Dictyostelium discoideum WS2162 plasmid Ddp5, complete sequence.
type: Entry
definition: Dictyostelium discoideum WS2162 plasmid Ddp5, complete sequence.
sequence version: NC_001889.1
sequence date: 2023-04-03
sequence: sequence
division: INV
label: NC_001889.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA927338
keyword: RefSeq
source: Dictyostelium discoideum
organism: Dictyostelium discoideum
taxonomy: Eukaryota; Amoebozoa; Evosea; Eumycetozoa; Dictyostelia; Dictyosteliales; Dictyosteliaceae; Dictyostelium.
reference: 1
references: 9539429
reference: 2
reference: 3
comment: PROVISIONAL REFSEQ: This record has not yet been subject to final\nNCBI review. The reference sequence was derived from AF000580.\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 14955
topology: circular
so has quality: SO_0000988
location: 1..14955
location: region:1-14955:1
RO_0002162: 44689

NC_001889
type: RefSeq
SIO_000068: refseq

PRJNA927338
type: BioProject
SIO_000068: bioproject

1
title: Dictyostelium discoideum nuclear plasmid Ddp5 is a chimera related to the Ddp1 and Ddp2 plasmid families
author: Rieben, W.K. Jr.
author: Gonzales, C.M.
author: Gonzales, S.T.
author: Pilkington, K.J.
author: Kiyosawa, H.
author: Hughes, J.E.
author: Welker, D.L.
journal: Genetics
volume: 148
issue: 3
pages: 1117-1125
year: 1998
pubmed: 9539429

9539429
type: PubMed
SIO_000068: pubmed

2
title: Direct Submission
journal: Submitted (30-NOV-2000) National Center for Biotechnology Information, NIH, Bethesda, MD 20894, USA

3
title: Direct Submission
author: Rieben, W.K.
author: Gonzales, C.
author: Gonzales, S.T.
author: Pilkington, K.
author: Kiyosawa, H.
author: Hughes, J.E.
author: Welker, D.L.
journal: Submitted (21-APR-1997) Biology, Utah State University, Logan, UT 84322-5305, USA

position:1:1
position: 1
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:14955:1
position: 14955
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-14955:1:source
so part of: sequence
organism: Dictyostelium discoideum
mol type: genomic DNA
strain: WS2162
plasmid: Ddp5
note: high copy number nuclear plasmid

44689
type: Taxonomy
SIO_000068: taxonomy

rep
type: Gene
subclass of: SO_0000704
RO_0002162: 44689
gene: rep
so part of: sequence
location: 1..3117
location: region:1-3117:1
so has part: feature:1-3117:1:exon
subclass of: SO_0000010

2544496
type: Gene
SIO_000068: ncbigene

position:3117:1
position: 3117
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-3117:1:exon

rep
type: Messenger RNA
subclass of: SO_0000234
RO_0002162: 44689
gene: rep
SIO_010081: rep
subclass of: SO_0000673
so part of: rep
location: 1..3117
location: region:1-3117:1
so has part: feature:1-3117:1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:1-3117:1:exon

rep
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 44689
gene: rep
note: replication and transcription factor
codon start: 1
product: Rep-like
translation: MNENKLISPHDFTQHFVNILELFSMPERVQTIKTPRIMPYSFSIEHLLFFEFFKSLSTKIKNDSFQISLDIKSIFDKLPLKNLSYHITLDLDVSFKKTICGDKNKKISISDCDQSIFIVDHFSRLFDRFIFSKPEIISYKRISALVSKQYQLVDYRMFGTKWFMFLRKVRRCCADMKGFEGFLKNLDFVSLYSSIQPIKVSQGHDEYIVSEIYKLYPSFNIENDPLPVQEGVNESDIEQIAINSENIQKINSQPNKRPNNQIYSRSQLSLVDFHARKLQKISIDPHKLSLNQAKEKFKNNTGSDDDTFNRFQNFSIDSEDGNDFSDTGDDDDDDDDDVDNDVDNDDDDDDDDNDDEFKEIHNICSVSHNGVSISNKVTEKIISVSNVIKLTLIEISKNKKEVNSEVVLSIFKNLQEGSFNSQLVDSFFGINKCDKVITFPNSILTYLASTDLNKIKINEISNEVFDLTKNLFLDESVNVLIPTISEQNKIGFIWVPIKDDNINTTINLIPMDIDPCHSQIKSISRFIQFCILIKKINQFIVNINISFDLFKKISMNLIGLSQNLLLMEAEVERLKSGRCSNDLFHSKRANDNEQRKFSLMVNEFLIENSNIIKMSILNNCLELRSLPLTNLNVEYDPVTLLHKLGFIFHCRQEISKFNYNHFISIDEVIKLFKPNNVTAKSCEIENNIKQYYALKSSDCSKHKQTEESFVPLNFIRFLNISITIAPYNVNNTFSFRNIKKGFSITNLELFSLLKSERPEKQFKDYVGDTRRIKLSFVSPCLIKITDITYCFSFSKSNEYNYRKIKSFKIHNLSIVPIDIKSNNKLIKTIEPISVENVDINHSSFNFSISCYDIIFSTIIISKARLDELKNYKIALPKNLSTVQDQFVKIVTNFASKINELKDLTDLEKHIISQYLLTQENKNKKAQERERQKIQEQQEQQEQQEQRERREQQEQQEQQEQQEQQEQQEQQEQQEQQEQQEQQEQQEQREQEEQEEQREQEEQEEQEEQEEQEEEEEEEEQTKKKKKQKKTKKNINKKK
SIO_010081: rep
subclass of: SO_0000673
so part of: rep
location: 1..3117
location: region:1-3117:1
so has part: feature:1-3117:1:exon

NP_046743.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-3117:1:exon

d2
type: Gene
subclass of: SO_0000704
RO_0002162: 44689
gene: d2
so part of: sequence
location: 3154..5760
location: region:3154-5760:1
so has part: feature:3154-5760:1:exon

2544499
type: Gene
SIO_000068: ncbigene

position:3154:1
position: 3154
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5760:1
position: 5760
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3154-5760:1:exon

mRNA
type: Messenger RNA
subclass of: SO_0000234
RO_0002162: 44689
so part of: sequence
location: complement(3154..5760)
location: region:3154-5760:-1
so has part: feature:3154-5760:-1:region

position:3154:-1
position: 3154
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5760:-1
position: 5760
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3154-5760:-1:region

CDS
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 44689
note: similar to plasmid Ddp1 D2 protein; may provide nonessential but beneficial phenotype
codon start: 1
product: D2-like
translation: MKTSLYLLFFIWLLNYSVVFCSFDAITYINGTYRFMSSDDPVWRDIEPTDPKSKQIQFDFLNIFVNKNDEGYTEIKKDNLLTQRKEIQNSNDSLTPKIFIGFGYVHITFKNVMNRTILLMAGENFLEVNTDKMFLRIDIAQQCSHAPNVQLSIGSGKHSFGKIIPCPAYISESLEKKMKREKINIIKKKQEKLGNSSEINNDLIERLEKEITNLHEDHKLIEEELEELGRIKKLINIFNFYIMFILLAICTSLYYILEAIDKNRRESRKNKEEIIKKYIQQSGSSIYIKKNSGSIKIPPISVILFIFLCVLPTDSINYDNHMCGTVIPLGKGVEKTTETEDNKAFTTYSKGFYSFQVPKNNYILCFNLDDEMGNIIETLYLDLSDYKYVSSGTFAYTTGEFIGHTSQYSACHHDQGCNQGRCGGIKPTDKTCQNSLRKENLATFYPGQSFCSSPAKGSAIGCGAVKELHDMCQYDRASVIPNGPPHDIYTITSTRLNFNYKLVIGSCENCIDYGMVNKSKPISISVSASSDKVDISLHSFEFVEVGDDVFLGQAANRDNPVSGMVGDIQASNHEIWTDKLRGHEISIPAQGLWSNRHFTYGHHTVITNFDYVDSAFKKTRTWEKNSFRRGDCLWNYNKSQKQYECSPSTHGQITGTIEFNQNYTISSNITKVCVEIRSFGPLKNGTRSSSSGSALYVEIRSTCLPGSVIVKSENKNITITTGALKVNKEFMNHTVTYQTNLKKVKAKFCFNEVCITFETELELEKFSLTKFVLDKVSGNGDKSDPGDGDTDTDVESPDRAPSGSGSSGAGIIKLFGKILSFYKGFWSGLLNLLGGKYKIYIYIALGLTCFVLLGLLISYIKNVFFFWK
so part of: sequence
location: complement(3154..5760)
location: region:3154-5760:-1
so has part: feature:3154-5760:-1:region

NP_046744.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3154-5760:-1:region

d1
type: Gene
subclass of: SO_0000704
RO_0002162: 44689
gene: d1
so part of: sequence
location: 5983..9877
location: region:5983-9877:1
so has part: feature:5983-9877:1:exon
subclass of: SO_0000010

2544497
type: Gene
SIO_000068: ncbigene

position:5983:1
position: 5983
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:9877:1
position: 9877
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5983-9877:1:exon

d1
type: Messenger RNA
subclass of: SO_0000234
RO_0002162: 44689
gene: d1
SIO_010081: d1
subclass of: SO_0000673
so part of: d1
location: join(5983..6059,6130..9877)
location: region:5983-9877:1
so has part: feature:5983-6059:1:exon
so has part: feature:6130-9877:1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:5983-6059:1:exon

position:6059:1
position: 6059
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:6130-9877:1:exon

position:6130:1
position: 6130
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

d1
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 44689
gene: d1
note: similar to plasmid Ddp1 d1/d3 protein; may be a transcription factor or may provide a nonessential but beneficial phenotype
codon start: 1
product: D1-like
translation: MPKSETNSIILVQPPTTFFSDHDFKIISRKNLKNLVDCFILDDKLVIKDGSDNKIIPESLDELYKLLCQIHTSKPIHLKYTDMVKQFKMLYHVSNIENSILSFLRCCEDASCKHYCLTLKPMIKNEKNNQLAIVSPKSKSKSQKIFATQNTIVDYDSDCNQVRIIRSYRDFSFLTPSPFFYNLYIQHLYTSYKKDPNFPRLISIDEFTAISLLYNQNNQSTAILDNLKNNSLTNEAIDFIMYKTMLQFSPISRKKNKFFKCLSTNSYPEIFYFFNLKSIFLDGNKSKRIFTNADGSLNELIIFPIAYGGHISLGALYMEKVEEKIRIQYMMHVDKFVKSTHCCIDVPSHTCKESDCYSLTCTYQKFVCWKKIKKAFIIQLMVENNENLTFLDTNDDSLIFENDFPVLPFSFGVNETIDCHLAFVRNLNLVVDCFYVEIPKLSMESILKSRFSTHSTQYTLDTSHFQQLELEISNSCKQFAMVQEMVEKEITPSGFAYDLKCLNPSVGFPPNIIFEFAIQTSFFGQVKQYFSYISTYCVMMSINKGFPSGSYNFTKIELNMSSLLEDVVFFYYYSTNNMLYYTTLKNSATIGNFHPSTSFKIYPEVSFFFVPNRSIPINYDQDHPSTFFKKIIDSYLKNVQKNEDHDNDIQPIFSTKILVLKSKKSDSLLSIPLDNNNLDLYNYEVFYKKDYKELEANEFYYHTNIKLQYKQINYIINKIRENHSINNAEKSSKSPSSPFMDCETKNKEYNTSSVNEPSLNQNQSHFQNQNQKKNEEINNIKNESDNSLKRRKCEYFDQNAQEKAETDINNLLDKLNLLTDENLKIQIINNDLKNENKLKDERIKMLLSKGSPKDHCDNILSTTLNSLKVQNEEKEAKINLLEKQVRHLNNVVSENANFLSQINNSIGNNFFENFVTMDILILILENCSKSIEFNTKKLEEYIEDKILLKNSINSVEYINLTKGSLQMFKNYLIEILSKDLGKVPQIYLNELLTKFSISEAQINPLIPDSHHIKHNIVNPISPYLNNFSTFPDNFIHFILYVEIEEEKRLQLSSIDISFMFNEFLEKLSKCQEITEVFKKIRDISKNSLDYVQKNKDKFLDVSSDALKRFLKKDELMLVSNENGKNIELDILNNIINRCNYCILFADLAVLKPKLVLFQEATCTVCYRPCIGNNVFLKCEKNYCNNVICSNCFKENIKNCSDEYSMSKRCNHCISRSISGKLCISCEKLNSISDKLEICDQIVFNDVDQPCVFKLCKDCKTKKLCPYVKHENVLN
SIO_010081: d1
subclass of: SO_0000673
so part of: d1
location: join(5983..6059,6130..9877)
location: region:5983-9877:1
so has part: feature:5983-6059:1:exon
so has part: feature:6130-9877:1:exon

NP_046745.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5983-6059:1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:6130-9877:1:exon

intron
type: Intron
subclass of: SO_0000188
RO_0002162: 44689
so part of: sequence
location: complement(6060..6129)
location: region:6060-6129:-1
so has part: feature:6060-6129:-1:region

position:6060:-1
position: 6060
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:6129:-1
position: 6129
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6060-6129:-1:region

repeat_region
type: Repeat Region
subclass of: SO_0000657
RO_0002162: 44689
rpt type: direct
so part of: sequence
location: 9949..10351
location: region:9949-10351:1
so has part: feature:9949-10351:1:region

position:9949:1
position: 9949
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:10351:1
position: 10351
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:9949-10351:1:region

g6
type: Gene
subclass of: SO_0000704
RO_0002162: 44689
gene: g6
so part of: sequence
location: 10509..11024
location: region:10509-11024:1
so has part: feature:10509-11024:1:exon

2544501
type: Gene
SIO_000068: ncbigene

position:10509:1
position: 10509
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:11024:1
position: 11024
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:10509-11024:1:exon

mRNA
type: Messenger RNA
subclass of: SO_0000234
RO_0002162: 44689
so part of: sequence
location: complement(10509..11024)
location: region:10509-11024:-1
so has part: feature:10509-11024:-1:region

position:10509:-1
position: 10509
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:11024:-1
position: 11024
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:10509-11024:-1:region

CDS
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 44689
note: similar to plasmid Ddp1 g6/g4/d5 protein; transcription factor
codon start: 1
product: G6-like
translation: MQIIFIMFILYIVCSSQITEIFYRDNKCTEGNEHKFFIYLEEEFMQNSTHVIQVKEEQHIIKELDKCTLDFNGGSILSKGYVNKKINKKMCGINIYNGNACDELKKKIVIYLDSMCIKNKGGYGMVLCNEKQTLFYDCADEFCKNCEIIQTEVHKKKCEKTELGYTNYFSN
so part of: sequence
location: complement(10509..11024)
location: region:10509-11024:-1
so has part: feature:10509-11024:-1:region

NP_046746.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:10509-11024:-1:region

g2
type: Gene
subclass of: SO_0000704
RO_0002162: 44689
gene: g2
so part of: sequence
location: 11232..12167
location: region:11232-12167:1
so has part: feature:11232-12167:1:exon
subclass of: SO_0000010

2544500
type: Gene
SIO_000068: ncbigene

position:11232:1
position: 11232
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:12167:1
position: 12167
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:11232-12167:1:exon

g2
type: Messenger RNA
subclass of: SO_0000234
RO_0002162: 44689
gene: g2
SIO_010081: g2
subclass of: SO_0000673
so part of: g2
location: 11232..12167
location: region:11232-12167:1
so has part: feature:11232-12167:1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:11232-12167:1:exon

g2
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 44689
gene: g2
note: similar to plasmid Ddp1 g2/g3/d4 protein; possible transcription factor
codon start: 1
product: G2-like
translation: MCKIILFFIISNIFFFFLLSYVDSYYSYLRGFVNSNSDLFVASEQKPSDDMLYILQKPKSIFILFIDYKERNVTLISGNFFNVFYSNEKKIELPLQEVCSDHMNTFKIIVSTKINMYQREFRCKTSFFDEVWYCTQDPINNVCLKVASKIFVLLFLFLYICITYYILAFFFKIMDLFSRRKNLPNQNKVNEQDVKLEALLTENKEAFDFIFKKIQEIETSMHTNNNEFNRLNSRSGYNFDNGNEYTNNGDSSIKGENQINIQQSDYNNTYTNNGNSSAKGGNQINNQQFESYNQNYFKNMYNNFKNKLNIN
SIO_010081: g2
subclass of: SO_0000673
so part of: g2
location: 11232..12167
location: region:11232-12167:1
so has part: feature:11232-12167:1:exon

NP_046747.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:11232-12167:1:exon

g5
type: Gene
subclass of: SO_0000704
RO_0002162: 44689
gene: g5
so part of: sequence
location: complement(12187..13280)
location: region:12187-13280:-1
so has part: feature:12187-13280:-1:exon
subclass of: SO_0000010

2544498
type: Gene
SIO_000068: ncbigene

position:12187:-1
position: 12187
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:13280:-1
position: 13280
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:12187-13280:-1:exon

g5
type: Messenger RNA
subclass of: SO_0000234
RO_0002162: 44689
gene: g5
SIO_010081: g5
subclass of: SO_0000673
so part of: g5
location: complement(join(12187..12926,12998..13280))
location: region:12187-13280:-1
so has part: feature:12998-13280:-1:exon
so has part: feature:12187-12926:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:12998-13280:-1:exon

position:12998:-1
position: 12998
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:12187-12926:-1:exon

position:12926:-1
position: 12926
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

g5
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 44689
gene: g5
note: similar to plasmid Ddp1 g5/d6 protein; transcription factor; contains HHCC zinc finger motif
codon start: 1
product: G5-like
translation: MESNYNEFYKNNLDIDHSQEIIRYLKNGNRVTVSNKHFFKDIFRSKFGDRTGRSKAYKSFVNSSFKRYLKIINKTYSLNGLDRNGDDILFNKIKGKKVFIGPIPKRYHYNEKDDNTIEHFNVDQMVKKIRDEGFYICKIDVENTFIDCVDCQTKTYVVSKKSTNLRKKTPDNEIHTPTLSPEQLTPLLTPQKTPPLSATLGEEISEEETSEEETSEEETLEEETSPSISISNSPEVVIPLLPTPTPTPTPLISSPQSKVQQDQQTSEGCLKFIPKLRYRNEIKASKLNKENTLEPTQKIIPVKKFKQSYWAKNPKLMSTTEIKVFQGCLSEKRSRVQIKK
SIO_010081: g5
subclass of: SO_0000673
so part of: g5
location: complement(join(12187..12926,12998..13280))
location: region:12187-13280:-1
so has part: feature:12998-13280:-1:exon
so has part: feature:12187-12926:-1:exon

NP_046748.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:12998-13280:-1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:12187-12926:-1:exon

g5
type: Intron
subclass of: SO_0000188
RO_0002162: 44689
gene: g5
SIO_010081: g5
subclass of: SO_0000673
so part of: g5
location: complement(12927..12997)
location: region:12927-12997:-1
so has part: feature:12927-12997:-1:exon

position:12927:-1
position: 12927
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:12997:-1
position: 12997
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:12927-12997:-1:exon

repeat_region
type: Repeat Region
subclass of: SO_0000657
RO_0002162: 44689
so part of: sequence
location: 13290..13978
location: region:13290-13978:1
so has part: feature:13290-13978:1:region

position:13290:1
position: 13290
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:13978:1
position: 13978
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:13290-13978:1:region

repeat_region
type: Repeat Region
subclass of: SO_0000657
RO_0002162: 44689
so part of: sequence
location: complement(14204..14908)
location: region:14204-14908:-1
so has part: feature:14204-14908:-1:region

position:14204:-1
position: 14204
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:14908:-1
position: 14908
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:14204-14908:-1:region