Gene loci information

Transcript annotation

  • This transcript has been annotated as Nucleoporin NUP188-like protein.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_2 g7603 g7603.t1 TSS g7603.t1 24895261 24895261
chr_2 g7603 g7603.t1 isoform g7603.t1 24895307 24901622
chr_2 g7603 g7603.t1 exon g7603.t1.exon1 24895307 24895332
chr_2 g7603 g7603.t1 cds g7603.t1.CDS1 24895307 24895332
chr_2 g7603 g7603.t1 exon g7603.t1.exon2 24895399 24897463
chr_2 g7603 g7603.t1 cds g7603.t1.CDS2 24895399 24897463
chr_2 g7603 g7603.t1 exon g7603.t1.exon3 24897527 24899827
chr_2 g7603 g7603.t1 cds g7603.t1.CDS3 24897527 24899827
chr_2 g7603 g7603.t1 exon g7603.t1.exon4 24899889 24900015
chr_2 g7603 g7603.t1 cds g7603.t1.CDS4 24899889 24900015
chr_2 g7603 g7603.t1 exon g7603.t1.exon5 24900655 24901622
chr_2 g7603 g7603.t1 cds g7603.t1.CDS5 24900655 24901622
chr_2 g7603 g7603.t1 TTS g7603.t1 NA NA

Sequences

>g7603.t1 Gene=g7603 Length=5487
ATGAGTGCCGCAGAAAATAAAATTACTCAATGGAAGAGAGTTTATCAACTTGTATCAGGA
ACATTTTACAATGAGAATCAAGAAGTAGTAAAAAAGAAACTATTAGAGCTTCAAAATGAA
ATTCAAGATGGAATTAAAATTTTTAAAAAACCAAAAGCAGACGCAACTGAAGAGACTGAA
AAACTCCTCAATGAAAAGCAACAAACAAAAATATTACCATTTGCACAAAAACTTCAAAAA
TATCTAGACCTTGATGTTAAACAATCATACAAAATTCTTTGCTATTATTTGGAAAATGAA
TATCGTGGATCAGCTTCCTCTTTGCAGAATTTTGTATCAAACGAATCTTTGATGATTAAA
TTACTCAATGATATTTGGTTTTATTATACACTCGAGAGGATGGTTTTGCTGAAAGTTGTG
AAATGTGTTTTAGAATATCATGAATCACCTGATCATCCATATAGAGAAGCTTTCAAAGCA
ATTGTTGATAAAATAGGCTTAGCAGTTCTTAGAAAATCATATATTGAACAATTTGAGATG
ATCTTAAAAGATGTACAGCAGGGAAAATTTTTACCTGGTGATATCTTTAACAGTCCTCAA
AAATTGCAATCATGGTCGGAAAGGAAACATCGTGAAATGAACGAAATATTACAAATAATT
CTATTGACAACATTCTATGATCCTATTCAAGCAGATGAGCTTCAAAATCTTTTAGATCTG
TTTAAAGCACATTCATTTGGAAAACAAAATCAATTTCTCAATGCTTCAAACAGTGTTCAT
ACAGATTTGATTCAGAAAGTCACATATAATGAAATTGCAGTTTTGATGGTAGCTCTTTCA
ACTAACAACAATTACGATGATACAAAATGGATTAATGAAGTTATTTCAAAATTAGATGAA
AAAATAATTGCAATGCATCATTATCAAGAGCATGGACCAATTCTTTTATCTTGGATGATT
TTTAAATTTTCATCGAAAAAGAATAATGACACAACAGCAATTGATCAATTCAATAATTAT
GGGAAATTAGGTGCAAGAGCAGTTCAATTGAATGTTTTTGAATACATGTATAAAATGATT
ATTCATAGACAATTTCAAGATAAAAGTCTTATTTCAAAAATAGTGTTCCGATGTATCTAC
GACAATTTAGTCACTTTATGTGACTTATTCAATGCAGACGGATCATTGTCGTATCATTCA
AAAATTTTCAATTTATTTAGTGAGGTTCTTAAGCAATCATCAATTGCAAAAGACTTTTGC
AAGAATGAAGAATCGGCAATAAGAACACTTTTTAATTCAGCTGTAGAGAAGTTTCCACAT
GAGTTTGTGCCTTTATCATTACTTGCAAAGTCATTGTCAACAGCAAGTATTACATCTTAT
AATTGGATAATGCAGTATCTTCAAAATTTACCTGTGTACACTGAACAGCCAAATGATCCT
TTGTATGAACTTCGTAAAAGTGATGATGATAATGAAGAAGATTCATATGTACTTCTTAGT
GATTATCAACCGTTCAGACGAATAAAAGAATTTATTGTTCGTGCTGATAACTCTGCTGTT
GTTCGCGAAGAGAAAGGTAAAATGTATGTATACTTTCTCATAAAACTCAATTATTTCCAT
GCTCTTCAAAATGAAATTCATGAACTACTCAATTGCATTGTAAGCTATGCTGAAATACAA
GAAAATACATTAAAACGTTTGGAATCTGGAATAAATTTATTGACATCAATAATCAGGCGT
ATTGATAGTCCTGATGACATCACAAATGAAATGATACATCCAACTGAAATGGTTCTTGAT
ATATTAGAAAAATTTAAAATTTTTCAACATCCTTCACTTGAACTTATGGCTGCCTGTGTG
AACGTTTGTGCAGAATTGGTTACAAATTTTGGTGAAGAAATTTTTCGAAGATTTCAAAAT
CTCAATATTTCACCAGTAGTCAACGTTATTCATCAAGACTTTAAAGTGTATTCAAACGGA
AATGGATTTGAATTGGGCCTTGTTGGTTATTATCTTATTAATATAGAACGATCATCAGGA
TGTTATAATTTTCTAAAAGCATATTTCAATTTCTTAAAAAAATGTTCAAAGCTCGAAATT
GGAGATGTTTATGCGATTGAGTTACCGGGACTATTGTTTATTATTCGTGAAGTATTTAAT
AACATTCACACTTGGTATTTTGAAAATGAACAAGACAGAATGGAGATTCTCCTTTTTATA
TTTGAATTTTTACATGATTTTCTGACAATACCAAATGAAGTCATTAAAGAAGATTTATCG
AAGAAATTGCTTCGTGATATATGTGTCTATAGTTTCCTATACTTAGACAATGCGTCGTCA
TTGCTACGATATGTTGCCATTGGAAATGCTGCATTACAAAATTTTATGGAAAATGAATCG
AACTGGTTTGTTGCCGCAGATTCACAATTAAACCTTCTTGTTATCAATGCAATGCGAATA
TTAATGCAAACATTAAGACTGAAAGAAACTGTAACACTAAATAATGAAGTTTTAACACCA
CTTGAGCAAATGATTTACACTCAACCTAAACAAAGAGATGCATTGAAAATAATTCCCATT
GTTGCCAATTACACAACATATTCATTCAATCGACGATTTGCTGTACTTTCATGCAGATTA
TTGAGAAGATTTGCAATTGAATTTCAAAGCTCACTTTCAGCATGCCTCGATTTGGAAGCG
GATCAAGTACGAATGATGTTTCTTCAACGCCTTCGTGATGAACTTGAAAGTGATGATCTT
AAAATTTCTATTCTCGATTTTGTTAATGCGTGCATCGATAAACAACCCGGATTGACTGAA
GCTTTTTTCAAAGTTTCATATGAACAAGATGTACGAAACAGTTATTTCTTCAAACGAGCA
AATCAAGATGAAGATTTATGTGAAGGAATTATTTCCTATATGGAAGAATTTCTCGAAGCT
GTATCAAAGGACCCGTCAAAAATTACAAATGATCAATTAAAGAGAATTATGAACTTGTTT
CATTCATTATGGAAGCAAGGATTACAATCTCTTGTTAGTAGTTTATTAAAAAAAGATACA
TTCTGGTTATCACTGTGTAGTCCTATATTGACTACACCAATTTCAAACTATCAATATTCA
CAGTTGCTCAACATTATGGGAATAGAGTTGTTTAAAATTCAAGACATGAAAGAGAATGAA
AATTTCAAGAAAATGATTGAAAAATTTCTTTCCAAGGATGTCTTTCAGAAGTGGCTTCGA
GTTGTATTTGAATTACCTACCATGAGTTTGAATGATTCATCAATTATTGAAGAAGTTCCA
GAATGGCTTGGTAGATTACAATCATTCAAAGATTTCCTCGTATTGCTACTTAAAAAGAAA
TCAGTTATTAAAATACCAAATGAAAGTATGAAAGAATTACTTGACAAATCTGTTGAAGCT
CTTTTATCTGCATCCGAGGAAATGGAAAATGGAAATGATACACGACCATTTGTTATTCTT
GCTGAATTGTATTTAATTATTTTGAACGATCAAAATTTAAAATACACAAATAATCATGAA
GAAGATGCACAGTTACTAAAGAATATTGAATCACTTTTAAAAGTTGTAACCAGTTGCTAT
GGTGGTTTACATAAACGTGCAAAGGACTCAATTTTAGCTATTGCCATTAAAATTTTAAGC
ATAGAGTCTGACGAAATAAAAAATTATCCTGCAGTTTCCAATTCATTTGTGAGATACAAT
TTGGAAATTTTGTGCATGGAGTTCTTTACAATTGAGAATGAGATGAAAGGAGATAAAAGT
ACTTTTGAACGAAATGATAAAACCGATTCAGTGATTCTTGCTATCAATTTATTGAAGAAA
ATCTTATTAATTAGCAATGAATTTTATGGAAACTGTAATTATTGGTTTAATTACTATAAA
GTATTTAACAGAATTTTGAACATTATCAGTGTAATTTGTCAAGATTCTACAAGACATAAA
ATTACGAGTGAATTGCTAAATTTACTTCTCATTTTGGCTAAAGATTCATACAGCAAAAAT
ATTATCTATTGTGACATAGGTGATTATTTGTGGATTAACATGATTACACCTAAATGCCTT
TTAGAGAAAGGTTTACCAACAATGAATAAAAGCGCAGAATGGACATCACAAGATTGGTGG
AACATTTATACAAAAGGAATTGAACTTGTTAGAGTATTACTTGAGCGAGAAGGCCATTTG
TTCATCAAAGACGCTCTGTTTTTTGTCGGTATTCATGAGCAATACTTGTCTGAAGCATTA
TCTCTTGCAAAATATTCATTAGAACCAAATGCATTGAAACTTATTAAATCGACACTAGAG
TTAATAGCAGAAGTAATAAAATATGAATGTTTCTGGACTGCTGATTATCAATTAACTATA
CACAATTTGATTAGACATATTCAATGTTTATTAGATTATGCAGTGTCCTTAATTCAACGT
CCAAAACTATTGAAACGTTTAACAGAAGCTTCAAAGGCTCATTTTCAAGAATATTCTGAT
TCAATTCTAAGTGATCCTAATGTTCAATTTGGAGCTCCAAAAATTAATGCAAACAACGTT
CCCCAACTAACTTATGGAACAGTTTTGAGTGTCATAGCATTAATAGTTAAAGCTTTAAAT
CTACAACATTTTACTTTTAAGCAAAAAGTACTGAACAAGATTCCGAGTGGTGAGAATGAT
CAAGAAAATGATACAATCACAATGCTATCAGTTGGTGATTCCCCATCTCATTTAGGACTG
CCATCAACTTCCCCATCTAGTCCTCGAAGACCATTTTCAAAATCATTGTCAATGAGTTCA
ATGACTAGTTCAGTCATACAACCTTCAAATGAACTATTAGCTCATCTTGATTCAAAAATA
TGCATTAATGTGTTGGAAGTCCTTTTGACATTACTTGCATCTCAAAGTCTTTTGGCACTC
AAAGCACGACATTTATCAAGTCGCGAAAAACAACTTATTCGTCGAGAGTTATCAACTGAA
CTTCATTGTCTTCATGATTTTGTTAAGAAAAAAATTCTTAAAGATTCAACAAAATCACCC
CTTTATAGAAACAAAATGGGAGCTTATCAGATTATAAATAAAGTTGATGATGATGATCTT
ATTCCAAGTACTTCAAAAGCTCCTACTGTATCACAACGTAGAAGTCAAGATTTGCGAGTG
AATGTTGTCCGAAAACTACATTTACAACAAAAATCAACAAGTCCATTCGAAATACCAACA
TCATTTTCACCAATTCAATCATCATCTGTGGAGAGCACACCTATAAGAGCAAACATCAAT
CCTACTACGAGCACATCAATTAAACGAGTTGGTTTCGATCTGTCATCTACACAATATAAA
GTCTCTTTACTTGAAGATAATGAACCATATATTGTTAATAGAGGAGATCCATCTTTCACT
GGTCTATCACTTGTAAAGTTTGTTGAGGAAGATTATATTCAACTATTATCAAATATTTTC
ATCTTTATTTGTCAAAATGAGAATTAA

>g7603.t1 Gene=g7603 Length=1828
MSAAENKITQWKRVYQLVSGTFYNENQEVVKKKLLELQNEIQDGIKIFKKPKADATEETE
KLLNEKQQTKILPFAQKLQKYLDLDVKQSYKILCYYLENEYRGSASSLQNFVSNESLMIK
LLNDIWFYYTLERMVLLKVVKCVLEYHESPDHPYREAFKAIVDKIGLAVLRKSYIEQFEM
ILKDVQQGKFLPGDIFNSPQKLQSWSERKHREMNEILQIILLTTFYDPIQADELQNLLDL
FKAHSFGKQNQFLNASNSVHTDLIQKVTYNEIAVLMVALSTNNNYDDTKWINEVISKLDE
KIIAMHHYQEHGPILLSWMIFKFSSKKNNDTTAIDQFNNYGKLGARAVQLNVFEYMYKMI
IHRQFQDKSLISKIVFRCIYDNLVTLCDLFNADGSLSYHSKIFNLFSEVLKQSSIAKDFC
KNEESAIRTLFNSAVEKFPHEFVPLSLLAKSLSTASITSYNWIMQYLQNLPVYTEQPNDP
LYELRKSDDDNEEDSYVLLSDYQPFRRIKEFIVRADNSAVVREEKGKMYVYFLIKLNYFH
ALQNEIHELLNCIVSYAEIQENTLKRLESGINLLTSIIRRIDSPDDITNEMIHPTEMVLD
ILEKFKIFQHPSLELMAACVNVCAELVTNFGEEIFRRFQNLNISPVVNVIHQDFKVYSNG
NGFELGLVGYYLINIERSSGCYNFLKAYFNFLKKCSKLEIGDVYAIELPGLLFIIREVFN
NIHTWYFENEQDRMEILLFIFEFLHDFLTIPNEVIKEDLSKKLLRDICVYSFLYLDNASS
LLRYVAIGNAALQNFMENESNWFVAADSQLNLLVINAMRILMQTLRLKETVTLNNEVLTP
LEQMIYTQPKQRDALKIIPIVANYTTYSFNRRFAVLSCRLLRRFAIEFQSSLSACLDLEA
DQVRMMFLQRLRDELESDDLKISILDFVNACIDKQPGLTEAFFKVSYEQDVRNSYFFKRA
NQDEDLCEGIISYMEEFLEAVSKDPSKITNDQLKRIMNLFHSLWKQGLQSLVSSLLKKDT
FWLSLCSPILTTPISNYQYSQLLNIMGIELFKIQDMKENENFKKMIEKFLSKDVFQKWLR
VVFELPTMSLNDSSIIEEVPEWLGRLQSFKDFLVLLLKKKSVIKIPNESMKELLDKSVEA
LLSASEEMENGNDTRPFVILAELYLIILNDQNLKYTNNHEEDAQLLKNIESLLKVVTSCY
GGLHKRAKDSILAIAIKILSIESDEIKNYPAVSNSFVRYNLEILCMEFFTIENEMKGDKS
TFERNDKTDSVILAINLLKKILLISNEFYGNCNYWFNYYKVFNRILNIISVICQDSTRHK
ITSELLNLLLILAKDSYSKNIIYCDIGDYLWINMITPKCLLEKGLPTMNKSAEWTSQDWW
NIYTKGIELVRVLLEREGHLFIKDALFFVGIHEQYLSEALSLAKYSLEPNALKLIKSTLE
LIAEVIKYECFWTADYQLTIHNLIRHIQCLLDYAVSLIQRPKLLKRLTEASKAHFQEYSD
SILSDPNVQFGAPKINANNVPQLTYGTVLSVIALIVKALNLQHFTFKQKVLNKIPSGEND
QENDTITMLSVGDSPSHLGLPSTSPSSPRRPFSKSLSMSSMTSSVIQPSNELLAHLDSKI
CINVLEVLLTLLASQSLLALKARHLSSREKQLIRRELSTELHCLHDFVKKKILKDSTKSP
LYRNKMGAYQIINKVDDDDLIPSTSKAPTVSQRRSQDLRVNVVRKLHLQQKSTSPFEIPT
SFSPIQSSSVESTPIRANINPTTSTSIKRVGFDLSSTQYKVSLLEDNEPYIVNRGDPSFT
GLSLVKFVEEDYIQLLSNIFIFICQNEN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
3 g7603.t1 Coils Coil Coil 52 72 -
2 g7603.t1 PANTHER PTHR31431 NUCLEOPORIN NUP188 HOMOLOG 11 1699 1.2E-193
1 g7603.t1 Pfam PF10487 Nucleoporin subcomplex protein binding to Pom34 30 945 4.4E-130
5 g7603.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 1621 -
6 g7603.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 1622 1640 -
4 g7603.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1641 1828 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0017056 structural constituent of nuclear pore MF

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.

Raw TPM values