Gene loci information

Transcript annotation

  • This transcript has been annotated as Nuclear pore complex protein Nup98-Nup96.

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_3 g388 g388.t1 TSS g388.t1 3134462 3134462
chr_3 g388 g388.t1 isoform g388.t1 3134679 3140347
chr_3 g388 g388.t1 exon g388.t1.exon1 3134679 3134889
chr_3 g388 g388.t1 cds g388.t1.CDS1 3134679 3134889
chr_3 g388 g388.t1 exon g388.t1.exon2 3134949 3136317
chr_3 g388 g388.t1 cds g388.t1.CDS2 3134949 3136317
chr_3 g388 g388.t1 exon g388.t1.exon3 3136378 3137819
chr_3 g388 g388.t1 cds g388.t1.CDS3 3136378 3137819
chr_3 g388 g388.t1 exon g388.t1.exon4 3137879 3139962
chr_3 g388 g388.t1 cds g388.t1.CDS4 3137879 3139962
chr_3 g388 g388.t1 exon g388.t1.exon5 3140027 3140347
chr_3 g388 g388.t1 cds g388.t1.CDS5 3140027 3140347
chr_3 g388 g388.t1 TTS g388.t1 3140486 3140486

Sequences

>g388.t1 Gene=g388 Length=5427
ATGTTTGGCTCAAAAAATACTTTTGGACAACCCACGACTGGAACTTTTTCAGGCTTTGGA
CAAAGTGCATTCTCAAAGCCAGCAAATACATTCGGAACAAATACTTTTGGACAGCAAAAT
CAATCTGTCTTTGGTGCTCAACAGCAGCCGAGTTCTTCTGGACTTTTTGGCTCTGGCGCT
GCAGCTTCTACGCCTCAATCAGCATTTGGAAGTGCTTTTGGTCAACAAACATCAATTTTT
GGAAATACAAGCACGACTGGTACAACTTCACTTTTTGGTAATCAGCAGCAGCCGACATCT
GCATTTGGTGCTCCTAAGCAACAAATTTTCGGCCAAACACAACAACCAACAACTTCTCTT
TTTGGACAACCTCAACAACAACAAACAACATCACTTTTCGGTCAAACTCCCACTAATACG
GGAACTGGACTTTTTGGTTCAACAACAACTTCTGCTTTTGCTCAACCAACGACTTTAGGC
AATCAACAAACTGGAACAGCTATTGCAAAATTTCAAGCACAACAAGAAACTGATACTTTG
CTAAAAGGGTCAACAACATCTTATATCCAAACTAAGCAACAATGCATAACATTTATGAAA
GAATATGCAGATAAATCTCTTGAAGAATTAAGAGTTGAAGATTATATTGCAAATCGAAAA
GGTCCACAGCCAGCTTCTGCAGGTCTTTTTGGTGGAAGCAATCAAAGTAATTTCTTCAAT
TCAAATCCAACATCGACTTCAGGAGGATTTACTGGTTTTGGTCAGCAATCGACTGCTCAA
CCGATTTTTGGTCAAACAAACACAAGTACATTAGGTCAAACATCTGCATTTGGAGCGACC
AATTCAGCGTTTAATCAAAGTAGTGGTGGTCTCTTTGGAAAGCCTCTTCAAACTCCTGCA
ACAACAGCATCAGCATTTGGTGGATTTGGTTCAAATACAAGTACATTTGGAGTTGCAAAA
CCATTTAACGCAACTGCTCCTACTACAAATTTATTCGGTCAAACTCCCGCAGCTACAGGC
TTTGGTCAACCTGCAACAAACACTTTTGGAGCTTCAACATTTGGTCAACCTCAACAACAG
CAAACACCTTCTCTTTTCGGTGCCTCATCAACAGCACCTCCTCCCGCATGGAATGCAGGA
ACTTCTACAGCAAATACTGGTTTTAATACGAGTGCGGGTACAAGTTTGTTCGGTTCATCT
GCAGCTAAACCTGCATTTGGGACGGGAGCATTTGGCAGTGCTCCAAGTGCATTTGGGACA
ACACAACCACCTGCATCAACTGGTTTTAATTTTGGTCAACCAACTACTGGAACTACTAGT
CTTTTTGGACAAAAACCAGCTACAAATTTATTTGGTCAACCTGCTGCTCAACCAAATACT
TCATTATCGTTTGGGACTGGAACTGGAACGTCACTTTTTGGCTCGAACACTCAGCCAGCT
ACAGGAGGTCTTTTTGGTTCAACGCCTGCTCAAAATACTACAAATACAGGTGGAGGTCTT
TTCGGGTCATCAAATACAAGCGGGTTTGGTACAAATTTAGGTTTATCATTTGGTCAAACT
CAGCCATCTCTCTTTGGAACCAATCAAACAAATATGCAACAACCACAACAGCAACAAAAC
AATACTGAAATTCATTCAAAAATACTTGCAATGACAGGAAATCCTTATGGTGATAATGAA
CTTTTTAAAGGACTCAAACCTAGTCCGATGCCTAATGATGCTTTTAAGCCAACAAATCCG
TTAGCTCAAAAAGCGTTACTTGAATCAAGCAGCAATTTTAAAATTTCACCTAATTCATCA
GTATCAAAAATCAAAATCAAACCTGTAACAGCTGTTGCTTCAAAAAAGAGTCTTTTTGAT
GGTTTAGAAGAGTACGATGCATCTCTTGAAGAAAGTTTCACTATCAAAACTAGCGCTAAA
CGATTAATCATTAAACCTCGTACACCGATTGATGCTAATAAGTCAATTAATGACTCGATT
TTGAAACATACTCGAGACGAATCAAAAGTAATTGAAAAAGAAAATGTTCCTGAAACTTTT
CAAAATCAAATTCCAACAACACCATTTGTTGACAATAATGTTGATCAAGATAGCGATCGA
AGAGTATCTTGGCTTCGAACGGCTCCGCAACACATTCGAGCTCGACCAAATATTCGTGAA
AATGCAGCCGATACGACAATCAATCAATTGATTCAGACATCAAACAAAGACACAGAGACA
ATAAAAGACAAATTAGAGACATCTGTTATGAATGCATCTATACTTAATGAGACTTTTAAT
TCAAATGCAGATGATACACAAAATGAAGCTGATATCTCGATTTATACTGGACCAGTTGAA
CCTCATCCAACCGGAATCGTTTTACGAAGAGTTGGTTATTATACTATTCCATCGCTTGAT
GAACTTATTGAATATATGGATGATGAAGGTCATTGCAAAGTACCAAACTTTACGATCGGT
CGCGGTGGTTATGGAAATGTTTATTTCGATGAGGAAATTGATGTTGCAGGACTTAATCTT
GATGAAATTTGTCATTTTCGAAACAAAGAAATTATACTTTATCAAGATGATGATAATAAG
CCTCCAGTTGGAGAAGGATTGAACAGGAGAGCTCAAGTCACATTAGATCAAATTTGGCCA
ATGGATAAAACAACACATGAGCCAATTAAAGATCCACTTCGATTAGAATCGATGGGATAT
GAAGCAAAATTACGAAGAATTTGTGAAAAACGAAACACGAAATTTTTGGAATATCGACCA
GAAACTGGTAGTTGTGTGTTTAAAGTTGAACATTTCTCAAAATATACCCTTGATGATTCC
GAAGACGAGGGAAATGAAGTAGAACCACGCAGTGATCCAAAGAAAGCTCGAATTACTCCA
TTACCGCAAAATGCAAAGAAGATTTTAAATGATAAAGAGAAAATGACTGCAGATATTCAA
AATGATAATCTTCAACGCATGAAGCAACAAGATGCAACTTTTGTTCTTGGGACACATGTG
GGACAAAGAGGATTTCAAACAAATTTTACAACAATGAATTTAGATGAAAATTTTAATTCT
GATCCAACAAGTCCGTCAATAAAGCTTGCAAAAGACATGCAAACAGATACACATAAATTG
CAATTAATGAAAGCATCATTTTTTGTTGAAGATGATGCTTTTTCAGTTATGAGTGATGCA
ACTGAAGGACGCGAGAGTCCAGATCAAATTGTTCCAACTGATTTTACTCCAAAACCATCG
ATTTTTGCAGTAACAGGATTATTGTCTAAACAATTTAAAATGTTTGATGATGCAGCCGCA
GTTCAAGAATATGAGACAAGAGATTTTGAACAATCTAGCGAGCCTAAACGACAAGAATTA
ATTCAAACAATTTTCAAAGCAGTTGGACCAAAATCACAGCCATTAATTGTTCGTCCTCGA
GTAATGCTCTTTGATATTAGCGACATCAGTTTGCCAATGAGTGAGTCAATTTTGAATAAC
ATGATACAGAAACCAAACAACACTGTTCCATTCTTTCACGGCAGAAAATTCAAAATTGGT
TGGAGTCACGGTAATGAATTTACAGTTCTGCAAAGTCATGCGAGCAAGTCATTGTTTAAA
GGACGTCTTCGTGATGATTTATCAAAATCATTTGTTAAATTAGCTCAAATCAAATCAATG
TCACATAAAACCAATGCAAAATTTGACAAATCACTTGTTGAGCATTTAAAAATTCAATTG
AAATATGATAAGAAAATTTCAATCAACGGATCTGACTGTAAATATTTTGAAGCTGATGGA
AAGGCATTAGGACTGCATGAACATTATGAATTGGCACAAAAATTGATAAAAGATTCACCC
AATGAAAAGAATAGTTATGATGCGACAGTCTGGTCTTTAATGGAATCTTTATGGGGGTGT
ATTGATAATATGAATATGGAAACACTCGATCATGGAACAATAATGCTACGAAGAGATCTT
TTATCTCTTTGGCTGGAGAATGTAGTTACTGATAACGATGTGTTTAAATCTAATCTTGAT
TATTTGGATCGATTAACAAATTTAATGATGTGTCACAAAGTGAATGATGCATGTGACTTA
GCGTTCGAAAATAACGATATAAATTTAAGTCTTTTGCTTTCACAAGCGAGTGGAAGTTCT
TCAACTAGACAATTATTACAACACCAGTTATCTTGTTGGCATGAAGTTGAAGCTGATGAG
TTCATTGACGATAGAAGATTGAAAATTCTTATGATGGTGAGCGGAATATCAGCGATGGAA
GGAGCGAAAAAGTCCACTCTTAACATTTTTGAAAATCTAAATTGGTTAAAATGCTTAGCA
CTTCAAGTGTGGTATGTTTCAACATTAGTTTCTTCAGCAACTGATTCAATTTTGGCATAT
GTGAAAAATTACCAAAATATCACTGCAAATGTTGCTCATCCAGTTCCACCATATTGCAAA
GCTAGCGATGCGGCTGATTGCAAATACTATGATCTAAGATTTCATTTAATGAAACTCTTT
AGTCAACGAAGTCATTCGCTTGAAGTTCTGCTAAATCCTGCAAATTATTCCAAAGATTTA
ATGGACTATAGGCTGTCATTTCTTGTTCTTCAAGTGCTCGAAACTTTAGGATATCGCCAC
ATCAGTGAATCTTGCCGTCTTAAAATTTATACTTCAATAGCTGAGCAATTAGAAACAAAT
GGCCTATGGGAATGGTCAATTTGGGTTATGCTACACATTGCAAACCAAAATTATCGTGAA
AGTGCTATTCAAAAATTACTCTATAGATATATCAAAATTGACGATGAACTTGATGATGCA
TATTCATTAAAGGAGAAATTCATTCAAGAAGACTTGCAAATTCCAGAGAAATGGATTTTC
TGGGCTAAAGCTGTTCGTGCAAAAGCACTAAATAATCATCAAGTAGAACTCAAGTATTTG
CTTAAAGCACAACATTGGTCAGAAGCGCATGAAGTTTTAATGACCCACATCGCACCAGAT
CTTTTTATTAATGATCAAACTGATTATTTGAAATCCTTACTGAAGCAGTTTCAAGCAACA
AATGAAATTCAACACTGGAAGACGCAGGGAGAGATTTTACTAAATTTTATTGAATTAAAT
GAGAATTTTTCATCATTGAATAGTGAAGAAAATATTAATGCAGATCTTTTCCTTCAACAA
TTAAGTCCGCTTCTCTCAGATTTGTGTTCAAATATTAAATTATTCCCATGTCCGACATCA
AAGCATCGTCTTTGTCAATGTGAGATCGCTAAACAACTCGCATTTATTATCAGAAACTTC
TATGCATCATCAAATGCCTATGGAACTCAAGCATTCTCGATGATTAGAACAGCACTAGAT
AAGCTACCTCTTCCTCAAGAGTATGCTCAATCTGAATTGCCATATGTTCTTACGACGTTT
TTATTAGAACGATTGAATACGAATTAA

>g388.t1 Gene=g388 Length=1808
MFGSKNTFGQPTTGTFSGFGQSAFSKPANTFGTNTFGQQNQSVFGAQQQPSSSGLFGSGA
AASTPQSAFGSAFGQQTSIFGNTSTTGTTSLFGNQQQPTSAFGAPKQQIFGQTQQPTTSL
FGQPQQQQTTSLFGQTPTNTGTGLFGSTTTSAFAQPTTLGNQQTGTAIAKFQAQQETDTL
LKGSTTSYIQTKQQCITFMKEYADKSLEELRVEDYIANRKGPQPASAGLFGGSNQSNFFN
SNPTSTSGGFTGFGQQSTAQPIFGQTNTSTLGQTSAFGATNSAFNQSSGGLFGKPLQTPA
TTASAFGGFGSNTSTFGVAKPFNATAPTTNLFGQTPAATGFGQPATNTFGASTFGQPQQQ
QTPSLFGASSTAPPPAWNAGTSTANTGFNTSAGTSLFGSSAAKPAFGTGAFGSAPSAFGT
TQPPASTGFNFGQPTTGTTSLFGQKPATNLFGQPAAQPNTSLSFGTGTGTSLFGSNTQPA
TGGLFGSTPAQNTTNTGGGLFGSSNTSGFGTNLGLSFGQTQPSLFGTNQTNMQQPQQQQN
NTEIHSKILAMTGNPYGDNELFKGLKPSPMPNDAFKPTNPLAQKALLESSSNFKISPNSS
VSKIKIKPVTAVASKKSLFDGLEEYDASLEESFTIKTSAKRLIIKPRTPIDANKSINDSI
LKHTRDESKVIEKENVPETFQNQIPTTPFVDNNVDQDSDRRVSWLRTAPQHIRARPNIRE
NAADTTINQLIQTSNKDTETIKDKLETSVMNASILNETFNSNADDTQNEADISIYTGPVE
PHPTGIVLRRVGYYTIPSLDELIEYMDDEGHCKVPNFTIGRGGYGNVYFDEEIDVAGLNL
DEICHFRNKEIILYQDDDNKPPVGEGLNRRAQVTLDQIWPMDKTTHEPIKDPLRLESMGY
EAKLRRICEKRNTKFLEYRPETGSCVFKVEHFSKYTLDDSEDEGNEVEPRSDPKKARITP
LPQNAKKILNDKEKMTADIQNDNLQRMKQQDATFVLGTHVGQRGFQTNFTTMNLDENFNS
DPTSPSIKLAKDMQTDTHKLQLMKASFFVEDDAFSVMSDATEGRESPDQIVPTDFTPKPS
IFAVTGLLSKQFKMFDDAAAVQEYETRDFEQSSEPKRQELIQTIFKAVGPKSQPLIVRPR
VMLFDISDISLPMSESILNNMIQKPNNTVPFFHGRKFKIGWSHGNEFTVLQSHASKSLFK
GRLRDDLSKSFVKLAQIKSMSHKTNAKFDKSLVEHLKIQLKYDKKISINGSDCKYFEADG
KALGLHEHYELAQKLIKDSPNEKNSYDATVWSLMESLWGCIDNMNMETLDHGTIMLRRDL
LSLWLENVVTDNDVFKSNLDYLDRLTNLMMCHKVNDACDLAFENNDINLSLLLSQASGSS
STRQLLQHQLSCWHEVEADEFIDDRRLKILMMVSGISAMEGAKKSTLNIFENLNWLKCLA
LQVWYVSTLVSSATDSILAYVKNYQNITANVAHPVPPYCKASDAADCKYYDLRFHLMKLF
SQRSHSLEVLLNPANYSKDLMDYRLSFLVLQVLETLGYRHISESCRLKIYTSIAEQLETN
GLWEWSIWVMLHIANQNYRESAIQKLLYRYIKIDDELDDAYSLKEKFIQEDLQIPEKWIF
WAKAVRAKALNNHQVELKYLLKAQHWSEAHEVLMTHIAPDLFINDQTDYLKSLLKQFQAT
NEIQHWKTQGEILLNFIELNENFSSLNSEENINADLFLQQLSPLLSDLCSNIKLFPCPTS
KHRLCQCEIAKQLAFIIRNFYASSNAYGTQAFSMIRTALDKLPLPQEYAQSELPYVLTTF
LLERLNTN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g388.t1 Gene3D G3DSA:1.10.10.2360 - 164 220 0.00000
11 g388.t1 Gene3D G3DSA:3.30.1610.10 - 785 939 0.00000
12 g388.t1 Gene3D G3DSA:1.25.40.690 - 1331 1417 0.00002
5 g388.t1 PANTHER PTHR23198:SF17 NUCLEAR PORE COMPLEX PROTEIN NUP98-NUP96 1 408 0.00000
7 g388.t1 PANTHER PTHR23198 NUCLEOPORIN 1 408 0.00000
6 g388.t1 PANTHER PTHR23198:SF17 NUCLEAR PORE COMPLEX PROTEIN NUP98-NUP96 333 1754 0.00000
8 g388.t1 PANTHER PTHR23198 NUCLEOPORIN 333 1754 0.00000
2 g388.t1 Pfam PF13634 Nucleoporin FG repeat region 68 146 0.03900
3 g388.t1 Pfam PF13634 Nucleoporin FG repeat region 222 307 9.40000
4 g388.t1 Pfam PF04096 Nucleoporin autopeptidase 792 937 0.00000
1 g388.t1 Pfam PF12110 Nuclear protein 96 1344 1626 0.00000
13 g388.t1 ProSiteProfiles PS51434 NUP C-terminal domain profile. 790 932 54.94100
9 g388.t1 SUPERFAMILY SSF82215 C-terminal autoproteolytic domain of nucleoporin nup98 783 939 0.00000

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:0005643 nuclear pore CC
GO:0006913 nucleocytoplasmic transport BP
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