Gene loci information

Transcript annotation

  • This transcript has been annotated as E3 SUMO-protein ligase RanBP2.

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_1 g10255 g10255.t1 TTS g10255.t1 8547418 8547418
chr_1 g10255 g10255.t1 isoform g10255.t1 8547545 8553329
chr_1 g10255 g10255.t1 exon g10255.t1.exon1 8547545 8547855
chr_1 g10255 g10255.t1 cds g10255.t1.CDS1 8547545 8547855
chr_1 g10255 g10255.t1 exon g10255.t1.exon2 8547924 8549362
chr_1 g10255 g10255.t1 cds g10255.t1.CDS2 8547924 8549362
chr_1 g10255 g10255.t1 exon g10255.t1.exon3 8549423 8552543
chr_1 g10255 g10255.t1 cds g10255.t1.CDS3 8549423 8552543
chr_1 g10255 g10255.t1 exon g10255.t1.exon4 8552594 8552819
chr_1 g10255 g10255.t1 cds g10255.t1.CDS4 8552594 8552819
chr_1 g10255 g10255.t1 exon g10255.t1.exon5 8553255 8553329
chr_1 g10255 g10255.t1 cds g10255.t1.CDS5 8553255 8553329
chr_1 g10255 g10255.t1 TSS g10255.t1 8553435 8553435

Sequences

>g10255.t1 Gene=g10255 Length=5172
ATGTTAAAGTTCTATACAAAACGTGATGTCGACAAGCATGTCTCTCATATGTTTCAAAAA
CTTAGCGAAAAAGAGCGGTCAAGTCGTGGTTTGCATATTGCAAGATGCTATGTTAAGGTA
AACGAATGGGATCTTGCTCGAGATTGGTTACAACGATATCTAGACACAAAACAGGATGAT
CCTGTAGCTCACAGACTTATGGCCGAAATATATGAGCGTCTTCATAAAACAGAAGAAGCC
ATTACATCATATCAGCGCTCATATAATTTAAATAACAAACAAAATGATATCATTAAACAT
GTCTGCCGGCTTTATCTGCTTAATGGTGGTTGGTCTTCATGCCCTGGAAAAGTTAAATAC
TGGTGTGAATTAGCAGAAAATGAAAATATTCGCGACGAGAATATAGCTGATCTCCAATCA
AAAATTGGAGTAAAAGTCACCGCCAGTGGTAGTACAAGCAGTAACAGTAACTTGAAGGAA
CGAAAAAGTGATGTAGGCAAAATTCGAACAGAGAAAAAACTACAACATGAACTTTCATCA
TCATTTAATGAAGAGTTTAATAATAATTCTCAAAATGGATATACTGATGACGAAATTTTT
CACAATGCTTCATCTAGTTCTTTTAGAACTACACAAATGTCATTTGCACCAATGCCAAAT
TACAATGAAAAGTTTGCAGATGTTGAAGATTTGATTCGAAAGCTTTCTGATTTGGTAATT
TCTGTAAAGGAAGATGTTCTATGTGTTCGAAATGATATAACAAGTTTGAGGGACGATATT
CTTAATATTCGTGGTGATATAACTGATTTGAGTGTTAACAAAGATGCAACTACAGCAAAG
GCAATCATTGATGTCAATAAATCTATTGAAGATCTTACTTGGAATGTGAGTTGCTTGATG
AATATTTTTCCAAGCGCACCTGGGCCTGTTTCACTTCCAACAAATATAAGATTTCCACCT
AATCAATTGCCCCCGCAATTTAATCAAATGTATAACACGGCTTATCCAATTTATCCACCT
ATACGTCCACAATTGCCACCACATTTACAATATAATGATCCTCTTGGAATGAATTTGATA
ATGAATGCTGCTGCTGCTGCCGCAAATTATGGTTCTCCACTCATTGCTTCTCCACAACAA
CCTCCACCTCCGCCTCAACCGCAACAGCCTATTCCACAACAACAAAATATTTCACCAGCA
ATCACAATTCAAAATGGGCAGAAATCGTCTTTAATGGAAGCTTTAAATACGCCATCAGTT
TTAAATACATGGAATAATACATATAATGCAGCTCAAGTTATGTCAACAACTATTCCGCAA
ATCCATAATTTCACGCCTCAACAGCCACCATCAACTTTAGTTGCTTCTCCCAGTGTTTCA
ATATCACAACAACAACCACCACCATCATCATCAATACAAACTATGCCAGTTAATCAAAAT
AAACTTGTCGAAAAAACGCCAGTTAATGTTGTCATCACTAGTTCTGATCCTCTGCCTACA
TCAAATTCTTTTGTTACACAACCAACATTGAGCGTGACAATTCCACCTCAACATATTAAA
CAATCACCAATTGTTTCAACAGAAACGTCAAAAACAGTTGAGACAAAATCACAAGAAAAT
GTAACATCTGGTAATGATTTAATAAAATCAACAATGTCGTTCAGAATTCCAAAGAAAACC
GAGACTCAAGTTACTACTACAACAACAACAACGCAAAGTAATTCGACTCCTAAAACTCAA
AGCATGACTTTTAGTGGATTCACTGGTGATTTGTCAAAACCAAGTCCTATAGCATTTGCA
ACTCCAACTAAGGATAAAGAAGTTATTGATAAAAGTAACAAACCAGCACAACAGAGTCCA
TTTGCAAACTTTACTTTTGGTGGTGGTTCATCAAATAAATCATTCACAGAGCTTTTCAGT
AATTTGAATTCAAATAAGTCGGATACGAACAACACTACTGAAACTAAGTTGAATACATCT
GCTACTATAACTACTCAGAATGAGGAAGAAGCAGATCATTTTGAGCCGACAGCACAATTT
GAACCAGTGATTCCATTGCCAGATCTTGTTGAAGCTAAAACTGGTGAAGAAGAAGAAAAT
GTCGTATTTTGTCATCGTGCTAAGCTATTGCGATATGATACAAATACAAAAGAATGGAAA
GAACGAGGACTAGGTGAAATGAAAGTACTTGTAAGCAAGACAGACTCATCAAAGGCACGT
TTGCTAATGCGCAGAGAACAAGTTTTGAAAATTTGCTGTAATATGCCAATAACAAAAGAG
TTGAAATTCACTCCACGCAATGCAACTGCTTCGTCATTTGGAGGGCAAGATTTTAGTGAA
GGTGAGATAAGATCTGAAACACTTACAATTAAATTCAAGACAGCAGATCTGCTTAAGAGT
TTCCAAGAGGCAGTTTTGAATGTTCAAAAGAATTTAACTACTGAGACAGTTCAACCAGAA
AAGAAAGAGGTAAAAAAGCAAGAAGAAAAGAAACAGGAAGTGAAGAAACAAGAAGAAAAG
AAACAGGAAGTGAAGAAACAAGAAGTAAAGAAACAAGAGGAAACTAAAGGATTTGGCGAT
ATGTTCAAACCAAAGGCTGGATCATGGACATGCGAAGCTTGTTATATTTCAAATAAACCA
GACACTTTGTATTGTGTTGCTTGTGAATCTCCAAAAGATAACACTGTGCCGAAGAAAGAG
CCAAAATCATTACTTGCTCCTGCTGCTGATGCACCTAAATTTAGTTTTGGTATGCCAAAC
TCTTCAGGATTTTCTTTCGGTATGCCTCAAAATCAAACAACCGTAGCACCCGTTATTGCA
CCAGCTCAATCAATTACAACAACAGCTTCATCAACCACTGGATTTTCTTTTGGTTCTACA
AATACAACATCAGCGCCATCAAATTTCACATTTGGGAAACCAGCTGATTCGTCAAGCAAT
GTGACATCTACGAAAACCGATTCAAATACTGAAAGTAGTGGTGGATTCAAGTTTAATGTT
CAAAACACTTTTTCATTTGGTATCAACAAAGAAAAATCGGCTGACGAAGTTCAGATTGAG
AAAACACCAGATCAAGAACTCGGATCAGGATCAGGAAGTTCTGGATTCAATTTTGTTTTT
AAGAAAAAATCACCTGCAAAAACTAAATCACCTGGTAAAACACGAAATGATAGCGTTAAT
AGCGAAGGAAACGATGGAGAGGAAGCTGATAATAATGAATATCATGAAGAAGAAGAAAAT
CAAGCATATTTCACACCAGTTATTCCACTGCCTGATAAAATTGATGTAAAAACTGGAGAA
GAAGATGAAGAAGTACTCTATTCGCATCGCTCGAAATTGTATCGATTTGTTGATAAGGAA
TGGAAAGAACGAGGGATTGGAGATATCAAGATATTGAAGCATAAGGAAACTGGCAAATTG
AGAGTTGTGATGCGCAGAGAACAAGTTTTGAAAATTTGTCTCAATTTTGTTCTCAATGAA
GAAATCGATTTTAAGCCAAAAGATGATACATCATTTAGATTTGCTGCAAATGATTTCTCT
GAAGGTGTTGCAGAACCAACATTTTTTGCAATTCGCTTCAAGACTAAGGAAATTAGAGAT
GGATTTAAGAAAGCAATTGACGATGCTTTAGCAGGAACTACTAAAAAATCAAATACATCT
TCAAGTGACAATGATGAGTTAATCAAAAGACTAATGTTGCCTGCAGATTTTTTCAATTAT
TTAAACAAACCTGATTGCACTGGTTGTATTGGATGTAAACCTGATGAATATGTCTACAAG
TCCGATTACAAATCTGAAGTTACTGAGGATGAAAATGCTTTACCATTGGACGCACCGAAA
TCAATCATCAAAATTGTAAAACCACGTCGAGCAAGCCAAGATAAACGAGTTTCATTTAAT
CTTTCTGACACAAAGGAAAACAATAATGTATTCAATTTATTTGGAGGAAAAAACGTGGAA
GCAACGCCTGATAAGGTTAAGACAGATTTATTTGGTATTAAAAAATCTGAAGCATCTACA
AATATTTTTGCTCAATTCAACGCTGAAAATCCACCGCCCCCACCGTCTGCAGTTTCAACT
AGTATCTTTGGATCTAATGCTCAAAATACAAGTTTGGGAGAAAATAAGAGCATTTTCGGG
TCATCTATCTTTTCATCGTCACTTAATACAACACCAACAACAAATGCAGATATTAAGAAA
GGTGATCAACAACAAAGTCTTTTTGGAAATCAAAATAGTTTTTCATTTTCTGCAGTATCA
AATGGTACCATCTTCGGAAATGCTAATAAAGAAAACAACTCATCACCATTTGGCAATTCA
TCACCTTTTGGATCGACAAGTATTTTTGGTTCAGCACTGAATAAAAGCAACAACAGTGAT
TCAAAATTAAACGACAATACTAAACCGACGAACATTTTTTCATCTAACACAAATAGCAGT
TTCAGTTTCGCAGAAGCAGCAAAACAATTGGATAAATCTTCAGACGCAAATAAATCAACA
GTTGAACCAGAATTTCTTAAAAAAACAAGTTCTATAGGAGGATTTGCAGAATTAGCAGCA
GCAAGTTCAAGTAATGCATTTAGTGGACAAAATAATTCATCTAGCGGCTTCTTTGGACTT
ACAGTAAAAGAGGATATTTTTAGCAGAAGCAAACAACTTAATGCATCTGGTAATGCTGAT
GCAAGTCAAGATGATTCAGAAAATGTTAATGATGATAATTACGATCCACATTATGACCCA
ATCATAAGTTTACCCGATGAAGTCAAAGTATCTACAGGCGAAGAGGATGAAGAAAAAATG
TTCGGCGAGAGAGCAAAACTCTTCCGTTACGATGCAAATACGAAAGAATGGAAAGAGAGA
GGCGTTGGCGAAATGAAAATTTTACATCATCCTATTAATAATACATACAGAATGATTTTG
CGACGTGAACAAATATTTAAACTTGTTCTCAATCAACTCTTAACACCAGATATTCACATG
GCACCAATGGGAAGTTCACCAAATGCATTTTGTTGGGCAGGTATGAACTATGCTGAAGTA
TCTTCTGGAGAAGCAGAGCAGCTAGCCGTGCGATTTAAAAATGAAGAGTTGGCAAATAGC
TTCAAGCGAAAAATCGAGGAATGCCAGTCTAAAATGGAATCACAAGGAAATTTACATCCA
GAAAATGATTAA

>g10255.t1 Gene=g10255 Length=1723
MLKFYTKRDVDKHVSHMFQKLSEKERSSRGLHIARCYVKVNEWDLARDWLQRYLDTKQDD
PVAHRLMAEIYERLHKTEEAITSYQRSYNLNNKQNDIIKHVCRLYLLNGGWSSCPGKVKY
WCELAENENIRDENIADLQSKIGVKVTASGSTSSNSNLKERKSDVGKIRTEKKLQHELSS
SFNEEFNNNSQNGYTDDEIFHNASSSSFRTTQMSFAPMPNYNEKFADVEDLIRKLSDLVI
SVKEDVLCVRNDITSLRDDILNIRGDITDLSVNKDATTAKAIIDVNKSIEDLTWNVSCLM
NIFPSAPGPVSLPTNIRFPPNQLPPQFNQMYNTAYPIYPPIRPQLPPHLQYNDPLGMNLI
MNAAAAAANYGSPLIASPQQPPPPPQPQQPIPQQQNISPAITIQNGQKSSLMEALNTPSV
LNTWNNTYNAAQVMSTTIPQIHNFTPQQPPSTLVASPSVSISQQQPPPSSSIQTMPVNQN
KLVEKTPVNVVITSSDPLPTSNSFVTQPTLSVTIPPQHIKQSPIVSTETSKTVETKSQEN
VTSGNDLIKSTMSFRIPKKTETQVTTTTTTTQSNSTPKTQSMTFSGFTGDLSKPSPIAFA
TPTKDKEVIDKSNKPAQQSPFANFTFGGGSSNKSFTELFSNLNSNKSDTNNTTETKLNTS
ATITTQNEEEADHFEPTAQFEPVIPLPDLVEAKTGEEEENVVFCHRAKLLRYDTNTKEWK
ERGLGEMKVLVSKTDSSKARLLMRREQVLKICCNMPITKELKFTPRNATASSFGGQDFSE
GEIRSETLTIKFKTADLLKSFQEAVLNVQKNLTTETVQPEKKEVKKQEEKKQEVKKQEEK
KQEVKKQEVKKQEETKGFGDMFKPKAGSWTCEACYISNKPDTLYCVACESPKDNTVPKKE
PKSLLAPAADAPKFSFGMPNSSGFSFGMPQNQTTVAPVIAPAQSITTTASSTTGFSFGST
NTTSAPSNFTFGKPADSSSNVTSTKTDSNTESSGGFKFNVQNTFSFGINKEKSADEVQIE
KTPDQELGSGSGSSGFNFVFKKKSPAKTKSPGKTRNDSVNSEGNDGEEADNNEYHEEEEN
QAYFTPVIPLPDKIDVKTGEEDEEVLYSHRSKLYRFVDKEWKERGIGDIKILKHKETGKL
RVVMRREQVLKICLNFVLNEEIDFKPKDDTSFRFAANDFSEGVAEPTFFAIRFKTKEIRD
GFKKAIDDALAGTTKKSNTSSSDNDELIKRLMLPADFFNYLNKPDCTGCIGCKPDEYVYK
SDYKSEVTEDENALPLDAPKSIIKIVKPRRASQDKRVSFNLSDTKENNNVFNLFGGKNVE
ATPDKVKTDLFGIKKSEASTNIFAQFNAENPPPPPSAVSTSIFGSNAQNTSLGENKSIFG
SSIFSSSLNTTPTTNADIKKGDQQQSLFGNQNSFSFSAVSNGTIFGNANKENNSSPFGNS
SPFGSTSIFGSALNKSNNSDSKLNDNTKPTNIFSSNTNSSFSFAEAAKQLDKSSDANKST
VEPEFLKKTSSIGGFAELAAASSSNAFSGQNNSSSGFFGLTVKEDIFSRSKQLNASGNAD
ASQDDSENVNDDNYDPHYDPIISLPDEVKVSTGEEDEEKMFGERAKLFRYDANTKEWKER
GVGEMKILHHPINNTYRMILRREQIFKLVLNQLLTPDIHMAPMGSSPNAFCWAGMNYAEV
SSGEAEQLAVRFKNEELANSFKRKIEECQSKMESQGNLHPEND

Protein features from InterProScan

Transcript Database ID Name Start End E.value
23 g10255.t1 CDD cd13174 RanBD4_RanBP2_insect-like 1592 1709 1.59939E-67
22 g10255.t1 Coils Coil Coil 817 855 -
17 g10255.t1 Gene3D G3DSA:1.25.40.10 - 3 144 1.4E-33
19 g10255.t1 Gene3D G3DSA:2.30.29.30 - 664 824 9.3E-50
18 g10255.t1 Gene3D G3DSA:4.10.1060.10 Znf265 838 893 2.0E-16
20 g10255.t1 Gene3D G3DSA:2.30.29.30 - 1067 1228 1.1E-54
21 g10255.t1 Gene3D G3DSA:2.30.29.30 - 1561 1720 1.6E-53
31 g10255.t1 MobiDBLite mobidb-lite consensus disorder prediction 560 579 -
33 g10255.t1 MobiDBLite mobidb-lite consensus disorder prediction 816 853 -
32 g10255.t1 MobiDBLite mobidb-lite consensus disorder prediction 974 994 -
30 g10255.t1 MobiDBLite mobidb-lite consensus disorder prediction 1013 1082 -
29 g10255.t1 MobiDBLite mobidb-lite consensus disorder prediction 1024 1038 -
7 g10255.t1 PANTHER PTHR23138 RAN BINDING PROTEIN 464 843 2.4E-157
10 g10255.t1 PANTHER PTHR23138:SF87 E3 SUMO-PROTEIN LIGASE RANBP2-RELATED 464 843 2.4E-157
6 g10255.t1 PANTHER PTHR23138 RAN BINDING PROTEIN 820 1221 2.4E-157
9 g10255.t1 PANTHER PTHR23138:SF87 E3 SUMO-PROTEIN LIGASE RANBP2-RELATED 820 1221 2.4E-157
8 g10255.t1 PANTHER PTHR23138 RAN BINDING PROTEIN 1339 1711 2.4E-157
11 g10255.t1 PANTHER PTHR23138:SF87 E3 SUMO-PROTEIN LIGASE RANBP2-RELATED 1339 1711 2.4E-157
5 g10255.t1 Pfam PF14559 Tetratricopeptide repeat 29 70 2.1E-6
1 g10255.t1 Pfam PF00638 RanBP1 domain 691 810 2.7E-33
4 g10255.t1 Pfam PF00641 Zn-finger in Ran binding protein and others 865 892 1.4E-7
2 g10255.t1 Pfam PF00638 RanBP1 domain 1095 1209 1.7E-37
3 g10255.t1 Pfam PF00638 RanBP1 domain 1590 1710 1.2E-39
28 g10255.t1 ProSitePatterns PS01358 Zinc finger RanBP2-type signature. 869 888 -
38 g10255.t1 ProSiteProfiles PS50293 TPR repeat region circular profile. 27 94 11.012
37 g10255.t1 ProSiteProfiles PS50196 Ran binding domain type 1 profile. 679 814 35.619
34 g10255.t1 ProSiteProfiles PS50199 Zinc finger RanBP2 type profile. 865 894 10.478
36 g10255.t1 ProSiteProfiles PS50196 Ran binding domain type 1 profile. 1083 1215 35.654
35 g10255.t1 ProSiteProfiles PS50196 Ran binding domain type 1 profile. 1577 1714 37.986
25 g10255.t1 SMART SM00160 ranbd_3 680 808 5.4E-47
27 g10255.t1 SMART SM00547 zf_4 867 891 3.4E-6
26 g10255.t1 SMART SM00160 ranbd_3 1084 1209 5.9E-47
24 g10255.t1 SMART SM00160 ranbd_3 1578 1708 1.0E-41
12 g10255.t1 SUPERFAMILY SSF48452 TPR-like 32 111 1.59E-10
13 g10255.t1 SUPERFAMILY SSF50729 PH domain-like 681 812 5.82E-35
16 g10255.t1 SUPERFAMILY SSF90209 Ran binding protein zinc finger-like 866 892 2.83E-6
15 g10255.t1 SUPERFAMILY SSF50729 PH domain-like 1086 1210 3.91E-40
14 g10255.t1 SUPERFAMILY SSF50729 PH domain-like 1573 1714 1.23E-37

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:0046907 intracellular transport BP
GO:0005515 protein binding 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