Gene loci information

Transcript annotation

  • This transcript has been annotated as Cytohesin-1.

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 g6548 g6548.t1 TSS g6548.t1 17598315 17598315
chr_2 g6548 g6548.t1 isoform g6548.t1 17598969 17607265
chr_2 g6548 g6548.t1 exon g6548.t1.exon1 17598969 17600000
chr_2 g6548 g6548.t1 cds g6548.t1.CDS1 17598969 17600000
chr_2 g6548 g6548.t1 exon g6548.t1.exon2 17602005 17602131
chr_2 g6548 g6548.t1 cds g6548.t1.CDS2 17602005 17602131
chr_2 g6548 g6548.t1 exon g6548.t1.exon3 17602463 17602561
chr_2 g6548 g6548.t1 cds g6548.t1.CDS3 17602463 17602561
chr_2 g6548 g6548.t1 exon g6548.t1.exon4 17602632 17602731
chr_2 g6548 g6548.t1 cds g6548.t1.CDS4 17602632 17602731
chr_2 g6548 g6548.t1 exon g6548.t1.exon5 17603803 17604023
chr_2 g6548 g6548.t1 cds g6548.t1.CDS5 17603803 17604023
chr_2 g6548 g6548.t1 exon g6548.t1.exon6 17604095 17604272
chr_2 g6548 g6548.t1 cds g6548.t1.CDS6 17604095 17604272
chr_2 g6548 g6548.t1 exon g6548.t1.exon7 17604343 17604436
chr_2 g6548 g6548.t1 cds g6548.t1.CDS7 17604343 17604436
chr_2 g6548 g6548.t1 exon g6548.t1.exon8 17604516 17604623
chr_2 g6548 g6548.t1 cds g6548.t1.CDS8 17604516 17604623
chr_2 g6548 g6548.t1 exon g6548.t1.exon9 17604697 17604844
chr_2 g6548 g6548.t1 cds g6548.t1.CDS9 17604697 17604844
chr_2 g6548 g6548.t1 exon g6548.t1.exon10 17606592 17606647
chr_2 g6548 g6548.t1 cds g6548.t1.CDS10 17606592 17606647
chr_2 g6548 g6548.t1 exon g6548.t1.exon11 17606902 17606933
chr_2 g6548 g6548.t1 cds g6548.t1.CDS11 17606902 17606933
chr_2 g6548 g6548.t1 exon g6548.t1.exon12 17606996 17607026
chr_2 g6548 g6548.t1 cds g6548.t1.CDS12 17606996 17607026
chr_2 g6548 g6548.t1 exon g6548.t1.exon13 17607092 17607265
chr_2 g6548 g6548.t1 cds g6548.t1.CDS13 17607092 17607265
chr_2 g6548 g6548.t1 TTS g6548.t1 17607339 17607339

Sequences

>g6548.t1 Gene=g6548 Length=2400
ATGTTTGGAAGCGATAAGAAATCGAATGGTGGTAGTGGTGGCGTAACAAATTGGTTTTTC
TCACTTCGTCGACAACCCAAAAAACAGAAATCACTTGATAGTAGTAAGCTCCTACAGAAG
AGCTGCGTAGATTTATCGAGCGCTGGCGTCAATGGCGGTTCTTCCGAACAAGACTTACTA
TTCCGCACAAAGCCTTCCAAACTGAAACTAAATAACAATAGTAGCAATAATAATAATAAT
AATAATGACGACTTATCGTCAAATAGCAATTCATGTACAAATTGTTGTTGTAAATTCTCA
TCAAAAACCTCCTCATCACCGTCATTTGGTGTATCACCAATCGATGACATTGAACAGTGT
GATCAAATGCGTAGAGTGTTAATTACAAGCGAGGAAAACTATTGTGCAACAGATTTTCAT
GATTACGACGATGTAGATATCGAAGAAGAGAATGATGATATGAAAATACCACCAGCCTCA
CAACAACAGCCACAGCCAAAGCAAAAAACAAGTAATTTTAATAGTAACATTTTATTGTAC
AACAAAAAAGAAGAATTTAGCAGAACGACGCGAACGGTGACAACGAGAGTCGTTACAAAA
GCAACAATTAACGGTAATGACACAATGACCCTTCCAACACAATCGCTAACATCATCATCA
TCAACGAGCTGTAGTAATACCAATCGAAATCTAAACAGCAACATTCACCATCGTATAGGC
TTAGTATTTAATGAAAATGGGCAATTAATCAATAGGAGACAATTATTAAATGCAAAGAAC
CGTGATGGTCTAATATTTGATGAATGTGGAAGGCTTTTGTATACGGACAATGATGAAACT
TCATCATCACTCACTCCCATTTCAATATTAGATGATAGTACAATTGAGTTTATAGATAGT
TCAACACAAAACAGTGATATACAGAATCGAGCAAATATGCAAAATAAGTGTAATAATTGC
AATGGTAGCAAATTGACGATAAGTAGCAGTATATTATCAAGTTGTAAATCAGATTGGGAA
TTTTCAAAACAGCAAATTAAGGATGAGCTTAGTGAAGTAGTACAAGAGATGGAATCACAT
GAGTCCGAAAATAAGCATTCCAGTAAGGAAAAGCAAATGTCGATAGGACGGAAAAAGTTC
AATATGGATCCGAAAAAAGGTATCGAATATCTTTACGAGAACCATCTTCTCAAACATGAT
CCACAAGATGTGGCGCAATTTTTGTATAAAGGAGAAGGATTAAATAAAACAGCAATCGGT
GACTATCTAGGCGAGAAAAATCCATTCAATGAGAAAGTTTTGAAAGCTTTTGTTGAACTT
CATGACTTTACAAATCTTATTTTAGTGCAAGCTTTAAGGCAATTTTTATGGAGCTTTCGA
CTGCCGGGTGAGGCACAGAAAATTGATAGAATGATGGAGTGCTTTGCACAACGCTACTGT
CAATTAAATCCTGACATCTTTACTAACGCCGACACATGTTATGTTTTGAGTTTCGCCATT
ATTATGTTGAACACTTCTCTTCATAATCCATCTGTTAAAGATAAACCAACTGTCGAGCAA
TTTATTTCAATGAATCGAGGTGTGAATAACGGAGATGATTTACCACGAGAGCTTTTAGAA
TCACTTTACGAATCAATAAGAACCGAGCCATTTAAAATTCCACAAGATGATGGCAATGAT
TTAATGCATACATTCTTCAATCCCGATAAAGAAGGTTGGTTATGGAAACAAGGAGGGCGC
TATAAGTCGTGGAAAAGACGATGGTTTATCCTTAACGATAATTGTCTTTATTACTTTGAA
TTTACAACTGATAAAGAACCAAGAGGCATTATACCGCTAGAAAACATTATGGTTCGTGAG
TGCAAGGCCACTGATAAAAGTAAACCACATTGCTTTGAATTGTATGCTTCGGGTGGTGCA
GAAATAATCAAGGCCTGTAAAACGGATTCAGAGGGCAAGGTTGTTGAGGGTAAACATACA
GTTTATCGAATGTCTGCTGCTACTGAGGAGGAAAAGAATGAATGGATAAGACTTTTGAAA
CATTCAATTGCCCATAATCCGTTTTATGACATTTTGGTACAAAGGAAGAAGAAGGCGCTT
GTTAAGAAGTCGTACGCAAGTTGCGTTGATTCTTTCTTTCTGAAATTTTTTTCAATCGTC
GAGGATCAAATTGATCACAGCATTAAACAAAAATGGCAAAGCGTACAAAGAAGGTCGGAA
TTGTTGCACGGCAAATATACATGCAGTTTCTGTGGTAAAGATGCAATGAAACGCACTTGT
GTTGGTATCTGGAGTTGCAAACGATGCAAGCGAGTAGTTGCTGGAGGAGCATGGGTTTTT
TCCACAACAGCAGCAGCCACCGTACGCTCAGCAGTCAGACGTTTGAGAGAATTGAACTAA

>g6548.t1 Gene=g6548 Length=799
MFGSDKKSNGGSGGVTNWFFSLRRQPKKQKSLDSSKLLQKSCVDLSSAGVNGGSSEQDLL
FRTKPSKLKLNNNSSNNNNNNNDDLSSNSNSCTNCCCKFSSKTSSSPSFGVSPIDDIEQC
DQMRRVLITSEENYCATDFHDYDDVDIEEENDDMKIPPASQQQPQPKQKTSNFNSNILLY
NKKEEFSRTTRTVTTRVVTKATINGNDTMTLPTQSLTSSSSTSCSNTNRNLNSNIHHRIG
LVFNENGQLINRRQLLNAKNRDGLIFDECGRLLYTDNDETSSSLTPISILDDSTIEFIDS
STQNSDIQNRANMQNKCNNCNGSKLTISSSILSSCKSDWEFSKQQIKDELSEVVQEMESH
ESENKHSSKEKQMSIGRKKFNMDPKKGIEYLYENHLLKHDPQDVAQFLYKGEGLNKTAIG
DYLGEKNPFNEKVLKAFVELHDFTNLILVQALRQFLWSFRLPGEAQKIDRMMECFAQRYC
QLNPDIFTNADTCYVLSFAIIMLNTSLHNPSVKDKPTVEQFISMNRGVNNGDDLPRELLE
SLYESIRTEPFKIPQDDGNDLMHTFFNPDKEGWLWKQGGRYKSWKRRWFILNDNCLYYFE
FTTDKEPRGIIPLENIMVRECKATDKSKPHCFELYASGGAEIIKACKTDSEGKVVEGKHT
VYRMSAATEEEKNEWIRLLKHSIAHNPFYDILVQRKKKALVKKSYASCVDSFFLKFFSIV
EDQIDHSIKQKWQSVQRRSELLHGKYTCSFCGKDAMKRTCVGIWSCKRCKRVVAGGAWVF
STTAAATVRSAVRRLRELN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g6548.t1 CDD cd00171 Sec7 369 551 2.42606E-92
15 g6548.t1 CDD cd01252 PH_GRP1-like 566 686 3.46983E-76
13 g6548.t1 Coils Coil Coil 343 370 -
12 g6548.t1 Gene3D G3DSA:1.10.220.20 - 364 442 5.7E-31
10 g6548.t1 Gene3D G3DSA:1.10.1000.11 - 443 566 1.3E-54
9 g6548.t1 Gene3D G3DSA:2.30.29.30 - 567 695 4.2E-40
11 g6548.t1 Gene3D G3DSA:2.20.25.30 - 721 799 3.2E-24
4 g6548.t1 PANTHER PTHR10663:SF340 CYTOHESIN-1 343 700 3.0E-176
5 g6548.t1 PANTHER PTHR10663 GUANYL-NUCLEOTIDE EXCHANGE FACTOR 343 700 3.0E-176
1 g6548.t1 Pfam PF01369 Sec7 domain 370 551 5.6E-74
2 g6548.t1 Pfam PF00169 PH domain 569 683 1.3E-24
3 g6548.t1 Pfam PF01780 Ribosomal L37ae protein family 731 797 1.6E-21
18 g6548.t1 ProSiteProfiles PS50190 SEC7 domain profile. 362 549 45.298
19 g6548.t1 ProSiteProfiles PS50003 PH domain profile. 567 684 18.613
17 g6548.t1 SMART SM00222 sec7_5 366 551 2.4E-101
16 g6548.t1 SMART SM00233 PH_update 568 686 3.0E-22
8 g6548.t1 SUPERFAMILY SSF48425 Sec7 domain 369 559 1.01E-78
7 g6548.t1 SUPERFAMILY SSF50729 PH domain-like 566 690 2.95E-30
6 g6548.t1 SUPERFAMILY SSF57829 Zn-binding ribosomal proteins 735 790 4.76E-16

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:0005840 ribosome CC
GO:0032012 regulation of ARF protein signal transduction BP
GO:0006412 translation BP
GO:0005085 guanyl-nucleotide exchange factor activity MF
GO:0003735 structural constituent of ribosome 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