General information for g6548.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cytohesin-1.
Parent gene
- The parent gene g6548 is located on chr_2: 17606925..17607974 (+ strand)
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.t3 | TSS | g6548.t3 | 17598315 | 17598315 |
| chr_2 | g6548 | g6548.t3 | isoform | g6548.t3 | 17598969 | 17604844 |
| chr_2 | g6548 | g6548.t3 | exon | g6548.t3.exon1 | 17598969 | 17600000 |
| chr_2 | g6548 | g6548.t3 | cds | g6548.t3.CDS1 | 17598969 | 17600000 |
| chr_2 | g6548 | g6548.t3 | exon | g6548.t3.exon2 | 17602005 | 17602131 |
| chr_2 | g6548 | g6548.t3 | cds | g6548.t3.CDS2 | 17602005 | 17602131 |
| chr_2 | g6548 | g6548.t3 | exon | g6548.t3.exon3 | 17602463 | 17602561 |
| chr_2 | g6548 | g6548.t3 | cds | g6548.t3.CDS3 | 17602463 | 17602561 |
| chr_2 | g6548 | g6548.t3 | exon | g6548.t3.exon4 | 17602632 | 17602731 |
| chr_2 | g6548 | g6548.t3 | cds | g6548.t3.CDS4 | 17602632 | 17602731 |
| chr_2 | g6548 | g6548.t3 | exon | g6548.t3.exon5 | 17603803 | 17604023 |
| chr_2 | g6548 | g6548.t3 | cds | g6548.t3.CDS5 | 17603803 | 17604023 |
| chr_2 | g6548 | g6548.t3 | exon | g6548.t3.exon6 | 17604095 | 17604272 |
| chr_2 | g6548 | g6548.t3 | cds | g6548.t3.CDS6 | 17604095 | 17604272 |
| chr_2 | g6548 | g6548.t3 | exon | g6548.t3.exon7 | 17604343 | 17604436 |
| chr_2 | g6548 | g6548.t3 | cds | g6548.t3.CDS7 | 17604343 | 17604436 |
| chr_2 | g6548 | g6548.t3 | exon | g6548.t3.exon8 | 17604516 | 17604623 |
| chr_2 | g6548 | g6548.t3 | cds | g6548.t3.CDS8 | 17604516 | 17604623 |
| chr_2 | g6548 | g6548.t3 | exon | g6548.t3.exon9 | 17604697 | 17604844 |
| chr_2 | g6548 | g6548.t3 | cds | g6548.t3.CDS9 | 17604697 | 17604843 |
| chr_2 | g6548 | g6548.t3 | TTS | g6548.t3 | NA | NA |
Sequences
>g6548.t3 Gene=g6548 Length=2107
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
GTTAAGA
>g6548.t3 Gene=g6548 Length=702
MFGSDKKSNGGSGGVTNWFFSLRRQPKKQKSLDSSKLLQKSCVDLSSAGVNGGSSEQDLL
FRTKPSKLKLNNNSSNNNNNNNDDLSSNSNSCTNCCCKFSSKTSSSPSFGVSPIDDIEQC
DQMRRVLITSEENYCATDFHDYDDVDIEEENDDMKIPPASQQQPQPKQKTSNFNSNILLY
NKKEEFSRTTRTVTTRVVTKATINGNDTMTLPTQSLTSSSSTSCSNTNRNLNSNIHHRIG
LVFNENGQLINRRQLLNAKNRDGLIFDECGRLLYTDNDETSSSLTPISILDDSTIEFIDS
STQNSDIQNRANMQNKCNNCNGSKLTISSSILSSCKSDWEFSKQQIKDELSEVVQEMESH
ESENKHSSKEKQMSIGRKKFNMDPKKGIEYLYENHLLKHDPQDVAQFLYKGEGLNKTAIG
DYLGEKNPFNEKVLKAFVELHDFTNLILVQALRQFLWSFRLPGEAQKIDRMMECFAQRYC
QLNPDIFTNADTCYVLSFAIIMLNTSLHNPSVKDKPTVEQFISMNRGVNNGDDLPRELLE
SLYESIRTEPFKIPQDDGNDLMHTFFNPDKEGWLWKQGGRYKSWKRRWFILNDNCLYYFE
FTTDKEPRGIIPLENIMVRECKATDKSKPHCFELYASGGAEIIKACKTDSEGKVVEGKHT
VYRMSAATEEEKNEWIRLLKHSIAHNPFYDILVQRKKKALVK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g6548.t3 | CDD | cd00171 | Sec7 | 369 | 551 | 7.88146E-92 |
| 12 | g6548.t3 | CDD | cd01252 | PH_GRP1-like | 566 | 686 | 5.39076E-77 |
| 10 | g6548.t3 | Coils | Coil | Coil | 343 | 370 | - |
| 9 | g6548.t3 | Gene3D | G3DSA:1.10.220.20 | - | 364 | 442 | 4.8E-31 |
| 8 | g6548.t3 | Gene3D | G3DSA:1.10.1000.11 | - | 443 | 566 | 1.1E-54 |
| 7 | g6548.t3 | Gene3D | G3DSA:2.30.29.30 | - | 567 | 695 | 3.4E-40 |
| 3 | g6548.t3 | PANTHER | PTHR10663:SF340 | CYTOHESIN-1 | 343 | 698 | 3.9E-176 |
| 4 | g6548.t3 | PANTHER | PTHR10663 | GUANYL-NUCLEOTIDE EXCHANGE FACTOR | 343 | 698 | 3.9E-176 |
| 1 | g6548.t3 | Pfam | PF01369 | Sec7 domain | 370 | 551 | 4.4E-74 |
| 2 | g6548.t3 | Pfam | PF00169 | PH domain | 569 | 683 | 1.1E-24 |
| 15 | g6548.t3 | ProSiteProfiles | PS50190 | SEC7 domain profile. | 362 | 549 | 45.298 |
| 16 | g6548.t3 | ProSiteProfiles | PS50003 | PH domain profile. | 567 | 684 | 18.613 |
| 14 | g6548.t3 | SMART | SM00222 | sec7_5 | 366 | 551 | 2.4E-101 |
| 13 | g6548.t3 | SMART | SM00233 | PH_update | 568 | 686 | 3.0E-22 |
| 6 | g6548.t3 | SUPERFAMILY | SSF48425 | Sec7 domain | 369 | 559 | 7.98E-79 |
| 5 | g6548.t3 | SUPERFAMILY | SSF50729 | PH domain-like | 566 | 690 | 2.41E-30 |
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:0032012 | regulation of ARF protein signal transduction | BP |
| GO:0005085 | guanyl-nucleotide exchange factor activity | MF |
KEGG
Orthology
- This transcript has been annotated with K18441 (cytohesin)
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. There were no conditions that were differentially expressed