General information for g6548.t6
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.t6 | isoform | g6548.t6 | 17602005 | 17604434 |
| chr_2 | g6548 | g6548.t6 | exon | g6548.t6.exon1 | 17602005 | 17602131 |
| chr_2 | g6548 | g6548.t6 | cds | g6548.t6.CDS1 | 17602041 | 17602131 |
| chr_2 | g6548 | g6548.t6 | exon | g6548.t6.exon2 | 17602463 | 17602561 |
| chr_2 | g6548 | g6548.t6 | cds | g6548.t6.CDS2 | 17602463 | 17602561 |
| chr_2 | g6548 | g6548.t6 | exon | g6548.t6.exon3 | 17602632 | 17602731 |
| chr_2 | g6548 | g6548.t6 | cds | g6548.t6.CDS3 | 17602632 | 17602731 |
| chr_2 | g6548 | g6548.t6 | exon | g6548.t6.exon4 | 17603803 | 17604023 |
| chr_2 | g6548 | g6548.t6 | cds | g6548.t6.CDS4 | 17603803 | 17604023 |
| chr_2 | g6548 | g6548.t6 | exon | g6548.t6.exon5 | 17604095 | 17604272 |
| chr_2 | g6548 | g6548.t6 | cds | g6548.t6.CDS5 | 17604095 | 17604272 |
| chr_2 | g6548 | g6548.t6 | exon | g6548.t6.exon6 | 17604343 | 17604434 |
| chr_2 | g6548 | g6548.t6 | cds | g6548.t6.CDS6 | 17604343 | 17604433 |
| chr_2 | g6548 | g6548.t6 | TSS | g6548.t6 | NA | NA |
| chr_2 | g6548 | g6548.t6 | TTS | g6548.t6 | NA | NA |
Sequences
>g6548.t6 Gene=g6548 Length=817
CAAATTAAGGATGAGCTTAGTGAAGTAGTACAAGAGATGGAATCACATGAGTCCGAAAAT
AAGCATTCCAGTAAGGAAAAGCAAATGTCGATAGGACGGAAAAAGTTCAATATGGATCCG
AAAAAAGGTATCGAATATCTTTACGAGAACCATCTTCTCAAACATGATCCACAAGATGTG
GCGCAATTTTTGTATAAAGGAGAAGGATTAAATAAAACAGCAATCGGTGACTATCTAGGC
GAGAAAAATCCATTCAATGAGAAAGTTTTGAAAGCTTTTGTTGAACTTCATGACTTTACA
AATCTTATTTTAGTGCAAGCTTTAAGGCAATTTTTATGGAGCTTTCGACTGCCGGGTGAG
GCACAGAAAATTGATAGAATGATGGAGTGCTTTGCACAACGCTACTGTCAATTAAATCCT
GACATCTTTACTAACGCCGACACATGTTATGTTTTGAGTTTCGCCATTATTATGTTGAAC
ACTTCTCTTCATAATCCATCTGTTAAAGATAAACCAACTGTCGAGCAATTTATTTCAATG
AATCGAGGTGTGAATAACGGAGATGATTTACCACGAGAGCTTTTAGAATCACTTTACGAA
TCAATAAGAACCGAGCCATTTAAAATTCCACAAGATGATGGCAATGATTTAATGCATACA
TTCTTCAATCCCGATAAAGAAGGTTGGTTATGGAAACAAGGAGGGCGCTATAAGTCGTGG
AAAAGACGATGGTTTATCCTTAACGATAATTGTCTTTATTACTTTGAATTTACAACTGAT
AAAGAACCAAGAGGCATTATACCGCTAGAAAACATTA
>g6548.t6 Gene=g6548 Length=260
MESHESENKHSSKEKQMSIGRKKFNMDPKKGIEYLYENHLLKHDPQDVAQFLYKGEGLNK
TAIGDYLGEKNPFNEKVLKAFVELHDFTNLILVQALRQFLWSFRLPGEAQKIDRMMECFA
QRYCQLNPDIFTNADTCYVLSFAIIMLNTSLHNPSVKDKPTVEQFISMNRGVNNGDDLPR
ELLESLYESIRTEPFKIPQDDGNDLMHTFFNPDKEGWLWKQGGRYKSWKRRWFILNDNCL
YYFEFTTDKEPRGIIPLENI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g6548.t6 | CDD | cd00171 | Sec7 | 13 | 195 | 5.84876E-97 |
| 9 | g6548.t6 | Gene3D | G3DSA:1.10.220.20 | - | 8 | 86 | 9.7E-32 |
| 8 | g6548.t6 | Gene3D | G3DSA:1.10.1000.11 | - | 87 | 209 | 1.6E-55 |
| 7 | g6548.t6 | Gene3D | G3DSA:2.30.29.30 | - | 210 | 260 | 4.3E-20 |
| 12 | g6548.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 22 | - |
| 3 | g6548.t6 | PANTHER | PTHR10663:SF315 | CYTOHESIN 4A-RELATED | 4 | 260 | 1.8E-146 |
| 4 | g6548.t6 | PANTHER | PTHR10663 | GUANYL-NUCLEOTIDE EXCHANGE FACTOR | 4 | 260 | 1.8E-146 |
| 1 | g6548.t6 | Pfam | PF01369 | Sec7 domain | 14 | 195 | 4.3E-75 |
| 2 | g6548.t6 | Pfam | PF00169 | PH domain | 213 | 260 | 1.8E-13 |
| 13 | g6548.t6 | ProSiteProfiles | PS50190 | SEC7 domain profile. | 6 | 193 | 45.298 |
| 14 | g6548.t6 | ProSiteProfiles | PS50003 | PH domain profile. | 211 | 260 | 12.28 |
| 11 | g6548.t6 | SMART | SM00222 | sec7_5 | 10 | 195 | 2.4E-101 |
| 6 | g6548.t6 | SUPERFAMILY | SSF48425 | Sec7 domain | 13 | 203 | 7.06E-80 |
| 5 | g6548.t6 | SUPERFAMILY | SSF50729 | PH domain-like | 207 | 259 | 8.77E-18 |
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 K18442 (brefeldin A-inhibited guanine nucleotide-exchange protein)
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