General information for g1456.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative ADP-ribosylation factor GTPase-activating protein 1.
Parent gene
- The parent gene g1456 is located on chr_3: 11045027..11045850 (- 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_3 | g1456 | g1456.t1 | TTS | g1456.t1 | 11044317 | 11044317 |
| chr_3 | g1456 | g1456.t1 | isoform | g1456.t1 | 11044496 | 11045850 |
| chr_3 | g1456 | g1456.t1 | exon | g1456.t1.exon1 | 11044496 | 11045578 |
| chr_3 | g1456 | g1456.t1 | cds | g1456.t1.CDS1 | 11044496 | 11045578 |
| chr_3 | g1456 | g1456.t1 | exon | g1456.t1.exon2 | 11045640 | 11045686 |
| chr_3 | g1456 | g1456.t1 | cds | g1456.t1.CDS2 | 11045640 | 11045686 |
| chr_3 | g1456 | g1456.t1 | exon | g1456.t1.exon3 | 11045751 | 11045850 |
| chr_3 | g1456 | g1456.t1 | cds | g1456.t1.CDS3 | 11045751 | 11045850 |
| chr_3 | g1456 | g1456.t1 | TSS | g1456.t1 | 11045916 | 11045916 |
Sequences
>g1456.t1 Gene=g1456 Length=1230
ATGAGTTCACCTCGTTCGCGAAGACTTTTTCAGGAAATAAAAACAAATGACGAGAGCAAT
AAGTTCTGCTTTGATTGTGGAGCACATGCTCCTCAATGGGCATCTGTACAATATGGAATT
TGGGTTTGCCTCGAATGTAGCGGAAAACATCGAGGATTGGGAGTACACATTTCATTCATT
CGTTCAATTACAATGGACAAATGGAAAGACCTTGAACTAGAGAAAATGAAAGTAGGAGGA
AATCGGAAGGCAAAACAATTCCTTGAAGCTGAAGATAGTTGGAATGAATCAACACGTTTC
AATGATCGCTACAATTCATTAGCAGCTGCTTTATATCGTGACAAAATTTCAGCTTTGGCA
GAAGGACGTGAATGGGATTATGATGAAGCAAAGAAGAGATTGGCAAAGAGACCATCAGCT
CACATTCCTCACTCGAAAAGCGCTGGCGCACTTTCATCGAATAATTATTCTTCAGGCAAT
AACTATGAAGCAAGTTCTGGTGGCGGTTATCAAAATGCAGAATTTAACATGAAAGACATC
AGTGATCAGAAAGAAAAATTCTTTGATAGAATTCAAGCTGAGAATGCAATGAGGCGAGAT
GATTTGCCGCCAAGTCAAGGTGGCCGTTATCAAGGCTTTGGGAATCAAGTTCAAAATAAT
TCTGTTAGAAAGAGTCAAAGTGAGTTCTTTGATACAACTTGGTCTTCATTCTCGAGTGGC
TGGGGATTGCTTTCAAATAGCGCTACAAAACTTGCTCAAACAGCTAAAGATTATGGGAAT
ATTGCATCTCAAAAAATGAAAGAATCGAATCTGCTTGATGTTGCTGGAAAAGAAGTTTTT
AATATCGCAAATAAAGTAACAGATCTGGGAAGAAAAGGTCTTCAAACCGCTACAAGCGCA
ATTAGTGGAGCTAACTATAACGACATTGACAATCCACAACAACAGCAAAAAAGCAATTAC
GAACAGAATCAATTTAATAATGATTGGACCAATGTCGATTCAAATGGTTTTACAGATGAC
GACCAATTCGAATCATATCAAAGTTACGAAAGCCCTAAAAGTGTTGCAAGCGAGAAAACT
AGTATAAAAGCCAGTCGTCCAAGACCGCAAGCATCAGATAGCTTAGTAAATGATTTTAAA
AATATGGATGTAAAGAGTGGTATAAAAGTAGATAGCTCAAAGAAAACAAATAAACAGGAA
GATGATTTATGGAATATGTTGAACAACTAG
>g1456.t1 Gene=g1456 Length=409
MSSPRSRRLFQEIKTNDESNKFCFDCGAHAPQWASVQYGIWVCLECSGKHRGLGVHISFI
RSITMDKWKDLELEKMKVGGNRKAKQFLEAEDSWNESTRFNDRYNSLAAALYRDKISALA
EGREWDYDEAKKRLAKRPSAHIPHSKSAGALSSNNYSSGNNYEASSGGGYQNAEFNMKDI
SDQKEKFFDRIQAENAMRRDDLPPSQGGRYQGFGNQVQNNSVRKSQSEFFDTTWSSFSSG
WGLLSNSATKLAQTAKDYGNIASQKMKESNLLDVAGKEVFNIANKVTDLGRKGLQTATSA
ISGANYNDIDNPQQQQKSNYEQNQFNNDWTNVDSNGFTDDDQFESYQSYESPKSVASEKT
SIKASRPRPQASDSLVNDFKNMDVKSGIKVDSSKKTNKQEDDLWNMLNN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g1456.t1 | CDD | cd08830 | ArfGap_ArfGap1 | 6 | 122 | 2.09696E-66 |
| 7 | g1456.t1 | Gene3D | G3DSA:3.30.40.160 | - | 3 | 129 | 8.4E-46 |
| 10 | g1456.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 348 | 409 | - |
| 11 | g1456.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 348 | 379 | - |
| 12 | g1456.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 384 | 401 | - |
| 2 | g1456.t1 | PANTHER | PTHR46395 | ADP-RIBOSYLATION FACTOR GTPASE-ACTIVATING PROTEIN 1 | 1 | 397 | 4.9E-101 |
| 5 | g1456.t1 | PRINTS | PR00405 | HIV Rev interacting protein signature | 20 | 39 | 1.3E-22 |
| 4 | g1456.t1 | PRINTS | PR00405 | HIV Rev interacting protein signature | 39 | 56 | 1.3E-22 |
| 3 | g1456.t1 | PRINTS | PR00405 | HIV Rev interacting protein signature | 60 | 81 | 1.3E-22 |
| 1 | g1456.t1 | Pfam | PF01412 | Putative GTPase activating protein for Arf | 11 | 115 | 1.7E-32 |
| 13 | g1456.t1 | ProSiteProfiles | PS50115 | ARF GTPase-activating proteins domain profile. | 7 | 125 | 26.73 |
| 9 | g1456.t1 | SMART | SM00105 | arf_gap_3 | 7 | 125 | 1.8E-42 |
| 6 | g1456.t1 | SUPERFAMILY | SSF57863 | ArfGap/RecO-like zinc finger | 16 | 105 | 8.37E-34 |
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:0005096 | GTPase activator activity | MF |
KEGG
Orthology
- This transcript has been annotated with K12492 (ADP-ribosylation factor GTPase-activating protein 1)
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.
