General information for g9613.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Stromal membrane-associated protein 2.
Parent gene
- The parent gene g9613 is located on chr_1: 4283973..4285738 (- 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_1 | g9613 | g9613.t1 | TTS | g9613.t1 | 4283237 | 4283237 |
| chr_1 | g9613 | g9613.t1 | isoform | g9613.t1 | 4283973 | 4285738 |
| chr_1 | g9613 | g9613.t1 | exon | g9613.t1.exon1 | 4283973 | 4285081 |
| chr_1 | g9613 | g9613.t1 | cds | g9613.t1.CDS1 | 4283973 | 4285081 |
| chr_1 | g9613 | g9613.t1 | exon | g9613.t1.exon2 | 4285143 | 4285275 |
| chr_1 | g9613 | g9613.t1 | cds | g9613.t1.CDS2 | 4285143 | 4285275 |
| chr_1 | g9613 | g9613.t1 | exon | g9613.t1.exon3 | 4285685 | 4285738 |
| chr_1 | g9613 | g9613.t1 | cds | g9613.t1.CDS3 | 4285685 | 4285738 |
| chr_1 | g9613 | g9613.t1 | TSS | g9613.t1 | 4285836 | 4285836 |
Sequences
>g9613.t1 Gene=g9613 Length=1296
ATGAATAAGAAAGATGATAAGAAAGCAAAGTTGATACAAGAAAAGTGCAATACGATTCTC
AATCAGTTGCTAAGAGATGAGGATAACAAGTATTGTTGTGATTGCGATCAGAAAGGACCT
AGATGGGCAAGTTGGAATTTAGGCATTTTCTTATGCATTCGTTGCGCTGGAATTCATCGT
AATTTAGGCGTTCATATTTCTCGGGTTAAATCAGTCAATCTGGATACTTGGTCACCAGAG
CAAGTTGTTTGTCTACAACAAATGGGAAACTCGCGAGCTCGGGCAGTTTATGAAGCCTTA
TTATCTGATAATTTTCGTCGTCCACAAACGGATTCAGGATTAGAGAGTTTTATCCGTGCA
AAATATGAGCAAAAGAAGTATATAGCACGAGAATGGATTCCGCCACCATTTCCACCAAAA
GTCAATTGGGATAAAGAAATTGAAGAAGAACTTGAAAATCAAAAACGAAAAAAGAAAGCA
TCCAACAATGTTTCATCTAATGTCACTGAAAGCACACCAACTACTGTAAAGCCTCCAAGT
GCACCATCAAAGAGCATTATACCCGCACCTCTACCAAAACCTCATTCTCCCAAAAACTCA
AGAGTTGAGGCAAGAAAGAGTGCAACTTCAAATTCAACGAATATTACAGACCTATTAGGG
TTAGACACTGAAACACCATCATCAGTGAATAATACATCTTTGAATTCAATTCCAAATTCA
GATCATTCAACAATTCAAACAAGCACTCAAAATGAAAATTCTCTTAATTTTCCTTTTACG
ATTACAACAAATCAAACGTCATCATCACCAGCAAATCAATTAAGTGGAACATCCAATGGA
GAAGCAAATAATAGCGCGAATCAATTGAAACAAGAAGAAGTTGACTTTTTCAATCAAACA
ACATTAGAGAATACTAGTAGTGGTGCTAAATTGACAAATGACAAAATTTTGGCGCTCTAT
GGAAATGCAAGCTCTTCTTCGCCTCAACTTCCTCAATTTAATATAAATTTCCAACAACAT
ACACAGCAACAACCATTATCACTTCAGGATTCATTTTTTTATGGCAATCAACAGCCAGCT
GTATTCAAGCCTCAAATTCCGTCTCAACAACAACATCAATTCTATCCGACTCAACCGATA
CAAAGTCAGCCATCATCTTTACTGTATAATGGTAATAATAACAACTTTGCAAATTTTGGT
AATTTCGGAGGAACAATGCAATCGCAGCAAATCAACAAGCTAAATGAGGAAAACATAAGG
AAAATTGAAAGTCTCAATTTTAATAATTTCAAGTAA
>g9613.t1 Gene=g9613 Length=431
MNKKDDKKAKLIQEKCNTILNQLLRDEDNKYCCDCDQKGPRWASWNLGIFLCIRCAGIHR
NLGVHISRVKSVNLDTWSPEQVVCLQQMGNSRARAVYEALLSDNFRRPQTDSGLESFIRA
KYEQKKYIAREWIPPPFPPKVNWDKEIEEELENQKRKKKASNNVSSNVTESTPTTVKPPS
APSKSIIPAPLPKPHSPKNSRVEARKSATSNSTNITDLLGLDTETPSSVNNTSLNSIPNS
DHSTIQTSTQNENSLNFPFTITTNQTSSSPANQLSGTSNGEANNSANQLKQEEVDFFNQT
TLENTSSGAKLTNDKILALYGNASSSSPQLPQFNINFQQHTQQQPLSLQDSFFYGNQQPA
VFKPQIPSQQQHQFYPTQPIQSQPSSLLYNGNNNNFANFGNFGGTMQSQQINKLNEENIR
KIESLNFNNFK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g9613.t1 | CDD | cd08839 | ArfGap_SMAP | 20 | 122 | 1.56841E-75 |
| 8 | g9613.t1 | Coils | Coil | Coil | 144 | 164 | - |
| 7 | g9613.t1 | Gene3D | G3DSA:3.30.40.160 | - | 4 | 132 | 8.2E-52 |
| 11 | g9613.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 152 | 223 | - |
| 13 | g9613.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 160 | 181 | - |
| 12 | g9613.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 203 | 223 | - |
| 2 | g9613.t1 | PANTHER | PTHR45705 | FI20236P1 | 1 | 412 | 1.6E-83 |
| 3 | g9613.t1 | PRINTS | PR00405 | HIV Rev interacting protein signature | 29 | 48 | 1.9E-21 |
| 4 | g9613.t1 | PRINTS | PR00405 | HIV Rev interacting protein signature | 48 | 65 | 1.9E-21 |
| 5 | g9613.t1 | PRINTS | PR00405 | HIV Rev interacting protein signature | 69 | 90 | 1.9E-21 |
| 1 | g9613.t1 | Pfam | PF01412 | Putative GTPase activating protein for Arf | 18 | 130 | 1.2E-40 |
| 14 | g9613.t1 | ProSiteProfiles | PS50115 | ARF GTPase-activating proteins domain profile. | 17 | 135 | 27.504 |
| 10 | g9613.t1 | SMART | SM00105 | arf_gap_3 | 18 | 135 | 2.7E-46 |
| 6 | g9613.t1 | SUPERFAMILY | SSF57863 | ArfGap/RecO-like zinc finger | 17 | 129 | 1.96E-42 |
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 K12486 (stromal membrane-associated 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.
