General information for g10942.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Ran GTPase-activating protein.
Parent gene
- The parent gene g10942 is located on chr_1: 12919408..12920626 (- 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 | g10942 | g10942.t2 | TTS | g10942.t2 | 12918563 | 12918563 |
| chr_1 | g10942 | g10942.t2 | isoform | g10942.t2 | 12918688 | 12920626 |
| chr_1 | g10942 | g10942.t2 | exon | g10942.t2.exon1 | 12918688 | 12919227 |
| chr_1 | g10942 | g10942.t2 | cds | g10942.t2.CDS1 | 12919220 | 12919227 |
| chr_1 | g10942 | g10942.t2 | exon | g10942.t2.exon2 | 12919402 | 12920400 |
| chr_1 | g10942 | g10942.t2 | cds | g10942.t2.CDS2 | 12919402 | 12920400 |
| chr_1 | g10942 | g10942.t2 | exon | g10942.t2.exon3 | 12920515 | 12920626 |
| chr_1 | g10942 | g10942.t2 | cds | g10942.t2.CDS3 | 12920515 | 12920626 |
| chr_1 | g10942 | g10942.t2 | TSS | g10942.t2 | 12920702 | 12920702 |
Sequences
>g10942.t2 Gene=g10942 Length=1651
ATGGCGCTATTTAATTTAGCAAGTGTAAGTGATGCATTGAAAGAGACAGAGCAAGAATCA
AGTGGTGTTTCATTTGTCGGCTTGGCAAAAAAATGGGAAAATGAAGAAGATGTAAAAGAA
GTCATAAAAGCAATGCATGAATGTAAACATCTTCATTTTCTAAACTTGGAGGGAAACACT
CTTGGCTGTGAAGGAGCAAAACATATTGGTAAAGCATTAGAGAAACATCCAGAATTCAAG
AAAGCACTATGGAAAGACCTCTTTACTGGAAGAATGAAAACTGAAATACCACCGGCACTT
ATGGATTTATCAAAAGGAATTATGGTGGCAAAAGCTCAACTCACAGTACTTGATTTAAGC
GATAATGCTCTTGGACCTAATGGCGCAACCGGTTTAGTTGATTTATTAAGTAGCTCAGCA
TGCTACTCTCTACAAGAACTTCGTTTAATGAATTGCGGTTTAGGAATTACTGGTGCAAAA
ATGTTGGCTAAATCTCTTATGGAATGCTATAAGGGAAGTGTAGAAGCTGGAACTCCTATG
GAGTTAAGAGTTTTTGCAGCTGGTCGCAATCGATTAGAAAATGAAGGAGCAAAAGCATTG
TCAAAAGTTTTTGAGGAAATTCAGACATTACAGGAAATTACAATTCCTCAAAATGGAATT
TATCATGTTGGAATGTCAGCTTTAGCAGAAGCACTCAAAAAGAATCCCAACATTCAAGTT
ATAAATTTCAATGATAACACTATCACAGCAAAAGGAGCTGAAGTTTTAGCAGAGGCATTT
TATGCAATTGAAGGTCTACGTGAAATTAATTTGGGTGATTGTCTATTGAAAGATGAGGGT
GGTCAAATTTTAAGTGATGTTTTGGCCGATTGTCATCCTGATTTAGAGTTTGTTAATTTA
AGTGGAAATGAAATCGGACCAGAAGTTGGAATTGCTCTTGCAAATACAATGGGACATAAA
GAAAATTTGAAAAAGTTTATTCTCGATTCGAATCAATTTGGTGATGAAGGTGTTGAACAA
ATTCAACAAATTATGGAAGAGTTTGGCAAGTTGGATGTATTGAGTATTGAAGATGATGAA
GGTTTAGCTGATGAAGAAGAAGATGAAGGAGGAGGATGAAGAAGACTGTATCATTACAAA
TGTATCAAATCTATCTCAAAATAATTTTGAGACATCTCTCGACAACAGTATATTGCTCAA
TAATAGCTCAACAGCAGATGATCCAATTGCAGCTTTTTGTAATGATAAATTATCACCGAC
ATTCGAGAAATTCCAACAAATAACTGACGAGGACAAACTAAAAGCATTTAAAGACTATCT
CTCACAAGCTCCTGAAGACGATTACCTAACACATCTCGTTTTCATTATTTTAAAATTGTC
GTCCATTAGTGATCAATCAGAAGAAGCTAAACAACTTGCCTTAGATCTATTTAAAGAAGC
TTTCGACTATGCGAAAACCAAAGACCGTTTGAAGAGTGTCAGAAATTTTTTCCTTATTCA
ATTGGGCCTTTTAAAATCTGAACAGAAAGAATTCAAGCCTAAATATAATGTTCAATCGTG
TCGATCAACACTTGAAAATGCTCTTAAAGTAAACACATTACCTGATGAAGAAAAAACTAT
CTTTGAAGTGTTTCTTAATTCTGCTAAATAA
>g10942.t2 Gene=g10942 Length=372
MALFNLASVSDALKETEQESSGVSFVGLAKKWENEEDVKEVIKAMHECKHLHFLNLEGNT
LGCEGAKHIGKALEKHPEFKKALWKDLFTGRMKTEIPPALMDLSKGIMVAKAQLTVLDLS
DNALGPNGATGLVDLLSSSACYSLQELRLMNCGLGITGAKMLAKSLMECYKGSVEAGTPM
ELRVFAAGRNRLENEGAKALSKVFEEIQTLQEITIPQNGIYHVGMSALAEALKKNPNIQV
INFNDNTITAKGAEVLAEAFYAIEGLREINLGDCLLKDEGGQILSDVLADCHPDLEFVNL
SGNEIGPEVGIALANTMGHKENLKKFILDSNQFGDEGVEQIQQIMEEFGKLDVLSIEDDE
GLADEEEDEGGG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 20 | g10942.t2 | CDD | cd00116 | LRR_RI | 28 | 358 | 0.0000 |
| 19 | g10942.t2 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 23 | 361 | 0.0000 |
| 7 | g10942.t2 | PANTHER | PTHR24113:SF5 | RAN GTPASE-ACTIVATING PROTEIN 1 | 23 | 369 | 0.0000 |
| 8 | g10942.t2 | PANTHER | PTHR24113 | RAN GTPASE-ACTIVATING PROTEIN 1 | 23 | 369 | 0.0000 |
| 6 | g10942.t2 | Pfam | PF13516 | Leucine Rich repeat | 48 | 69 | 0.2200 |
| 5 | g10942.t2 | Pfam | PF13516 | Leucine Rich repeat | 113 | 132 | 0.0120 |
| 3 | g10942.t2 | Pfam | PF13516 | Leucine Rich repeat | 141 | 163 | 1.4000 |
| 4 | g10942.t2 | Pfam | PF13516 | Leucine Rich repeat | 234 | 257 | 0.1000 |
| 2 | g10942.t2 | Pfam | PF13516 | Leucine Rich repeat | 294 | 314 | 1.4000 |
| 1 | g10942.t2 | Pfam | PF13516 | Leucine Rich repeat | 320 | 341 | 0.1200 |
| 15 | g10942.t2 | SMART | SM00368 | LRR_RI_2 | 48 | 75 | 0.0095 |
| 12 | g10942.t2 | SMART | SM00368 | LRR_RI_2 | 111 | 138 | 0.0290 |
| 11 | g10942.t2 | SMART | SM00368 | LRR_RI_2 | 141 | 168 | 0.2900 |
| 17 | g10942.t2 | SMART | SM00368 | LRR_RI_2 | 179 | 206 | 85.0000 |
| 10 | g10942.t2 | SMART | SM00368 | LRR_RI_2 | 207 | 234 | 12.0000 |
| 18 | g10942.t2 | SMART | SM00368 | LRR_RI_2 | 235 | 262 | 0.5600 |
| 14 | g10942.t2 | SMART | SM00368 | LRR_RI_2 | 263 | 290 | 0.3100 |
| 13 | g10942.t2 | SMART | SM00368 | LRR_RI_2 | 292 | 319 | 22.0000 |
| 16 | g10942.t2 | SMART | SM00368 | LRR_RI_2 | 320 | 347 | 4.6000 |
| 9 | g10942.t2 | SUPERFAMILY | SSF52047 | RNI-like | 34 | 357 | 0.0000 |
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:0005515 | protein binding | MF |
KEGG
Orthology
- This transcript has been annotated with K14319 (Ran 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.
