Gene loci information

Transcript annotation

  • This transcript has been annotated as Ran GTPase-activating protein.

Parent gene

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.t1 TTS g10942.t1 12918563 12918563
chr_1 g10942 g10942.t1 isoform g10942.t1 12918688 12920626
chr_1 g10942 g10942.t1 exon g10942.t1.exon1 12918688 12919227
chr_1 g10942 g10942.t1 cds g10942.t1.CDS1 12918688 12919227
chr_1 g10942 g10942.t1 exon g10942.t1.exon2 12919283 12919344
chr_1 g10942 g10942.t1 cds g10942.t1.CDS2 12919283 12919344
chr_1 g10942 g10942.t1 exon g10942.t1.exon3 12919402 12920400
chr_1 g10942 g10942.t1 cds g10942.t1.CDS3 12919402 12920400
chr_1 g10942 g10942.t1 exon g10942.t1.exon4 12920515 12920626
chr_1 g10942 g10942.t1 cds g10942.t1.CDS4 12920515 12920626
chr_1 g10942 g10942.t1 TSS g10942.t1 12920702 12920702

Sequences

>g10942.t1 Gene=g10942 Length=1713
ATGGCGCTATTTAATTTAGCAAGTGTAAGTGATGCATTGAAAGAGACAGAGCAAGAATCA
AGTGGTGTTTCATTTGTCGGCTTGGCAAAAAAATGGGAAAATGAAGAAGATGTAAAAGAA
GTCATAAAAGCAATGCATGAATGTAAACATCTTCATTTTCTAAACTTGGAGGGAAACACT
CTTGGCTGTGAAGGAGCAAAACATATTGGTAAAGCATTAGAGAAACATCCAGAATTCAAG
AAAGCACTATGGAAAGACCTCTTTACTGGAAGAATGAAAACTGAAATACCACCGGCACTT
ATGGATTTATCAAAAGGAATTATGGTGGCAAAAGCTCAACTCACAGTACTTGATTTAAGC
GATAATGCTCTTGGACCTAATGGCGCAACCGGTTTAGTTGATTTATTAAGTAGCTCAGCA
TGCTACTCTCTACAAGAACTTCGTTTAATGAATTGCGGTTTAGGAATTACTGGTGCAAAA
ATGTTGGCTAAATCTCTTATGGAATGCTATAAGGGAAGTGTAGAAGCTGGAACTCCTATG
GAGTTAAGAGTTTTTGCAGCTGGTCGCAATCGATTAGAAAATGAAGGAGCAAAAGCATTG
TCAAAAGTTTTTGAGGAAATTCAGACATTACAGGAAATTACAATTCCTCAAAATGGAATT
TATCATGTTGGAATGTCAGCTTTAGCAGAAGCACTCAAAAAGAATCCCAACATTCAAGTT
ATAAATTTCAATGATAACACTATCACAGCAAAAGGAGCTGAAGTTTTAGCAGAGGCATTT
TATGCAATTGAAGGTCTACGTGAAATTAATTTGGGTGATTGTCTATTGAAAGATGAGGGT
GGTCAAATTTTAAGTGATGTTTTGGCCGATTGTCATCCTGATTTAGAGTTTGTTAATTTA
AGTGGAAATGAAATCGGACCAGAAGTTGGAATTGCTCTTGCAAATACAATGGGACATAAA
GAAAATTTGAAAAAGTTTATTCTCGATTCGAATCAATTTGGTGATGAAGGTGTTGAACAA
ATTCAACAAATTATGGAAGAGTTTGGCAAGTTGGATGTATTGAGTATTGAAGATGATGAA
GGTTTAGCTGATGAAGAAGAAGATGAAGGAGAATACCAAAGTGAAGAAGAAGAAGAACAA
GAGGATGAAGAAGATGAGGGTGAATATGATGAGGAGGATGAAGAAGACTGTATCATTACA
AATGTATCAAATCTATCTCAAAATAATTTTGAGACATCTCTCGACAACAGTATATTGCTC
AATAATAGCTCAACAGCAGATGATCCAATTGCAGCTTTTTGTAATGATAAATTATCACCG
ACATTCGAGAAATTCCAACAAATAACTGACGAGGACAAACTAAAAGCATTTAAAGACTAT
CTCTCACAAGCTCCTGAAGACGATTACCTAACACATCTCGTTTTCATTATTTTAAAATTG
TCGTCCATTAGTGATCAATCAGAAGAAGCTAAACAACTTGCCTTAGATCTATTTAAAGAA
GCTTTCGACTATGCGAAAACCAAAGACCGTTTGAAGAGTGTCAGAAATTTTTTCCTTATT
CAATTGGGCCTTTTAAAATCTGAACAGAAAGAATTCAAGCCTAAATATAATGTTCAATCG
TGTCGATCAACACTTGAAAATGCTCTTAAAGTAAACACATTACCTGATGAAGAAAAAACT
ATCTTTGAAGTGTTTCTTAATTCTGCTAAATAA

>g10942.t1 Gene=g10942 Length=570
MALFNLASVSDALKETEQESSGVSFVGLAKKWENEEDVKEVIKAMHECKHLHFLNLEGNT
LGCEGAKHIGKALEKHPEFKKALWKDLFTGRMKTEIPPALMDLSKGIMVAKAQLTVLDLS
DNALGPNGATGLVDLLSSSACYSLQELRLMNCGLGITGAKMLAKSLMECYKGSVEAGTPM
ELRVFAAGRNRLENEGAKALSKVFEEIQTLQEITIPQNGIYHVGMSALAEALKKNPNIQV
INFNDNTITAKGAEVLAEAFYAIEGLREINLGDCLLKDEGGQILSDVLADCHPDLEFVNL
SGNEIGPEVGIALANTMGHKENLKKFILDSNQFGDEGVEQIQQIMEEFGKLDVLSIEDDE
GLADEEEDEGEYQSEEEEEQEDEEDEGEYDEEDEEDCIITNVSNLSQNNFETSLDNSILL
NNSSTADDPIAAFCNDKLSPTFEKFQQITDEDKLKAFKDYLSQAPEDDYLTHLVFIILKL
SSISDQSEEAKQLALDLFKEAFDYAKTKDRLKSVRNFFLIQLGLLKSEQKEFKPKYNVQS
CRSTLENALKVNTLPDEEKTIFEVFLNSAK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g10942.t1 CDD cd00116 LRR_RI 28 358 9.17943E-63
12 g10942.t1 Coils Coil Coil 362 395 -
11 g10942.t1 Gene3D G3DSA:3.80.10.10 Ribonuclease Inhibitor 23 361 3.3E-82
10 g10942.t1 Gene3D G3DSA:1.25.40.200 - 422 570 6.0E-15
23 g10942.t1 MobiDBLite mobidb-lite consensus disorder prediction 360 394 -
6 g10942.t1 PANTHER PTHR24113:SF5 RAN GTPASE-ACTIVATING PROTEIN 1 23 416 3.8E-110
7 g10942.t1 PANTHER PTHR24113 RAN GTPASE-ACTIVATING PROTEIN 1 23 416 3.8E-110
5 g10942.t1 Pfam PF13516 Leucine Rich repeat 48 69 0.37
4 g10942.t1 Pfam PF13516 Leucine Rich repeat 113 132 0.021
3 g10942.t1 Pfam PF13516 Leucine Rich repeat 234 257 0.18
2 g10942.t1 Pfam PF13516 Leucine Rich repeat 320 341 0.2
1 g10942.t1 Pfam PF07834 RanGAP1 C-terminal domain 472 567 2.4E-7
19 g10942.t1 SMART SM00368 LRR_RI_2 48 75 0.0095
16 g10942.t1 SMART SM00368 LRR_RI_2 111 138 0.029
15 g10942.t1 SMART SM00368 LRR_RI_2 141 168 0.29
21 g10942.t1 SMART SM00368 LRR_RI_2 179 206 85.0
14 g10942.t1 SMART SM00368 LRR_RI_2 207 234 12.0
22 g10942.t1 SMART SM00368 LRR_RI_2 235 262 0.56
18 g10942.t1 SMART SM00368 LRR_RI_2 263 290 0.31
17 g10942.t1 SMART SM00368 LRR_RI_2 292 319 22.0
20 g10942.t1 SMART SM00368 LRR_RI_2 320 347 4.6
9 g10942.t1 SUPERFAMILY SSF52047 RNI-like 34 360 1.33E-57
8 g10942.t1 SUPERFAMILY SSF69099 Ran-GTPase activating protein 1 (RanGAP1), C-terminal domain 439 567 7.85E-24

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:0007165 signal transduction BP
GO:0005515 protein binding MF
GO:0005096 GTPase activator activity MF

KEGG

Orthology

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.

Raw TPM values