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.t4 TTS g10942.t4 12918563 12918563
chr_1 g10942 g10942.t4 isoform g10942.t4 12918688 12920626
chr_1 g10942 g10942.t4 exon g10942.t4.exon1 12918688 12919227
chr_1 g10942 g10942.t4 cds g10942.t4.CDS1 12918688 12919227
chr_1 g10942 g10942.t4 exon g10942.t4.exon2 12919283 12919344
chr_1 g10942 g10942.t4 cds g10942.t4.CDS2 12919283 12919344
chr_1 g10942 g10942.t4 exon g10942.t4.exon3 12919402 12920626
chr_1 g10942 g10942.t4 cds g10942.t4.CDS3 12919402 12920380
chr_1 g10942 g10942.t4 TSS g10942.t4 12920702 12920702

Sequences

>g10942.t4 Gene=g10942 Length=1827
ATGGCGCTATTTAATTTAGCAAGTGTAAGTGATGCATTGAAAGAGACAGAGCAAGAATCA
AGTGGTGTTTCATTTGTCGGCTTGGCAAAAAAATGGGAAAATGAAGAAGATGGTAAGAAA
ACGTGGCTAAACAAAAATATCCTGAATATCCTTGTAGAATAGTATTTAATATGATCTAAT
TTAGGGGTTATATAATGTACTATTTCTTTTTATTTATAAAATATAGTAAAAGAAGTCATA
AAAGCAATGCATGAATGTAAACATCTTCATTTTCTAAACTTGGAGGGAAACACTCTTGGC
TGTGAAGGAGCAAAACATATTGGTAAAGCATTAGAGAAACATCCAGAATTCAAGAAAGCA
CTATGGAAAGACCTCTTTACTGGAAGAATGAAAACTGAAATACCACCGGCACTTATGGAT
TTATCAAAAGGAATTATGGTGGCAAAAGCTCAACTCACAGTACTTGATTTAAGCGATAAT
GCTCTTGGACCTAATGGCGCAACCGGTTTAGTTGATTTATTAAGTAGCTCAGCATGCTAC
TCTCTACAAGAACTTCGTTTAATGAATTGCGGTTTAGGAATTACTGGTGCAAAAATGTTG
GCTAAATCTCTTATGGAATGCTATAAGGGAAGTGTAGAAGCTGGAACTCCTATGGAGTTA
AGAGTTTTTGCAGCTGGTCGCAATCGATTAGAAAATGAAGGAGCAAAAGCATTGTCAAAA
GTTTTTGAGGAAATTCAGACATTACAGGAAATTACAATTCCTCAAAATGGAATTTATCAT
GTTGGAATGTCAGCTTTAGCAGAAGCACTCAAAAAGAATCCCAACATTCAAGTTATAAAT
TTCAATGATAACACTATCACAGCAAAAGGAGCTGAAGTTTTAGCAGAGGCATTTTATGCA
ATTGAAGGTCTACGTGAAATTAATTTGGGTGATTGTCTATTGAAAGATGAGGGTGGTCAA
ATTTTAAGTGATGTTTTGGCCGATTGTCATCCTGATTTAGAGTTTGTTAATTTAAGTGGA
AATGAAATCGGACCAGAAGTTGGAATTGCTCTTGCAAATACAATGGGACATAAAGAAAAT
TTGAAAAAGTTTATTCTCGATTCGAATCAATTTGGTGATGAAGGTGTTGAACAAATTCAA
CAAATTATGGAAGAGTTTGGCAAGTTGGATGTATTGAGTATTGAAGATGATGAAGGTTTA
GCTGATGAAGAAGAAGATGAAGGAGAATACCAAAGTGAAGAAGAAGAAGAACAAGAGGAT
GAAGAAGATGAGGGTGAATATGATGAGGAGGATGAAGAAGACTGTATCATTACAAATGTA
TCAAATCTATCTCAAAATAATTTTGAGACATCTCTCGACAACAGTATATTGCTCAATAAT
AGCTCAACAGCAGATGATCCAATTGCAGCTTTTTGTAATGATAAATTATCACCGACATTC
GAGAAATTCCAACAAATAACTGACGAGGACAAACTAAAAGCATTTAAAGACTATCTCTCA
CAAGCTCCTGAAGACGATTACCTAACACATCTCGTTTTCATTATTTTAAAATTGTCGTCC
ATTAGTGATCAATCAGAAGAAGCTAAACAACTTGCCTTAGATCTATTTAAAGAAGCTTTC
GACTATGCGAAAACCAAAGACCGTTTGAAGAGTGTCAGAAATTTTTTCCTTATTCAATTG
GGCCTTTTAAAATCTGAACAGAAAGAATTCAAGCCTAAATATAATGTTCAATCGTGTCGA
TCAACACTTGAAAATGCTCTTAAAGTAAACACATTACCTGATGAAGAAAAAACTATCTTT
GAAGTGTTTCTTAATTCTGCTAAATAA

>g10942.t4 Gene=g10942 Length=526
MHECKHLHFLNLEGNTLGCEGAKHIGKALEKHPEFKKALWKDLFTGRMKTEIPPALMDLS
KGIMVAKAQLTVLDLSDNALGPNGATGLVDLLSSSACYSLQELRLMNCGLGITGAKMLAK
SLMECYKGSVEAGTPMELRVFAAGRNRLENEGAKALSKVFEEIQTLQEITIPQNGIYHVG
MSALAEALKKNPNIQVINFNDNTITAKGAEVLAEAFYAIEGLREINLGDCLLKDEGGQIL
SDVLADCHPDLEFVNLSGNEIGPEVGIALANTMGHKENLKKFILDSNQFGDEGVEQIQQI
MEEFGKLDVLSIEDDEGLADEEEDEGEYQSEEEEEQEDEEDEGEYDEEDEEDCIITNVSN
LSQNNFETSLDNSILLNNSSTADDPIAAFCNDKLSPTFEKFQQITDEDKLKAFKDYLSQA
PEDDYLTHLVFIILKLSSISDQSEEAKQLALDLFKEAFDYAKTKDRLKSVRNFFLIQLGL
LKSEQKEFKPKYNVQSCRSTLENALKVNTLPDEEKTIFEVFLNSAK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g10942.t4 CDD cd00116 LRR_RI 5 314 2.88937E-61
12 g10942.t4 Coils Coil Coil 318 351 -
11 g10942.t4 Gene3D G3DSA:3.80.10.10 Ribonuclease Inhibitor 1 317 1.0E-78
10 g10942.t4 Gene3D G3DSA:1.25.40.200 - 378 526 5.2E-15
23 g10942.t4 MobiDBLite mobidb-lite consensus disorder prediction 316 350 -
6 g10942.t4 PANTHER PTHR24113:SF5 RAN GTPASE-ACTIVATING PROTEIN 1 4 372 2.8E-105
7 g10942.t4 PANTHER PTHR24113 RAN GTPASE-ACTIVATING PROTEIN 1 4 372 2.8E-105
5 g10942.t4 Pfam PF13516 Leucine Rich repeat 4 25 0.34
2 g10942.t4 Pfam PF13516 Leucine Rich repeat 69 88 0.019
4 g10942.t4 Pfam PF13516 Leucine Rich repeat 190 213 0.16
3 g10942.t4 Pfam PF13516 Leucine Rich repeat 276 297 0.18
1 g10942.t4 Pfam PF07834 RanGAP1 C-terminal domain 428 523 2.1E-7
17 g10942.t4 SMART SM00368 LRR_RI_2 4 31 0.0095
18 g10942.t4 SMART SM00368 LRR_RI_2 67 94 0.029
16 g10942.t4 SMART SM00368 LRR_RI_2 97 124 0.29
19 g10942.t4 SMART SM00368 LRR_RI_2 135 162 85.0
15 g10942.t4 SMART SM00368 LRR_RI_2 163 190 12.0
14 g10942.t4 SMART SM00368 LRR_RI_2 191 218 0.56
22 g10942.t4 SMART SM00368 LRR_RI_2 219 246 0.31
20 g10942.t4 SMART SM00368 LRR_RI_2 248 275 22.0
21 g10942.t4 SMART SM00368 LRR_RI_2 276 303 4.6
9 g10942.t4 SUPERFAMILY SSF52047 RNI-like 3 316 9.16E-56
8 g10942.t4 SUPERFAMILY SSF69099 Ran-GTPase activating protein 1 (RanGAP1), C-terminal domain 395 523 6.8E-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