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.t5 TTS g10942.t5 12918563 12918563
chr_1 g10942 g10942.t5 isoform g10942.t5 12918688 12920626
chr_1 g10942 g10942.t5 exon g10942.t5.exon1 12918688 12919229
chr_1 g10942 g10942.t5 cds g10942.t5.CDS1 12919056 12919229
chr_1 g10942 g10942.t5 exon g10942.t5.exon2 12919283 12919344
chr_1 g10942 g10942.t5 cds g10942.t5.CDS2 12919283 12919344
chr_1 g10942 g10942.t5 exon g10942.t5.exon3 12919402 12920626
chr_1 g10942 g10942.t5 cds g10942.t5.CDS3 12919402 12920380
chr_1 g10942 g10942.t5 TSS g10942.t5 12920702 12920702

Sequences

>g10942.t5 Gene=g10942 Length=1829
ATGGCGCTATTTAATTTAGCAAGTGTAAGTGATGCATTGAAAGAGACAGAGCAAGAATCA
AGTGGTGTTTCATTTGTCGGCTTGGCAAAAAAATGGGAAAATGAAGAAGATGGTAAGAAA
ACGTGGCTAAACAAAAATATCCTGAATATCCTTGTAGAATAGTATTTAATATGATCTAAT
TTAGGGGTTATATAATGTACTATTTCTTTTTATTTATAAAATATAGTAAAAGAAGTCATA
AAAGCAATGCATGAATGTAAACATCTTCATTTTCTAAACTTGGAGGGAAACACTCTTGGC
TGTGAAGGAGCAAAACATATTGGTAAAGCATTAGAGAAACATCCAGAATTCAAGAAAGCA
CTATGGAAAGACCTCTTTACTGGAAGAATGAAAACTGAAATACCACCGGCACTTATGGAT
TTATCAAAAGGAATTATGGTGGCAAAAGCTCAACTCACAGTACTTGATTTAAGCGATAAT
GCTCTTGGACCTAATGGCGCAACCGGTTTAGTTGATTTATTAAGTAGCTCAGCATGCTAC
TCTCTACAAGAACTTCGTTTAATGAATTGCGGTTTAGGAATTACTGGTGCAAAAATGTTG
GCTAAATCTCTTATGGAATGCTATAAGGGAAGTGTAGAAGCTGGAACTCCTATGGAGTTA
AGAGTTTTTGCAGCTGGTCGCAATCGATTAGAAAATGAAGGAGCAAAAGCATTGTCAAAA
GTTTTTGAGGAAATTCAGACATTACAGGAAATTACAATTCCTCAAAATGGAATTTATCAT
GTTGGAATGTCAGCTTTAGCAGAAGCACTCAAAAAGAATCCCAACATTCAAGTTATAAAT
TTCAATGATAACACTATCACAGCAAAAGGAGCTGAAGTTTTAGCAGAGGCATTTTATGCA
ATTGAAGGTCTACGTGAAATTAATTTGGGTGATTGTCTATTGAAAGATGAGGGTGGTCAA
ATTTTAAGTGATGTTTTGGCCGATTGTCATCCTGATTTAGAGTTTGTTAATTTAAGTGGA
AATGAAATCGGACCAGAAGTTGGAATTGCTCTTGCAAATACAATGGGACATAAAGAAAAT
TTGAAAAAGTTTATTCTCGATTCGAATCAATTTGGTGATGAAGGTGTTGAACAAATTCAA
CAAATTATGGAAGAGTTTGGCAAGTTGGATGTATTGAGTATTGAAGATGATGAAGGTTTA
GCTGATGAAGAAGAAGATGAAGGAGAATACCAAAGTGAAGAAGAAGAAGAACAAGAGGAT
GAAGAAGATGAGGGTGAATATGATGAGAGGAGGATGAAGAAGACTGTATCATTACAAATG
TATCAAATCTATCTCAAAATAATTTTGAGACATCTCTCGACAACAGTATATTGCTCAATA
ATAGCTCAACAGCAGATGATCCAATTGCAGCTTTTTGTAATGATAAATTATCACCGACAT
TCGAGAAATTCCAACAAATAACTGACGAGGACAAACTAAAAGCATTTAAAGACTATCTCT
CACAAGCTCCTGAAGACGATTACCTAACACATCTCGTTTTCATTATTTTAAAATTGTCGT
CCATTAGTGATCAATCAGAAGAAGCTAAACAACTTGCCTTAGATCTATTTAAAGAAGCTT
TCGACTATGCGAAAACCAAAGACCGTTTGAAGAGTGTCAGAAATTTTTTCCTTATTCAAT
TGGGCCTTTTAAAATCTGAACAGAAAGAATTCAAGCCTAAATATAATGTTCAATCGTGTC
GATCAACACTTGAAAATGCTCTTAAAGTAAACACATTACCTGATGAAGAAAAAACTATCT
TTGAAGTGTTTCTTAATTCTGCTAAATAA

>g10942.t5 Gene=g10942 Length=404
MHECKHLHFLNLEGNTLGCEGAKHIGKALEKHPEFKKALWKDLFTGRMKTEIPPALMDLS
KGIMVAKAQLTVLDLSDNALGPNGATGLVDLLSSSACYSLQELRLMNCGLGITGAKMLAK
SLMECYKGSVEAGTPMELRVFAAGRNRLENEGAKALSKVFEEIQTLQEITIPQNGIYHVG
MSALAEALKKNPNIQVINFNDNTITAKGAEVLAEAFYAIEGLREINLGDCLLKDEGGQIL
SDVLADCHPDLEFVNLSGNEIGPEVGIALANTMGHKENLKKFILDSNQFGDEGVEQIQQI
MEEFGKLDVLSIEDDEGLADEEEDEGEYQSEEEEEQEDEEDEGEYDERRMKKTVSLQMYQ
IYLKIILRHLSTTVYCSIIAQQQMIQLQLFVMINYHRHSRNSNK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g10942.t5 CDD cd00116 LRR_RI 5 314 8.27194E-64
11 g10942.t5 Coils Coil Coil 318 338 -
10 g10942.t5 Gene3D G3DSA:3.80.10.10 Ribonuclease Inhibitor 1 317 4.5E-79
22 g10942.t5 MobiDBLite mobidb-lite consensus disorder prediction 316 344 -
23 g10942.t5 MobiDBLite mobidb-lite consensus disorder prediction 316 349 -
7 g10942.t5 PANTHER PTHR24113:SF5 RAN GTPASE-ACTIVATING PROTEIN 1 4 343 1.6E-105
8 g10942.t5 PANTHER PTHR24113 RAN GTPASE-ACTIVATING PROTEIN 1 4 343 1.6E-105
6 g10942.t5 Pfam PF13516 Leucine Rich repeat 4 25 0.25
3 g10942.t5 Pfam PF13516 Leucine Rich repeat 69 88 0.014
1 g10942.t5 Pfam PF13516 Leucine Rich repeat 97 119 1.5
5 g10942.t5 Pfam PF13516 Leucine Rich repeat 190 213 0.12
2 g10942.t5 Pfam PF13516 Leucine Rich repeat 250 270 1.5
4 g10942.t5 Pfam PF13516 Leucine Rich repeat 276 297 0.13
16 g10942.t5 SMART SM00368 LRR_RI_2 4 31 0.0095
17 g10942.t5 SMART SM00368 LRR_RI_2 67 94 0.029
15 g10942.t5 SMART SM00368 LRR_RI_2 97 124 0.29
18 g10942.t5 SMART SM00368 LRR_RI_2 135 162 85.0
14 g10942.t5 SMART SM00368 LRR_RI_2 163 190 12.0
13 g10942.t5 SMART SM00368 LRR_RI_2 191 218 0.56
21 g10942.t5 SMART SM00368 LRR_RI_2 219 246 0.31
19 g10942.t5 SMART SM00368 LRR_RI_2 248 275 22.0
20 g10942.t5 SMART SM00368 LRR_RI_2 276 303 4.6
9 g10942.t5 SUPERFAMILY SSF52047 RNI-like 3 316 3.66E-56

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

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