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.t6 TTS g10942.t6 12918563 12918563
chr_1 g10942 g10942.t6 isoform g10942.t6 12919282 12920626
chr_1 g10942 g10942.t6 exon g10942.t6.exon1 12919282 12919344
chr_1 g10942 g10942.t6 cds g10942.t6.CDS1 12919283 12919344
chr_1 g10942 g10942.t6 exon g10942.t6.exon2 12919402 12920400
chr_1 g10942 g10942.t6 cds g10942.t6.CDS2 12919402 12920400
chr_1 g10942 g10942.t6 exon g10942.t6.exon3 12920515 12920626
chr_1 g10942 g10942.t6 cds g10942.t6.CDS3 12920515 12920626
chr_1 g10942 g10942.t6 TSS g10942.t6 12920702 12920702

Sequences

>g10942.t6 Gene=g10942 Length=1174
ATGGCGCTATTTAATTTAGCAAGTGTAAGTGATGCATTGAAAGAGACAGAGCAAGAATCA
AGTGGTGTTTCATTTGTCGGCTTGGCAAAAAAATGGGAAAATGAAGAAGATGTAAAAGAA
GTCATAAAAGCAATGCATGAATGTAAACATCTTCATTTTCTAAACTTGGAGGGAAACACT
CTTGGCTGTGAAGGAGCAAAACATATTGGTAAAGCATTAGAGAAACATCCAGAATTCAAG
AAAGCACTATGGAAAGACCTCTTTACTGGAAGAATGAAAACTGAAATACCACCGGCACTT
ATGGATTTATCAAAAGGAATTATGGTGGCAAAAGCTCAACTCACAGTACTTGATTTAAGC
GATAATGCTCTTGGACCTAATGGCGCAACCGGTTTAGTTGATTTATTAAGTAGCTCAGCA
TGCTACTCTCTACAAGAACTTCGTTTAATGAATTGCGGTTTAGGAATTACTGGTGCAAAA
ATGTTGGCTAAATCTCTTATGGAATGCTATAAGGGAAGTGTAGAAGCTGGAACTCCTATG
GAGTTAAGAGTTTTTGCAGCTGGTCGCAATCGATTAGAAAATGAAGGAGCAAAAGCATTG
TCAAAAGTTTTTGAGGAAATTCAGACATTACAGGAAATTACAATTCCTCAAAATGGAATT
TATCATGTTGGAATGTCAGCTTTAGCAGAAGCACTCAAAAAGAATCCCAACATTCAAGTT
ATAAATTTCAATGATAACACTATCACAGCAAAAGGAGCTGAAGTTTTAGCAGAGGCATTT
TATGCAATTGAAGGTCTACGTGAAATTAATTTGGGTGATTGTCTATTGAAAGATGAGGGT
GGTCAAATTTTAAGTGATGTTTTGGCCGATTGTCATCCTGATTTAGAGTTTGTTAATTTA
AGTGGAAATGAAATCGGACCAGAAGTTGGAATTGCTCTTGCAAATACAATGGGACATAAA
GAAAATTTGAAAAAGTTTATTCTCGATTCGAATCAATTTGGTGATGAAGGTGTTGAACAA
ATTCAACAAATTATGGAAGAGTTTGGCAAGTTGGATGTATTGAGTATTGAAGATGATGAA
GGTTTAGCTGATGAAGAAGAAGATGAAGGAGAATACCAAAGTGAAGAAGAAGAAGAACAA
GAGGATGAAGAAGATGAGGGTGAATATGATGAGG

>g10942.t6 Gene=g10942 Length=391
MALFNLASVSDALKETEQESSGVSFVGLAKKWENEEDVKEVIKAMHECKHLHFLNLEGNT
LGCEGAKHIGKALEKHPEFKKALWKDLFTGRMKTEIPPALMDLSKGIMVAKAQLTVLDLS
DNALGPNGATGLVDLLSSSACYSLQELRLMNCGLGITGAKMLAKSLMECYKGSVEAGTPM
ELRVFAAGRNRLENEGAKALSKVFEEIQTLQEITIPQNGIYHVGMSALAEALKKNPNIQV
INFNDNTITAKGAEVLAEAFYAIEGLREINLGDCLLKDEGGQILSDVLADCHPDLEFVNL
SGNEIGPEVGIALANTMGHKENLKKFILDSNQFGDEGVEQIQQIMEEFGKLDVLSIEDDE
GLADEEEDEGEYQSEEEEEQEDEEDEGEYDE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g10942.t6 CDD cd00116 LRR_RI 28 358 1.19805E-64
11 g10942.t6 Coils Coil Coil 362 382 -
10 g10942.t6 Gene3D G3DSA:3.80.10.10 Ribonuclease Inhibitor 23 361 1.0E-82
22 g10942.t6 MobiDBLite mobidb-lite consensus disorder prediction 356 391 -
23 g10942.t6 MobiDBLite mobidb-lite consensus disorder prediction 358 391 -
7 g10942.t6 PANTHER PTHR24113:SF5 RAN GTPASE-ACTIVATING PROTEIN 1 23 386 1.1E-109
8 g10942.t6 PANTHER PTHR24113 RAN GTPASE-ACTIVATING PROTEIN 1 23 386 1.1E-109
6 g10942.t6 Pfam PF13516 Leucine Rich repeat 48 69 0.24
5 g10942.t6 Pfam PF13516 Leucine Rich repeat 113 132 0.013
3 g10942.t6 Pfam PF13516 Leucine Rich repeat 141 163 1.5
4 g10942.t6 Pfam PF13516 Leucine Rich repeat 234 257 0.11
2 g10942.t6 Pfam PF13516 Leucine Rich repeat 294 314 1.5
1 g10942.t6 Pfam PF13516 Leucine Rich repeat 320 341 0.13
18 g10942.t6 SMART SM00368 LRR_RI_2 48 75 0.0095
15 g10942.t6 SMART SM00368 LRR_RI_2 111 138 0.029
14 g10942.t6 SMART SM00368 LRR_RI_2 141 168 0.29
20 g10942.t6 SMART SM00368 LRR_RI_2 179 206 85.0
13 g10942.t6 SMART SM00368 LRR_RI_2 207 234 12.0
21 g10942.t6 SMART SM00368 LRR_RI_2 235 262 0.56
17 g10942.t6 SMART SM00368 LRR_RI_2 263 290 0.31
16 g10942.t6 SMART SM00368 LRR_RI_2 292 319 22.0
19 g10942.t6 SMART SM00368 LRR_RI_2 320 347 4.6
9 g10942.t6 SUPERFAMILY SSF52047 RNI-like 34 359 6.54E-58

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