Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Ras-related protein Rab-8A.

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 g11563 g11563.t12 TSS g11563.t12 17159420 17159420
chr_1 g11563 g11563.t12 isoform g11563.t12 17159511 17161704
chr_1 g11563 g11563.t12 exon g11563.t12.exon1 17159511 17159565
chr_1 g11563 g11563.t12 exon g11563.t12.exon2 17159662 17159733
chr_1 g11563 g11563.t12 exon g11563.t12.exon3 17160068 17160132
chr_1 g11563 g11563.t12 exon g11563.t12.exon4 17160349 17160601
chr_1 g11563 g11563.t12 exon g11563.t12.exon5 17160668 17160709
chr_1 g11563 g11563.t12 exon g11563.t12.exon6 17161175 17161464
chr_1 g11563 g11563.t12 cds g11563.t12.CDS1 17161177 17161464
chr_1 g11563 g11563.t12 exon g11563.t12.exon7 17161525 17161704
chr_1 g11563 g11563.t12 cds g11563.t12.CDS2 17161525 17161620
chr_1 g11563 g11563.t12 TTS g11563.t12 17161974 17161974

Sequences

>g11563.t12 Gene=g11563 Length=957
ATGTCTACGAAGACCTACGATTATTTGTTTAAACTTCTTTTGATCGGCGATAGTGGTGTA
GGAAAAACCTGTATACTGTTCAGATTTTCGGAAAATAATTTCAACACAACATTTATATCA
ACAATTGGAATTGACTTCAAAATTCGAACAATAGAGCTGGATGGAAAGAAAATAAAACTG
CAGATATGGTGAAACGATGATATAATAAGACAAAACAATAACATCGTGATATATAGTGAC
TAGTCATGTTCAGTTATCGTTCTATTAAACTAAAAAACGAGTAGTTCATGTATGACAATT
TAGTCATAAGTACATTTAAAAAAATGAATGCAAGTCTAGTATTTAACAAATGATATATTT
TAAAAATTCAACTTTATTGAAAAGTGCTCTACATTATAGACAAGTTAAAAAATTGCAAAT
TACAAATTATTCAATTAGTGATTGTCTGGACAAGAACGGTTTCGTACAATCACTACAGCG
TATTATCCAATGGGTATCATGCTTGTATATGACATCACTCAAGAGAAGTCATTTGAAAAT
ATTAAAAATTGGATAAGAAACATAGAAGAAAATGCTTCGACTGACGTTGAAAAGATGTTG
TTAGGTAATAAGTGTGAGTTAAATGAGAAGAGACAAGTCACAAAGGAACGAGGAGAGCAG
TTAGCTGTTGAATACGGAATCAAATTTCTTGAAACATCAGCGAAGAATAGCATCAATGTA
GAAGAAGCATTCTTTACATTAGCTCGAGATATAAAAATTAAAATGGAGAAGAGAATGGAA
GCAAATAATCCACCGAAGGGCCATCAATTGAAAGCAAATGAACCGCCACGAAAACCTGGT
CTCGGATGGCTATCAAAGTGTAACTTCTTTTAGCCTTATTGCATTATATTGTGTAGTTAT
TCCATGATGATAACGATGTAAGGAAAATTCTCAAATTTTTTGCAAATTTTGTATACA

>g11563.t12 Gene=g11563 Length=127
MGIMLVYDITQEKSFENIKNWIRNIEENASTDVEKMLLGNKCELNEKRQVTKERGEQLAV
EYGIKFLETSAKNSINVEEAFFTLARDIKIKMEKRMEANNPPKGHQLKANEPPRKPGLGW
LSKCNFF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g11563.t12 Gene3D G3DSA:3.40.50.300 - 1 115 0.0000000
2 g11563.t12 PANTHER PTHR47980 LD44762P 1 115 0.0000000
3 g11563.t12 PANTHER PTHR47980:SF33 RAS-RELATED PROTEIN RAB-8A 1 115 0.0000000
5 g11563.t12 PRINTS PR00449 Transforming protein P21 ras signature 31 44 0.0000000
4 g11563.t12 PRINTS PR00449 Transforming protein P21 ras signature 66 88 0.0000000
1 g11563.t12 Pfam PF00071 Ras family 2 89 0.0000000
10 g11563.t12 ProSiteProfiles PS51419 small GTPase Rab1 family profile. 1 124 19.2470000
7 g11563.t12 SMART SM00173 ras_sub_4 1 91 0.0000004
8 g11563.t12 SMART SM00175 rab_sub_5 1 91 0.0000000
6 g11563.t12 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 2 118 0.0000000

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:0005525 GTP binding MF
GO:0003924 GTPase activity MF

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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