Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Ras-related protein Rap-1b.

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 g10429 g10429.t8 TSS g10429.t8 9748706 9748706
chr_1 g10429 g10429.t8 isoform g10429.t8 9749060 9751459
chr_1 g10429 g10429.t8 exon g10429.t8.exon1 9749060 9749369
chr_1 g10429 g10429.t8 exon g10429.t8.exon2 9750067 9750531
chr_1 g10429 g10429.t8 cds g10429.t8.CDS1 9750457 9750531
chr_1 g10429 g10429.t8 exon g10429.t8.exon3 9751238 9751459
chr_1 g10429 g10429.t8 cds g10429.t8.CDS2 9751238 9751459
chr_1 g10429 g10429.t8 TTS g10429.t8 9752435 9752435

Sequences

>g10429.t8 Gene=g10429 Length=997
AGAAAAAGAGTGAATATTTTAAAATAGCCCCCATAAATACTTACTACTGATGATGATAAA
ACGAAGAAAAAAAGAATATGTATTTTATATATGTGTAATGGAATCATACTAATAAGGGAA
AATTCCAAAAAAATATATACATACCAAAAATTTAGTTCATTTAGTGGCTCGCTGCTCTCT
GTCAATTGTTTTATATAGAGGAGCATATTTTACGGCATAAATTAACATTTTTTGTGTATT
ATTCAATTCAATTCATACTTGGTAGACAGTTATGGTTTATTTTCCGTAGACGATGAAAAC
ATAAAAAAATGCGTGGAAACACAACAATCAAAAGTAAAAAGAGAGAAAATTAGTGTCTGA
GTACACATTAAGAGAAACAAAGAGCGTGAGCATAATACACTTGACTGAAATTGATTTATT
AGCCGGAAATCTTGTACTGTGAGGTGCATAAATCAGTGGTGGTGATTCATAAGCCACAAA
AGGAATTAAAAAGTCAAAGACGCATTGTTACTTAGAGTGACTCATTTGGATCGTTCTGAA
CTCAAAAGAATATCCGATTAAAGTGTGAGTGAATCAGCTGTTGATTTTCTCATTCATTTG
TACACTTAGATATCATTTTCGTCCTCGCACAAAGCAAGTGCAAGGCGACAAATTTCTGCG
GCTGCCAAGGATAAAATAAAAATCTGCCAAAATTTCGAGAATGCGTGAATACAAAATTGT
TATTTTAGGCTCTGGAGGAGTCGGTAAAAGTGCGCTTACGGTGCAATTTGTGCAGGGTAT
CTTTGTCGAGAAATATGATCCGACTATAGAAGACTCTTACCGAAAGCAAGTGGAAGTTGA
TGGACAGCAATGCATGTTGGAAATTCTTGATACGGCTGGAACAGAACAATTTACAGCCAT
GCGAGATTTATACATGAAAAATGGACAAGGTTTCATACTTGTATATTCCATCACGGCACA
ATCGATTTTCAATGATTTACAAGATTTACGGGAACAA

>g10429.t8 Gene=g10429 Length=99
MREYKIVILGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDGQQCMLEILDTAG
TEQFTAMRDLYMKNGQGFILVYSITAQSIFNDLQDLREQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g10429.t8 Gene3D G3DSA:3.40.50.300 - 1 99 0.00000
2 g10429.t8 PANTHER PTHR24070:SF427 RAP1A, MEMBER OF RAS ONCOGENE FAMILY B 1 99 0.00000
3 g10429.t8 PANTHER PTHR24070 RAS, DI-RAS, AND RHEB FAMILY MEMBERS OF SMALL GTPASE SUPERFAMILY 1 99 0.00000
6 g10429.t8 PRINTS PR00449 Transforming protein P21 ras signature 4 25 0.00000
4 g10429.t8 PRINTS PR00449 Transforming protein P21 ras signature 27 43 0.00000
5 g10429.t8 PRINTS PR00449 Transforming protein P21 ras signature 44 66 0.00000
1 g10429.t8 Pfam PF00071 Ras family 5 98 0.00000
11 g10429.t8 ProSiteProfiles PS51421 small GTPase Ras family profile. 1 99 27.36700
9 g10429.t8 SMART SM00173 ras_sub_4 1 99 0.00000
10 g10429.t8 SMART SM00175 rab_sub_5 4 99 0.00012
7 g10429.t8 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 2 98 0.00000
12 g10429.t8 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 1 87 0.00000

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:0016020 membrane CC
GO:0007165 signal transduction BP
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