Gene loci information

Transcript annotation

  • This transcript has been annotated as Ras-related protein Rap1.

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.t4 isoform g10429.t4 9748677 9751866
chr_1 g10429 g10429.t4 exon g10429.t4.exon1 9748677 9748862
chr_1 g10429 g10429.t4 TSS g10429.t4 9748706 9748706
chr_1 g10429 g10429.t4 exon g10429.t4.exon2 9750067 9750320
chr_1 g10429 g10429.t4 exon g10429.t4.exon3 9750485 9750531
chr_1 g10429 g10429.t4 exon g10429.t4.exon4 9751238 9751474
chr_1 g10429 g10429.t4 cds g10429.t4.CDS1 9751316 9751474
chr_1 g10429 g10429.t4 exon g10429.t4.exon5 9751555 9751707
chr_1 g10429 g10429.t4 cds g10429.t4.CDS2 9751555 9751707
chr_1 g10429 g10429.t4 exon g10429.t4.exon6 9751777 9751866
chr_1 g10429 g10429.t4 cds g10429.t4.CDS3 9751777 9751866
chr_1 g10429 g10429.t4 TTS g10429.t4 9752435 9752435

Sequences

>g10429.t4 Gene=g10429 Length=967
GGAGTCCTATGCTCTCACCAATACAAGTGTAGATTATAACGATAATTTGAAATTCTTTTA
GCAGAATTGAAAAATTAAACAGCATTTTGACAAGTAATTGATAGCAATTATCAATAAATA
AACACTTGACTGCGTAGTTAAGATTACAATACAGTGGATAATAGTGAAATTAAGTGATTA
AATCGTGCGTGGAAACACAACAATCAAAAGTAAAAAGAGAGAAAATTAGTGTCTGAGTAC
ACATTAAGAGAAACAAAGAGCGTGAGCATAATACACTTGACTGAAATTGATTTATTAGCC
GGAAATCTTGTACTGTGAGGTGCATAAATCAGTGGTGGTGATTCATAAGCCACAAAAGGA
ATTAAAAAGTCAAAGACGCATTGTTACTTAGAGTGACTCATTTGGATCGTTCTGAACTCA
AAAGAATATCCGATTAAAGTGCTCTGGAGGAGTCGGTAAAAGTGCGCTTACGGTGCAATT
TGTGCAGGGTATCTTTGTCGAGAAATATGATCCGACTATAGAAGACTCTTACCGAAAGCA
AGTGGAAGTTGATGGACAGCAATGCATGTTGGAAATTCTTGATACGGCTGGAACAGAACA
ATTTACAGCCATGCGAGATTTATACATGAAAAATGGACAAGGTTTCATACTTGTATATTC
CATCACGGCACAATCGATTTTCAATGATTTACAAGATTTACGGGAACAAATTTTGAGAGT
TAAGGACACTGATGACGTTCCAATGGTTTTGGTTGGCAATAAATGTGATTTGGAGGATGA
GAGAGTAGTAGGAAAAGAGTTAGGAAAGCAACTTGCACAACAATTCAATTGCTCGTTCAT
GGAAACATCCGCCAAAGCAAAAATTAACGTTAATGATATATTCAATGATTTAGTTCAGCA
AATTAACAAGAAATCACCAGAAAAGAAGCAGAGCAAGAAGAAAAAATCATTATGCACTTT
GCTATAA

>g10429.t4 Gene=g10429 Length=133
MLEILDTAGTEQFTAMRDLYMKNGQGFILVYSITAQSIFNDLQDLREQILRVKDTDDVPM
VLVGNKCDLEDERVVGKELGKQLAQQFNCSFMETSAKAKINVNDIFNDLVQQINKKSPEK
KQSKKKKSLCTLL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g10429.t4 Gene3D G3DSA:3.40.50.300 - 1 120 0.0000
2 g10429.t4 PANTHER PTHR24070 RAS, DI-RAS, AND RHEB FAMILY MEMBERS OF SMALL GTPASE SUPERFAMILY 1 133 0.0000
3 g10429.t4 PANTHER PTHR24070:SF424 RAP1A, MEMBER OF RAS ONCOGENE FAMILY 1 133 0.0000
4 g10429.t4 PRINTS PR00449 Transforming protein P21 ras signature 56 69 0.0000
5 g10429.t4 PRINTS PR00449 Transforming protein P21 ras signature 91 113 0.0000
1 g10429.t4 Pfam PF00071 Ras family 2 114 0.0000
11 g10429.t4 ProSiteProfiles PS51421 small GTPase Ras family profile. 1 133 31.7850
8 g10429.t4 SMART SM00173 ras_sub_4 1 116 0.0000
10 g10429.t4 SMART SM00174 rho_sub_3 1 116 0.0009
9 g10429.t4 SMART SM00175 rab_sub_5 2 116 0.0000
6 g10429.t4 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 2 125 0.0000
12 g10429.t4 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 2 107 0.0000

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