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.t5 isoform g10429.t5 9748677 9751866
chr_1 g10429 g10429.t5 exon g10429.t5.exon1 9748677 9748860
chr_1 g10429 g10429.t5 TSS g10429.t5 9748706 9748706
chr_1 g10429 g10429.t5 exon g10429.t5.exon2 9750067 9750531
chr_1 g10429 g10429.t5 cds g10429.t5.CDS1 9750457 9750531
chr_1 g10429 g10429.t5 exon g10429.t5.exon3 9751238 9751474
chr_1 g10429 g10429.t5 cds g10429.t5.CDS2 9751238 9751474
chr_1 g10429 g10429.t5 exon g10429.t5.exon4 9751555 9751707
chr_1 g10429 g10429.t5 cds g10429.t5.CDS3 9751555 9751707
chr_1 g10429 g10429.t5 exon g10429.t5.exon5 9751777 9751866
chr_1 g10429 g10429.t5 cds g10429.t5.CDS4 9751777 9751866
chr_1 g10429 g10429.t5 TTS g10429.t5 9752435 9752435

Sequences

>g10429.t5 Gene=g10429 Length=1129
GGAGTCCTATGCTCTCACCAATACAAGTGTAGATTATAACGATAATTTGAAATTCTTTTA
GCAGAATTGAAAAATTAAACAGCATTTTGACAAGTAATTGATAGCAATTATCAATAAATA
AACACTTGACTGCGTAGTTAAGATTACAATACAGTGGATAATAGTGAAATTAAGTGATTA
AATCGCGTGGAAACACAACAATCAAAAGTAAAAAGAGAGAAAATTAGTGTCTGAGTACAC
ATTAAGAGAAACAAAGAGCGTGAGCATAATACACTTGACTGAAATTGATTTATTAGCCGG
AAATCTTGTACTGTGAGGTGCATAAATCAGTGGTGGTGATTCATAAGCCACAAAAGGAAT
TAAAAAGTCAAAGACGCATTGTTACTTAGAGTGACTCATTTGGATCGTTCTGAACTCAAA
AGAATATCCGATTAAAGTGTGAGTGAATCAGCTGTTGATTTTCTCATTCATTTGTACACT
TAGATATCATTTTCGTCCTCGCACAAAGCAAGTGCAAGGCGACAAATTTCTGCGGCTGCC
AAGGATAAAATAAAAATCTGCCAAAATTTCGAGAATGCGTGAATACAAAATTGTTATTTT
AGGCTCTGGAGGAGTCGGTAAAAGTGCGCTTACGGTGCAATTTGTGCAGGGTATCTTTGT
CGAGAAATATGATCCGACTATAGAAGACTCTTACCGAAAGCAAGTGGAAGTTGATGGACA
GCAATGCATGTTGGAAATTCTTGATACGGCTGGAACAGAACAATTTACAGCCATGCGAGA
TTTATACATGAAAAATGGACAAGGTTTCATACTTGTATATTCCATCACGGCACAATCGAT
TTTCAATGATTTACAAGATTTACGGGAACAAATTTTGAGAGTTAAGGACACTGATGACGT
TCCAATGGTTTTGGTTGGCAATAAATGTGATTTGGAGGATGAGAGAGTAGTAGGAAAAGA
GTTAGGAAAGCAACTTGCACAACAATTCAATTGCTCGTTCATGGAAACATCCGCCAAAGC
AAAAATTAACGTTAATGATATATTCAATGATTTAGTTCAGCAAATTAACAAGAAATCACC
AGAAAAGAAGCAGAGCAAGAAGAAAAAATCATTATGCACTTTGCTATAA

>g10429.t5 Gene=g10429 Length=184
MREYKIVILGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDGQQCMLEILDTAG
TEQFTAMRDLYMKNGQGFILVYSITAQSIFNDLQDLREQILRVKDTDDVPMVLVGNKCDL
EDERVVGKELGKQLAQQFNCSFMETSAKAKINVNDIFNDLVQQINKKSPEKKQSKKKKSL
CTLL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g10429.t5 CDD cd04175 Rap1 3 165 0.0000
10 g10429.t5 Gene3D G3DSA:3.40.50.300 - 1 170 0.0000
2 g10429.t5 PANTHER PTHR24070 RAS, DI-RAS, AND RHEB FAMILY MEMBERS OF SMALL GTPASE SUPERFAMILY 1 184 0.0000
3 g10429.t5 PANTHER PTHR24070:SF424 RAP1A, MEMBER OF RAS ONCOGENE FAMILY 1 184 0.0000
8 g10429.t5 PRINTS PR00449 Transforming protein P21 ras signature 4 25 0.0000
4 g10429.t5 PRINTS PR00449 Transforming protein P21 ras signature 27 43 0.0000
6 g10429.t5 PRINTS PR00449 Transforming protein P21 ras signature 44 66 0.0000
7 g10429.t5 PRINTS PR00449 Transforming protein P21 ras signature 107 120 0.0000
5 g10429.t5 PRINTS PR00449 Transforming protein P21 ras signature 142 164 0.0000
1 g10429.t5 Pfam PF00071 Ras family 5 165 0.0000
17 g10429.t5 ProSiteProfiles PS51421 small GTPase Ras family profile. 1 184 44.9460
12 g10429.t5 SMART SM00173 ras_sub_4 1 167 0.0000
13 g10429.t5 SMART SM00175 rab_sub_5 4 167 0.0000
15 g10429.t5 SMART SM00174 rho_sub_3 6 167 0.0000
14 g10429.t5 SMART SM00176 ran_sub_2 9 183 0.0034
9 g10429.t5 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 2 176 0.0000
16 g10429.t5 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 1 158 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:0032486 Rap protein signal transduction BP
GO:0003924 GTPase activity 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