Gene loci information

Transcript annotation

  • This transcript has been annotated as hypothetical.

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_2 g4729 g4729.t2 isoform g4729.t2 4438273 4439395
chr_2 g4729 g4729.t2 exon g4729.t2.exon1 4438273 4439395
chr_2 g4729 g4729.t2 TTS g4729.t2 4438289 4438289
chr_2 g4729 g4729.t2 cds g4729.t2.CDS1 4438870 4439367
chr_2 g4729 g4729.t2 TSS g4729.t2 NA NA

Sequences

>g4729.t2 Gene=g4729 Length=1123
TTCACGTAATAATTCCCTTGATCGCAACATGACGCCACCATTAAATGCATCACTCTTGTC
AGCTGCAAGTAGCGTCTCATCGTCTTCACTCTCAATGGAGTCAACGACATCGAGCAGTCA
AAATCACAGCACGAAAACTCCCTCGAAAAAATCATCATCAAACCATGAGGTTCTTCCATC
ACATATTAATGCTCAGCTACAACCAAATTCACCATTGTTGAAAGGTAACGCGAATGGAGC
AGCGCCAGATTTTTATATTATCAAAGTAACATATGAAACAGATGGTGTTGAGAAAGATGG
AATTGTGCTATATAAAAGCATCATGTTGTGCAATAATGAGAGAACGCCGACTGTTATTCG
AAATGCAATGATAAAACTTGGCTTGGAAGGTGATCCTGATCGATATACATTATCACAAGT
TTTGCCAGACAAAGAATTGATGCTGCCAGCTAATGCTAATGTCTATTATGCTGTAAACAC
ACAATATAATTTGAATTTCATTCTTCGAAATAAGAAAGATTCATAAATAGACCAAAATAA
CTGCCTTTAAGAGCAATAATTGAATTGAGTCATTTAAATTTTAGTATTAAAATACCAGTG
GGTCCAATTTATTATATATTTAAATCTAAAAAATTACCAGTGAATTATTAAAGAAGCAAT
TTATAATCAAAACAAATGAATAATTTATCAAAAAAAAATTTTTGCTTATTTATGTTGAAG
CTTAAGCCGCACATTTTTTGAGCAGAGAATGCGTATTTTTTTGTGATTGATGGATTGGAT
TAAAAATAAACTTTTTAAAAGATTAATCATCATGTACTCTGTCTGTCTCTCATGCACAAT
TTTATGTCAAAAAAAATTAATGAATCTAATGAGAGTAACATAAAATTAATTTTTTTAGGA
ATTTATTTTGTAAATTTTTACATAGTCATGAATTTATGACTTTATTTTAAATTAAGTGAA
ATTTAAAAATAGAGCAGGAAATTTTTATGTATTCTAATTGTGTAATTAATTTAAATATTA
GATATGATAAATAAATATGATACTTGTAGAATTTCTAATTAGAATTTACAAAATGAAAAA
TTTCAATAAAAACCAAAATTTAATTCAAAAAATTCTCTATCAA

>g4729.t2 Gene=g4729 Length=165
MTPPLNASLLSAASSVSSSSLSMESTTSSSQNHSTKTPSKKSSSNHEVLPSHINAQLQPN
SPLLKGNANGAAPDFYIIKVTYETDGVEKDGIVLYKSIMLCNNERTPTVIRNAMIKLGLE
GDPDRYTLSQVLPDKELMLPANANVYYAVNTQYNLNFILRNKKDS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g4729.t2 CDD cd00153 RA_RalGDS_like 74 162 3.79638E-34
5 g4729.t2 Coils Coil Coil 162 165 -
4 g4729.t2 Gene3D G3DSA:3.10.20.90 - 12 165 3.3E-33
13 g4729.t2 MobiDBLite mobidb-lite consensus disorder prediction 15 48 -
1 g4729.t2 Pfam PF00788 Ras association (RalGDS/AF-6) domain 76 164 1.7E-12
7 g4729.t2 Phobius SIGNAL_PEPTIDE Signal peptide region 1 22 -
8 g4729.t2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 6 -
9 g4729.t2 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 7 17 -
10 g4729.t2 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 18 22 -
6 g4729.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 23 165 -
14 g4729.t2 ProSiteProfiles PS50200 Ras-associating (RA) domain profile. 74 164 17.461
12 g4729.t2 SMART SM00314 RA_5 74 164 1.2E-7
2 g4729.t2 SUPERFAMILY SSF54236 Ubiquitin-like 69 162 6.79E-29
3 g4729.t2 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 30 -

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:0007165 signal transduction BP

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