Gene loci information

Transcript annotation

  • This transcript has been annotated as Ras-related GTP-binding protein D.

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_3 g1930 g1930.t1 TTS g1930.t1 13954367 13954367
chr_3 g1930 g1930.t1 isoform g1930.t1 13954488 13955691
chr_3 g1930 g1930.t1 exon g1930.t1.exon1 13954488 13955234
chr_3 g1930 g1930.t1 cds g1930.t1.CDS1 13954488 13955234
chr_3 g1930 g1930.t1 exon g1930.t1.exon2 13955294 13955455
chr_3 g1930 g1930.t1 cds g1930.t1.CDS2 13955294 13955455
chr_3 g1930 g1930.t1 exon g1930.t1.exon3 13955515 13955691
chr_3 g1930 g1930.t1 cds g1930.t1.CDS3 13955515 13955691
chr_3 g1930 g1930.t1 TSS g1930.t1 13955886 13955886

Sequences

>g1930.t1 Gene=g1930 Length=1086
ATGTCTAGTTTTAATGAAAATGAAGAGGAAGATGATAACTTTTTTAATAATGATGAATAT
GTTAAACCAAAAATATTACTCTTTGGTTTGCGAAGAAGTGGAAAGAGCTCAATTCAAAAA
GTAGTTTTTCACAAGATGAGTCCAAATGAAACCCTTTTTCTTGAATCTACAAATAAGATT
GTTAAAGAAGATATCAACAACTCAAGCTTTGTGCAATTTGAGATTTGGGATTTTCCTGGT
CAAATAGATTTCTTTGATCCTACATTCGATAGTGAACTCATTTTTGGAGACTGTGGAGCA
TTAGTATTTGTGATCGATGCACAAGACGATTATCTAGAGGCTCTTTCAAAACTTAATCAA
ACAGTCACAAAGGCATATAAAGTGAATCCTAGAATTAAATTTGAAGTTTTTATTCATAAA
GTTGATGGTGTGTCTGATGATTTCAAAATTGAATCACAACGTGACATTCATCAAAGAGCT
ACAGATGACTTACAAGATGCTGGTTTAGATATTCATTTAAGCTTTCACCTCACATCTATA
TATGATCATTCTATATTTGAAGCATTTAGTAAAGTTGTTCAGAAGTTGATTTCGCAATTA
CCAACACTTGAAAATCTCCTTAACATTTTGATTACTAATTCTGGAATTGAAAAGGCCTTT
TTGTTTGATGTTGTATCTAAAATTTATATTGCTACTGATTCTGCACCTGTTGATATGCAA
ACCTATGAACTCTGTTGCGATATGATCGATGTGGTTATTGATCTAAGTGACATTTATGGT
GTATCAGCTGAAGAGAGAGCAAACCAAGAGCAAACAGCGTTTGATAATCTAAGTTCATCA
CTTATCAAGCTTAATAATTCAACAATTCTTTATCTCAAGGAAGTTAACAAATTTTTGGCT
CTTGTATGCATACTTCGCGAAGAAAATTTTACTCGACAAGGTGTAATTGATTATAATTTT
CTTATTTTTCGTGAATCGATTGGTCGTGTTTTTGAGTTGAGATCGAAGAAATTAAAAAGT
AACAATGATGATTTAAGTGAAGATTATAATTATCAACAACCATCATCTGTTACTGATTCT
GTTTAA

>g1930.t1 Gene=g1930 Length=361
MSSFNENEEEDDNFFNNDEYVKPKILLFGLRRSGKSSIQKVVFHKMSPNETLFLESTNKI
VKEDINNSSFVQFEIWDFPGQIDFFDPTFDSELIFGDCGALVFVIDAQDDYLEALSKLNQ
TVTKAYKVNPRIKFEVFIHKVDGVSDDFKIESQRDIHQRATDDLQDAGLDIHLSFHLTSI
YDHSIFEAFSKVVQKLISQLPTLENLLNILITNSGIEKAFLFDVVSKIYIATDSAPVDMQ
TYELCCDMIDVVIDLSDIYGVSAEERANQEQTAFDNLSSSLIKLNNSTILYLKEVNKFLA
LVCILREENFTRQGVIDYNFLIFRESIGRVFELRSKKLKSNNDDLSEDYNYQQPSSVTDS
V

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g1930.t1 CDD cd11385 RagC_like 24 197 0
5 g1930.t1 Gene3D G3DSA:3.40.50.300 - 20 198 0
6 g1930.t1 Gene3D G3DSA:3.30.450.190 - 201 330 0
2 g1930.t1 PANTHER PTHR11259:SF5 RAS-RELATED GTP-BINDING PROTEIN D 18 343 0
3 g1930.t1 PANTHER PTHR11259 RAS-RELATED GTP BINDING RAG/GTR YEAST 18 343 0
1 g1930.t1 Pfam PF04670 Gtr1/RagA G protein conserved region 24 249 0
4 g1930.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 22 202 0

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

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