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.t2 TTS g1930.t2 13954367 13954367
chr_3 g1930 g1930.t2 isoform g1930.t2 13954488 13955691
chr_3 g1930 g1930.t2 exon g1930.t2.exon1 13954488 13955234
chr_3 g1930 g1930.t2 cds g1930.t2.CDS1 13954488 13955234
chr_3 g1930 g1930.t2 exon g1930.t2.exon2 13955294 13955455
chr_3 g1930 g1930.t2 cds g1930.t2.CDS2 13955294 13955455
chr_3 g1930 g1930.t2 exon g1930.t2.exon3 13955511 13955691
chr_3 g1930 g1930.t2 cds g1930.t2.CDS3 13955511 13955546
chr_3 g1930 g1930.t2 TSS g1930.t2 13955886 13955886

Sequences

>g1930.t2 Gene=g1930 Length=1090
ATGTCTAGTTTTAATGAAAATGAAGAGGAAGATGATAACTTTTTTAATAATGATGAATAT
GTTAAACCAAAAATATTACTCTTTGGTTTGCGAAGAAGTGGAAAGAGCTCAATTCAAAAA
GTAGTTTTTCACAAGATGAGTCCAAATGAAACCCTTTTTCTTGAATCTACAAATAAGGTT
TATTGTTAAAGAAGATATCAACAACTCAAGCTTTGTGCAATTTGAGATTTGGGATTTTCC
TGGTCAAATAGATTTCTTTGATCCTACATTCGATAGTGAACTCATTTTTGGAGACTGTGG
AGCATTAGTATTTGTGATCGATGCACAAGACGATTATCTAGAGGCTCTTTCAAAACTTAA
TCAAACAGTCACAAAGGCATATAAAGTGAATCCTAGAATTAAATTTGAAGTTTTTATTCA
TAAAGTTGATGGTGTGTCTGATGATTTCAAAATTGAATCACAACGTGACATTCATCAAAG
AGCTACAGATGACTTACAAGATGCTGGTTTAGATATTCATTTAAGCTTTCACCTCACATC
TATATATGATCATTCTATATTTGAAGCATTTAGTAAAGTTGTTCAGAAGTTGATTTCGCA
ATTACCAACACTTGAAAATCTCCTTAACATTTTGATTACTAATTCTGGAATTGAAAAGGC
CTTTTTGTTTGATGTTGTATCTAAAATTTATATTGCTACTGATTCTGCACCTGTTGATAT
GCAAACCTATGAACTCTGTTGCGATATGATCGATGTGGTTATTGATCTAAGTGACATTTA
TGGTGTATCAGCTGAAGAGAGAGCAAACCAAGAGCAAACAGCGTTTGATAATCTAAGTTC
ATCACTTATCAAGCTTAATAATTCAACAATTCTTTATCTCAAGGAAGTTAACAAATTTTT
GGCTCTTGTATGCATACTTCGCGAAGAAAATTTTACTCGACAAGGTGTAATTGATTATAA
TTTTCTTATTTTTCGTGAATCGATTGGTCGTGTTTTTGAGTTGAGATCGAAGAAATTAAA
AAGTAACAATGATGATTTAAGTGAAGATTATAATTATCAACAACCATCATCTGTTACTGA
TTCTGTTTAA

>g1930.t2 Gene=g1930 Length=314
MKPFFLNLQIRFIVKEDINNSSFVQFEIWDFPGQIDFFDPTFDSELIFGDCGALVFVIDA
QDDYLEALSKLNQTVTKAYKVNPRIKFEVFIHKVDGVSDDFKIESQRDIHQRATDDLQDA
GLDIHLSFHLTSIYDHSIFEAFSKVVQKLISQLPTLENLLNILITNSGIEKAFLFDVVSK
IYIATDSAPVDMQTYELCCDMIDVVIDLSDIYGVSAEERANQEQTAFDNLSSSLIKLNNS
TILYLKEVNKFLALVCILREENFTRQGVIDYNFLIFRESIGRVFELRSKKLKSNNDDLSE
DYNYQQPSSVTDSV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g1930.t2 CDD cd11385 RagC_like 13 150 0
5 g1930.t2 Gene3D G3DSA:3.40.50.300 - 3 151 0
6 g1930.t2 Gene3D G3DSA:3.30.450.190 - 154 283 0
2 g1930.t2 PANTHER PTHR11259:SF5 RAS-RELATED GTP-BINDING PROTEIN D 12 296 0
3 g1930.t2 PANTHER PTHR11259 RAS-RELATED GTP BINDING RAG/GTR YEAST 12 296 0
1 g1930.t2 Pfam PF04670 Gtr1/RagA G protein conserved region 14 202 0
4 g1930.t2 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 17 155 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

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. There were no conditions that were differentially expressed