Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Ras-related protein Rab-14.

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 g5904 g5904.t6 TTS g5904.t6 12700643 12700643
chr_2 g5904 g5904.t6 isoform g5904.t6 12700893 12702292
chr_2 g5904 g5904.t6 exon g5904.t6.exon1 12700893 12702006
chr_2 g5904 g5904.t6 cds g5904.t6.CDS1 12701554 12701940
chr_2 g5904 g5904.t6 exon g5904.t6.exon2 12702148 12702292
chr_2 g5904 g5904.t6 TSS g5904.t6 12703071 12703071

Sequences

>g5904.t6 Gene=g5904 Length=1259
GCGACATGGGTGTCGGAAAGAGTTGCCTCTTACATCAATTCACAGAGAAAAAATTTATGG
CATCATGTCCACATACGATCGGAGTCGAATTCGGAACAAGAATTATTGAAGTTGATAAGC
AAAAGATAAAGGTATTTTATGATTTACTGCTGGACAGGAAAGATTTCGTGCGGTAACAAG
AAGTTATTATAGAGGTGCAGCTGGATGTTTAATGGTCTATGACATTACACGACGGTCGAC
ATACAACCATTTGAGTTCATGGCTTACAGACACTAAAAATTTAACTAATCCGTCTACTGT
GATTTTCCTTATTGGAAACAAATCAGATCTCGAATCTACGAGAGAAGTTACATATGAAGA
GGCGAAAAAGTTTGCAGATGAAAATGGTTTGATGTTTGCCGAAACAAGTGCGATGTCTGG
ACAAAATGTTGAAGAAGCATTTTTAGAGACAGCGAGAAAGATTTATCAGAGCGTGCAAGA
TGGTAGATTAGATTTGAATAGCGCAGAGAGTGGTGTCCAACAGAAAACCCAACAACGACC
GGGTAGAACTTCTTTAACAGATGATACTCAAACTAACAAAGATAATTGTTCATGCTAATT
CTAAAATTTAATGAAAACATCTGGTGCAAATATTTCTTTCTTCTTCGTAAATTTCTAACT
AAAATACCTAAACACAATTTAATATAGGATGAGTCTTTTTTTGTGGTAATAACCAAACAT
TGTCGAAAATGAGATCTAAACATCTTTCTTTTTATCCTCTCTAATCTCATCATAAAAATA
TTCTTATTCATTTTATGTTACATTTAATGCGAAAGAATATATTACATTACCAAACCAAAC
AAATAGAATCGCCCATAATCTATATATTTTACTTAGCTGATAAAAAAGTGAGAACAGAGC
CCATGTATAATAATGATATTCTTTTGTTATGCAAGCGTGATGATTCAGTATTTCAATTAT
TTTCTTGCATATTATTACATCCAATAATATGATTTTCTTTAATAACACAAAAGTATGATG
CATGCATATTGATCGCACGATGACTAATGATGGGCAGCAGTGAGTTTTTGTTGGAAAACA
AAAATAAAATAATATAATTATAAAGTGAATGTATAAAGTTGATGTGTATTAAGTTCTTTA
CCAATAATGATGTAGATGTTAGCATAGCAGAATTTATATCTTCCTTTGTTTATCTTTTTA
TTAATCTATTGCAGCATATTTGCATAAATGCATTTTTTGAACTATTTTTTTTATCGACA

>g5904.t6 Gene=g5904 Length=128
MVYDITRRSTYNHLSSWLTDTKNLTNPSTVIFLIGNKSDLESTREVTYEEAKKFADENGL
MFAETSAMSGQNVEEAFLETARKIYQSVQDGRLDLNSAESGVQQKTQQRPGRTSLTDDTQ
TNKDNCSC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g5904.t6 Gene3D G3DSA:3.40.50.300 - 1 128 3.7E-28
10 g5904.t6 MobiDBLite mobidb-lite consensus disorder prediction 95 128 -
2 g5904.t6 PANTHER PTHR47979:SF73 RAS-RELATED PROTEIN RAB-4A 1 128 4.7E-43
3 g5904.t6 PANTHER PTHR47979 DRAB11-RELATED 1 128 4.7E-43
4 g5904.t6 PRINTS PR00449 Transforming protein P21 ras signature 27 40 1.5E-10
5 g5904.t6 PRINTS PR00449 Transforming protein P21 ras signature 62 84 1.5E-10
1 g5904.t6 Pfam PF00071 Ras family 1 85 1.9E-23
11 g5904.t6 ProSiteProfiles PS51419 small GTPase Rab1 family profile. 1 126 18.208
8 g5904.t6 SMART SM00173 ras_sub_4 1 87 1.3E-4
9 g5904.t6 SMART SM00175 rab_sub_5 1 87 7.8E-12
6 g5904.t6 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 2 97 1.47E-22

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5904/g5904.t6; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5904.t6.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
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