Gene loci information

Transcript annotation

  • This transcript has been annotated as Ras-related protein rab7.

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 g2988 g2988.t8 TSS g2988.t8 21748744 21748744
chr_3 g2988 g2988.t8 isoform g2988.t8 21748820 21750217
chr_3 g2988 g2988.t8 exon g2988.t8.exon1 21748820 21748847
chr_3 g2988 g2988.t8 exon g2988.t8.exon2 21749261 21749502
chr_3 g2988 g2988.t8 exon g2988.t8.exon3 21749571 21749639
chr_3 g2988 g2988.t8 cds g2988.t8.CDS1 21749603 21749639
chr_3 g2988 g2988.t8 exon g2988.t8.exon4 21749719 21749924
chr_3 g2988 g2988.t8 cds g2988.t8.CDS2 21749719 21749924
chr_3 g2988 g2988.t8 exon g2988.t8.exon5 21749987 21750217
chr_3 g2988 g2988.t8 cds g2988.t8.CDS3 21749987 21750217
chr_3 g2988 g2988.t8 TTS g2988.t8 21750766 21750766

Sequences

>g2988.t8 Gene=g2988 Length=776
TCTACAGTAATATAAACAATTTTAAAAGTTTTACTATACATTTTCTTGTTATTTCATACA
CAATTCATAAGAATTAATTTGTAAAGTAAAATGGCAACAAGAAAGAAGGTTTTGTTGAAA
GTGATCATATTGGGAGATTCAAGTGTGGGAAAGACATCTCTAATGAATCAATATGTGAAT
AAACGTTTTTCAAACCAGTATAAAGCTACTATCGGGGCTGATTTCTTAACAAAGGAAGTA
GTTGTTGATGATCGAGTCGTCACAATGCAAACTCAATTTTTTTCTCTTTTTTTACAATCT
TCATGCGACGTCATAATTATTTAAAGATATGGGACACAGCTGGTCAAGAAAGATTTCAAT
CACTCGGAGTTGCATTTTATCGTGGAGCGGATTGTTGTGTATTGGTATTTGATACAACAG
CACCAAACACATTTAAAAATCTTGATTCTTGGCGTGATGAGTTTTTAATACAAGCAAGTC
CAAGAAATCCTGAACATTTTCCATTTGTAGTTTTGGGCAATAAAGTAGATTTGGAAAATC
GAGCTGTTTCAACAAAACGTGCACAGCAATGGTGCCAATCGAAAAATGATATTCCATATT
TTGAGACATCTGCTAAAGAGGGTATAAATGTTGACATTGCTTTCCAAACGATCGCTAAAA
ACGCACTCGCGCAAGAAAGTGATGAGGGTATTGATTCTGCATTCAGTCCATCTCTAACAT
TGGGCTCATCGTCAGACTCTAATAATAGACCCAACAGTAGTGACTGTTCATGCTAA

>g2988.t8 Gene=g2988 Length=157
MRRHNYLKIWDTAGQERFQSLGVAFYRGADCCVLVFDTTAPNTFKNLDSWRDEFLIQASP
RNPEHFPFVVLGNKVDLENRAVSTKRAQQWCQSKNDIPYFETSAKEGINVDIAFQTIAKN
ALAQESDEGIDSAFSPSLTLGSSSDSNNRPNSSDCSC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g2988.t8 Gene3D G3DSA:3.40.50.300 - 2 135 0.000e+00
2 g2988.t8 PANTHER PTHR47981 RAB FAMILY 6 157 0.000e+00
3 g2988.t8 PANTHER PTHR47981:SF3 RAB7B, MEMBER RAS ONCOGENE FAMILY-RELATED 6 157 0.000e+00
4 g2988.t8 PRINTS PR00449 Transforming protein P21 ras signature 64 77 0.000e+00
5 g2988.t8 PRINTS PR00449 Transforming protein P21 ras signature 99 121 0.000e+00
1 g2988.t8 Pfam PF00071 Ras family 5 121 0.000e+00
11 g2988.t8 ProSiteProfiles PS51419 small GTPase Rab1 family profile. 1 157 2.202e+01
8 g2988.t8 SMART SM00173 ras_sub_4 1 124 2.000e-07
10 g2988.t8 SMART SM00174 rho_sub_3 1 124 2.300e-05
9 g2988.t8 SMART SM00175 rab_sub_5 3 124 0.000e+00
6 g2988.t8 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 6 121 0.000e+00
12 g2988.t8 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 7 118 0.000e+00

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
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