Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Ras-related protein Rab-7A.

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.t6 TSS g2988.t6 21748744 21748744
chr_3 g2988 g2988.t6 isoform g2988.t6 21748820 21749908
chr_3 g2988 g2988.t6 exon g2988.t6.exon1 21748820 21748847
chr_3 g2988 g2988.t6 exon g2988.t6.exon2 21749261 21749502
chr_3 g2988 g2988.t6 cds g2988.t6.CDS1 21749323 21749502
chr_3 g2988 g2988.t6 exon g2988.t6.exon3 21749719 21749908
chr_3 g2988 g2988.t6 cds g2988.t6.CDS2 21749719 21749847
chr_3 g2988 g2988.t6 TTS g2988.t6 21750766 21750766

Sequences

>g2988.t6 Gene=g2988 Length=460
TCTACAGTAATATAAACAATTTTAAAAGTTTTACTATACATTTTCTTGTTATTTCATACA
CAATTCATAAGAATTAATTTGTAAAGTAAAATGGCAACAAGAAAGAAGGTTTTGTTGAAA
GTGATCATATTGGGAGATTCAAGTGTGGGAAAGACATCTCTAATGAATCAATATGTGAAT
AAACGTTTTTCAAACCAGTATAAAGCTACTATCGGGGCTGATTTCTTAACAAAGGAAGTA
GTTGTTGATGATCGAGTCGTCACAATGCAACTGGTCAAGAAAGATTTCAATCACTCGGAG
TTGCATTTTATCGTGGAGCGGATTGTTGTGTATTGGTATTTGATACAACAGCACCAAACA
CATTTAAAAATCTTGATTCTTGGCGTGATGAGTTTTTAATACAAGCAAGTCCAAGAAATC
CTGAACATTTTCCATTTGTAGTTTTGGGCAATAAAGTAGA

>g2988.t6 Gene=g2988 Length=102
MATRKKVLLKVIILGDSSVGKTSLMNQYVNKRFSNQYKATIGADFLTKEVVVDDRVVTMQ
LVKKDFNHSELHFIVERIVVYWYLIQQHQTHLKILILGVMSF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g2988.t6 Gene3D G3DSA:3.40.50.300 - 1 70 2.5E-18
2 g2988.t6 PANTHER PTHR47981 RAB FAMILY 1 62 9.2E-31
3 g2988.t6 PANTHER PTHR47981:SF3 RAB7B, MEMBER RAS ONCOGENE FAMILY-RELATED 1 62 9.2E-31
4 g2988.t6 PRINTS PR00449 Transforming protein P21 ras signature 9 30 1.2E-12
5 g2988.t6 PRINTS PR00449 Transforming protein P21 ras signature 32 48 1.2E-12
1 g2988.t6 Pfam PF00071 Ras family 10 62 2.9E-16
9 g2988.t6 Phobius SIGNAL_PEPTIDE Signal peptide region 1 20 -
10 g2988.t6 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 6 -
11 g2988.t6 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 7 15 -
12 g2988.t6 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 16 20 -
8 g2988.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 21 102 -
14 g2988.t6 ProSiteProfiles PS51419 small GTPase Rab1 family profile. 4 102 11.128
13 g2988.t6 SMART SM00175 rab_sub_5 9 85 7.0E-6
6 g2988.t6 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 5 62 3.34E-16

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

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