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.t1 TSS g2988.t1 21748744 21748744
chr_3 g2988 g2988.t1 isoform g2988.t1 21749323 21750217
chr_3 g2988 g2988.t1 exon g2988.t1.exon1 21749323 21749502
chr_3 g2988 g2988.t1 cds g2988.t1.CDS1 21749323 21749502
chr_3 g2988 g2988.t1 exon g2988.t1.exon2 21749627 21749639
chr_3 g2988 g2988.t1 cds g2988.t1.CDS2 21749627 21749639
chr_3 g2988 g2988.t1 exon g2988.t1.exon3 21749719 21749924
chr_3 g2988 g2988.t1 cds g2988.t1.CDS3 21749719 21749924
chr_3 g2988 g2988.t1 exon g2988.t1.exon4 21749987 21750217
chr_3 g2988 g2988.t1 cds g2988.t1.CDS4 21749987 21750217
chr_3 g2988 g2988.t1 TTS g2988.t1 21750766 21750766

Sequences

>g2988.t1 Gene=g2988 Length=630
ATGGCAACAAGAAAGAAGGTTTTGTTGAAAGTGATCATATTGGGAGATTCAAGTGTGGGA
AAGACATCTCTAATGAATCAATATGTGAATAAACGTTTTTCAAACCAGTATAAAGCTACT
ATCGGGGCTGATTTCTTAACAAAGGAAGTAGTTGTTGATGATCGAGTCGTCACAATGCAA
ATATGGGACACAGCTGGTCAAGAAAGATTTCAATCACTCGGAGTTGCATTTTATCGTGGA
GCGGATTGTTGTGTATTGGTATTTGATACAACAGCACCAAACACATTTAAAAATCTTGAT
TCTTGGCGTGATGAGTTTTTAATACAAGCAAGTCCAAGAAATCCTGAACATTTTCCATTT
GTAGTTTTGGGCAATAAAGTAGATTTGGAAAATCGAGCTGTTTCAACAAAACGTGCACAG
CAATGGTGCCAATCGAAAAATGATATTCCATATTTTGAGACATCTGCTAAAGAGGGTATA
AATGTTGACATTGCTTTCCAAACGATCGCTAAAAACGCACTCGCGCAAGAAAGTGATGAG
GGTATTGATTCTGCATTCAGTCCATCTCTAACATTGGGCTCATCGTCAGACTCTAATAAT
AGACCCAACAGTAGTGACTGTTCATGCTAA

>g2988.t1 Gene=g2988 Length=209
MATRKKVLLKVIILGDSSVGKTSLMNQYVNKRFSNQYKATIGADFLTKEVVVDDRVVTMQ
IWDTAGQERFQSLGVAFYRGADCCVLVFDTTAPNTFKNLDSWRDEFLIQASPRNPEHFPF
VVLGNKVDLENRAVSTKRAQQWCQSKNDIPYFETSAKEGINVDIAFQTIAKNALAQESDE
GIDSAFSPSLTLGSSSDSNNRPNSSDCSC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g2988.t1 CDD cd01862 Rab7 9 178 1.94057E-134
10 g2988.t1 Gene3D G3DSA:3.40.50.300 - 1 186 5.6E-69
2 g2988.t1 PANTHER PTHR47981 RAB FAMILY 1 209 6.3E-112
3 g2988.t1 PANTHER PTHR47981:SF3 RAB7B, MEMBER RAS ONCOGENE FAMILY-RELATED 1 209 6.3E-112
5 g2988.t1 PRINTS PR00449 Transforming protein P21 ras signature 9 30 2.5E-39
8 g2988.t1 PRINTS PR00449 Transforming protein P21 ras signature 32 48 2.5E-39
7 g2988.t1 PRINTS PR00449 Transforming protein P21 ras signature 50 72 2.5E-39
4 g2988.t1 PRINTS PR00449 Transforming protein P21 ras signature 116 129 2.5E-39
6 g2988.t1 PRINTS PR00449 Transforming protein P21 ras signature 151 173 2.5E-39
1 g2988.t1 Pfam PF00071 Ras family 10 173 2.8E-56
12 g2988.t1 Phobius SIGNAL_PEPTIDE Signal peptide region 1 20 -
13 g2988.t1 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 6 -
14 g2988.t1 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 7 15 -
15 g2988.t1 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 16 20 -
11 g2988.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 21 209 -
22 g2988.t1 ProSiteProfiles PS51419 small GTPase Rab1 family profile. 4 209 33.031
17 g2988.t1 SMART SM00173 ras_sub_4 6 176 5.2E-28
18 g2988.t1 SMART SM00175 rab_sub_5 9 176 2.9E-93
20 g2988.t1 SMART SM00174 rho_sub_3 11 176 1.4E-12
19 g2988.t1 SMART SM00176 ran_sub_2 14 209 2.2E-9
9 g2988.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 5 176 1.01E-54
21 g2988.t1 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 10 170 7.4E-27

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