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.t20 TSS g2988.t20 21748744 21748744
chr_3 g2988 g2988.t20 isoform g2988.t20 21749323 21750619
chr_3 g2988 g2988.t20 exon g2988.t20.exon1 21749323 21749502
chr_3 g2988 g2988.t20 cds g2988.t20.CDS1 21749480 21749502
chr_3 g2988 g2988.t20 exon g2988.t20.exon2 21749711 21749924
chr_3 g2988 g2988.t20 cds g2988.t20.CDS2 21749711 21749924
chr_3 g2988 g2988.t20 exon g2988.t20.exon3 21749987 21750619
chr_3 g2988 g2988.t20 cds g2988.t20.CDS3 21749987 21750217
chr_3 g2988 g2988.t20 TTS g2988.t20 21750766 21750766

Sequences

>g2988.t20 Gene=g2988 Length=1027
ATGGCAACAAGAAAGAAGGTTTTGTTGAAAGTGATCATATTGGGAGATTCAAGTGTGGGA
AAGACATCTCTAATGAATCAATATGTGAATAAACGTTTTTCAAACCAGTATAAAGCTACT
ATCGGGGCTGATTTCTTAACAAAGGAAGTAGTTGTTGATGATCGAGTCGTCACAATGCAA
TACTGTAGCTGGTCAAGAAAGATTTCAATCACTCGGAGTTGCATTTTATCGTGGAGCGGA
TTGTTGTGTATTGGTATTTGATACAACAGCACCAAACACATTTAAAAATCTTGATTCTTG
GCGTGATGAGTTTTTAATACAAGCAAGTCCAAGAAATCCTGAACATTTTCCATTTGTAGT
TTTGGGCAATAAAGTAGATTTGGAAAATCGAGCTGTTTCAACAAAACGTGCACAGCAATG
GTGCCAATCGAAAAATGATATTCCATATTTTGAGACATCTGCTAAAGAGGGTATAAATGT
TGACATTGCTTTCCAAACGATCGCTAAAAACGCACTCGCGCAAGAAAGTGATGAGGGTAT
TGATTCTGCATTCAGTCCATCTCTAACATTGGGCTCATCGTCAGACTCTAATAATAGACC
CAACAGTAGTGACTGTTCATGCTAATTGCTAATTACGAGCGATAAGTTTATTACTTTTAT
CAAGCGAAATTTTGCATCGATGCATATGAACAAAAACACACAGACAACGGAAAATGCAAA
AAATAAAAAAAGTTATAAAAAGTGCATGTGAAGATATATAAAAAAAATAATTATGATTTT
TTTCCTATTTACTACCATATCTCTCATTTCAAAAAAAAATCTTATCTTTTCTGTGAAAAT
CAAAAAATAAAATATTTTATTAAAGAAAAAAGATTTTAAATTTGGAATAGGTAAAGTGAG
AGGTTGGATAGTTCTTTTAGAGAAGAAGAGTCCAATCTTGTATATTGTAGCATAATTTGA
AACGTAACATAAAATATATATATAAATCACTCTTGATAAAAATTCCTTTGATTTTTGATC
CCTACAA

>g2988.t20 Gene=g2988 Length=155
MIESSQCNTVAGQERFQSLGVAFYRGADCCVLVFDTTAPNTFKNLDSWRDEFLIQASPRN
PEHFPFVVLGNKVDLENRAVSTKRAQQWCQSKNDIPYFETSAKEGINVDIAFQTIAKNAL
AQESDEGIDSAFSPSLTLGSSSDSNNRPNSSDCSC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g2988.t20 Gene3D G3DSA:3.40.50.300 - 5 133 0.0000000
2 g2988.t20 PANTHER PTHR47981 RAB FAMILY 6 155 0.0000000
3 g2988.t20 PANTHER PTHR47981:SF3 RAB7B, MEMBER RAS ONCOGENE FAMILY-RELATED 6 155 0.0000000
5 g2988.t20 PRINTS PR00449 Transforming protein P21 ras signature 62 75 0.0000000
4 g2988.t20 PRINTS PR00449 Transforming protein P21 ras signature 97 119 0.0000000
1 g2988.t20 Pfam PF00071 Ras family 11 119 0.0000000
11 g2988.t20 ProSiteProfiles PS51419 small GTPase Rab1 family profile. 1 155 21.5510000
7 g2988.t20 SMART SM00173 ras_sub_4 2 122 0.0000085
8 g2988.t20 SMART SM00175 rab_sub_5 4 122 0.0000000
9 g2988.t20 SMART SM00174 rho_sub_3 5 122 0.0007100
6 g2988.t20 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 10 119 0.0000000

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