Gene loci information

Transcript annotation

  • This transcript has been annotated as 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.t9 TTS g5904.t9 12700643 12700643
chr_2 g5904 g5904.t9 isoform g5904.t9 12700893 12703136
chr_2 g5904 g5904.t9 exon g5904.t9.exon1 12700893 12701994
chr_2 g5904 g5904.t9 cds g5904.t9.CDS1 12701554 12701994
chr_2 g5904 g5904.t9 exon g5904.t9.exon2 12702162 12702350
chr_2 g5904 g5904.t9 cds g5904.t9.CDS2 12702162 12702287
chr_2 g5904 g5904.t9 exon g5904.t9.exon3 12702952 12703136
chr_2 g5904 g5904.t9 TSS g5904.t9 12703071 12703071

Sequences

>g5904.t9 Gene=g5904 Length=1476
AATAACGGCTTTTAGTTTATTAATTTTTACAATTCTATAAAGTAATTTTTCCCCTTATTG
CTTTTGATTGAAGAAAAATAGAAAGGAAGATAGAAAGAAAAAATAATTTTCTGCAATTTA
ACAATATTCTCGCTGGAATCGAGTTATAAAACATTCTTTTATTGATATTAAAGACGTCAA
AAAATTTTCTCTTAATTGACTTAATTTTAATCTTTTCATTTTTATGCAGATATATTATAA
TTGGCGACATGGGTGTCGGAAAGAGTTGCCTCTTACATCAATTCACAGAGAAAAAATTTA
TGGCATCATGTCCACATACGATCGGAGTCGAATTCGGAACAAGAATTATTGAAGTTGATA
AGCAAAAGATAAAGGAAAGATTTCGTGCGGTAACAAGAAGTTATTATAGAGGTGCAGCTG
GATGTTTAATGGTCTATGACATTACACGACGGTCGACATACAACCATTTGAGTTCATGGC
TTACAGACACTAAAAATTTAACTAATCCGTCTACTGTGATTTTCCTTATTGGAAACAAAT
CAGATCTCGAATCTACGAGAGAAGTTACATATGAAGAGGCGAAAAAGTTTGCAGATGAAA
ATGGTTTGATGTTTGCCGAAACAAGTGCGATGTCTGGACAAAATGTTGAAGAAGCATTTT
TAGAGACAGCGAGAAAGATTTATCAGAGCGTGCAAGATGGTAGATTAGATTTGAATAGCG
CAGAGAGTGGTGTCCAACAGAAAACCCAACAACGACCGGGTAGAACTTCTTTAACAGATG
ATACTCAAACTAACAAAGATAATTGTTCATGCTAATTCTAAAATTTAATGAAAACATCTG
GTGCAAATATTTCTTTCTTCTTCGTAAATTTCTAACTAAAATACCTAAACACAATTTAAT
ATAGGATGAGTCTTTTTTTGTGGTAATAACCAAACATTGTCGAAAATGAGATCTAAACAT
CTTTCTTTTTATCCTCTCTAATCTCATCATAAAAATATTCTTATTCATTTTATGTTACAT
TTAATGCGAAAGAATATATTACATTACCAAACCAAACAAATAGAATCGCCCATAATCTAT
ATATTTTACTTAGCTGATAAAAAAGTGAGAACAGAGCCCATGTATAATAATGATATTCTT
TTGTTATGCAAGCGTGATGATTCAGTATTTCAATTATTTTCTTGCATATTATTACATCCA
ATAATATGATTTTCTTTAATAACACAAAAGTATGATGCATGCATATTGATCGCACGATGA
CTAATGATGGGCAGCAGTGAGTTTTTGTTGGAAAACAAAAATAAAATAATATAATTATAA
AGTGAATGTATAAAGTTGATGTGTATTAAGTTCTTTACCAATAATGATGTAGATGTTAGC
ATAGCAGAATTTATATCTTCCTTTGTTTATCTTTTTATTAATCTATTGCAGCATATTTGC
ATAAATGCATTTTTTGAACTATTTTTTTTATCGACA

>g5904.t9 Gene=g5904 Length=188
MGVGKSCLLHQFTEKKFMASCPHTIGVEFGTRIIEVDKQKIKERFRAVTRSYYRGAAGCL
MVYDITRRSTYNHLSSWLTDTKNLTNPSTVIFLIGNKSDLESTREVTYEEAKKFADENGL
MFAETSAMSGQNVEEAFLETARKIYQSVQDGRLDLNSAESGVQQKTQQRPGRTSLTDDTQ
TNKDNCSC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g5904.t9 Gene3D G3DSA:3.40.50.300 - 1 188 3.5E-49
12 g5904.t9 MobiDBLite mobidb-lite consensus disorder prediction 158 188 -
2 g5904.t9 PANTHER PTHR47979:SF73 RAS-RELATED PROTEIN RAB-4A 1 188 9.5E-75
3 g5904.t9 PANTHER PTHR47979 DRAB11-RELATED 1 188 9.5E-75
6 g5904.t9 PRINTS PR00449 Transforming protein P21 ras signature 16 32 3.1E-14
4 g5904.t9 PRINTS PR00449 Transforming protein P21 ras signature 87 100 3.1E-14
5 g5904.t9 PRINTS PR00449 Transforming protein P21 ras signature 122 144 3.1E-14
1 g5904.t9 Pfam PF00071 Ras family 2 145 1.1E-41
14 g5904.t9 ProSiteProfiles PS51419 small GTPase Rab1 family profile. 1 186 28.115
10 g5904.t9 SMART SM00175 rab_sub_5 1 147 1.9E-70
9 g5904.t9 SMART SM00173 ras_sub_4 2 147 1.5E-11
11 g5904.t9 SMART SM00174 rho_sub_3 2 147 2.5E-4
7 g5904.t9 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 2 156 5.07E-41
13 g5904.t9 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 2 137 4.5E-16

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5904/g5904.t9; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5904.t9.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