Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Vacuolar protein sorting-associated protein VTA1-like protein.

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 g7654 g7654.t1 TSS g7654.t1 25092084 25092084
chr_2 g7654 g7654.t1 isoform g7654.t1 25092159 25093186
chr_2 g7654 g7654.t1 exon g7654.t1.exon1 25092159 25092240
chr_2 g7654 g7654.t1 cds g7654.t1.CDS1 25092159 25092240
chr_2 g7654 g7654.t1 exon g7654.t1.exon2 25092305 25092442
chr_2 g7654 g7654.t1 cds g7654.t1.CDS2 25092305 25092442
chr_2 g7654 g7654.t1 exon g7654.t1.exon3 25092501 25093186
chr_2 g7654 g7654.t1 cds g7654.t1.CDS3 25092501 25093186
chr_2 g7654 g7654.t1 TTS g7654.t1 25093267 25093267

Sequences

>g7654.t1 Gene=g7654 Length=906
ATGGCTGAAGCACCAACAGGTTTAAAACATATTCAAGCTTATTTGAAAATTGCAGCCGAT
CATGATCAAAGAGATGCTGTTGTCGCTTATTGGGCAAGAGTTTATTCATTACAAACTGGA
ATTAAGAGTGCAAAACAGCCTGATGAAAAAAGATTTCTTTTGAAAATTATGGATTGGTTA
GAAGGATTCAAAAAAGCTAACAAAGATAATGAATCAATTACGAATGATACAGTTGCGCAA
GCCTATCTCGAGAATTATGCTCATCGTCTCTTTACTTATGCTGATCAGCAAGACAGAGCA
TCAAATTTTGGAAAAAATGTCGTTAAATCATTTTATACATCAGCAATGATTTATGACATT
CTTACAGTTCTCGGAGAATTGAGTGAAGAAGCAAAGCAAAATCGAAAATACGCAAAGTGG
AAAGCTGCTTATATTCATAATTGTTTGAAAAATGGTGAACAACCACATCCCGGTCCACTT
CCTAATGAAGAAGATGATGAATTACTCAATCTTGATGGATCTAATTCGACTCCAAGTGAG
CCTGGTTCATCTTCATCTATGGGCTGGAATACTCAACCTAATCAACCTGAAACTTCTCCT
CAGCAACCATCACCTCCTTCAAATACAAACACATTTAATAATGATCCATTCATGAACATT
AGAGCTCCTTCTCCACCAAAAGATCCTGAAGAGAAAAATCCAGGTGGTTTTGTTGCTTTT
GATCCTGAACAATCAAATATTCCTGTGCCTCCACAATCGAAGGCAGCTATTTCCCCTGAA
ATGATGATAAAGGCGCAAAAGTATTGCAAATTTGCTGGCAGTGCTCTTACATATGAAGAT
GTTCCTACTGCTATTGAAAATTTGCAAAAAGCATTAAGATTACTCACAACTGGACAAGAT
TCATAA

>g7654.t1 Gene=g7654 Length=301
MAEAPTGLKHIQAYLKIAADHDQRDAVVAYWARVYSLQTGIKSAKQPDEKRFLLKIMDWL
EGFKKANKDNESITNDTVAQAYLENYAHRLFTYADQQDRASNFGKNVVKSFYTSAMIYDI
LTVLGELSEEAKQNRKYAKWKAAYIHNCLKNGEQPHPGPLPNEEDDELLNLDGSNSTPSE
PGSSSSMGWNTQPNQPETSPQQPSPPSNTNTFNNDPFMNIRAPSPPKDPEEKNPGGFVAF
DPEQSNIPVPPQSKAAISPEMMIKAQKYCKFAGSALTYEDVPTAIENLQKALRLLTTGQD
S

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g7654.t1 Gene3D G3DSA:1.25.40.270 - 1 155 3.5E-56
7 g7654.t1 Gene3D G3DSA:1.20.5.420 Immunoglobulin FC 259 297 7.3E-14
5 g7654.t1 MobiDBLite mobidb-lite consensus disorder prediction 174 208 -
6 g7654.t1 MobiDBLite mobidb-lite consensus disorder prediction 174 197 -
3 g7654.t1 PANTHER PTHR46009 VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN VTA1 HOMOLOG 3 231 8.2E-81
4 g7654.t1 PANTHER PTHR46009 VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN VTA1 HOMOLOG 177 298 8.2E-81
1 g7654.t1 Pfam PF04652 Vta1 like 11 151 1.7E-43
2 g7654.t1 Pfam PF18097 Vta1 C-terminal domain 259 296 5.4E-18

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

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