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.t2 isoform g7654.t2 25091758 25093186
chr_2 g7654 g7654.t2 exon g7654.t2.exon1 25091758 25092029
chr_2 g7654 g7654.t2 exon g7654.t2.exon2 25092305 25092442
chr_2 g7654 g7654.t2 cds g7654.t2.CDS1 25092391 25092442
chr_2 g7654 g7654.t2 exon g7654.t2.exon3 25092501 25093186
chr_2 g7654 g7654.t2 cds g7654.t2.CDS2 25092501 25093186
chr_2 g7654 g7654.t2 TTS g7654.t2 25093267 25093267
chr_2 g7654 g7654.t2 TSS g7654.t2 NA NA

Sequences

>g7654.t2 Gene=g7654 Length=1096
TGCTTAATTTTGGGTTGCCGCATACTCTTCTTTGCACAACTACTATCACATGTTTCGAAT
TTCTTCAACCGTTACGTTATATTGAAAAACTAGCATTCTTGCACATCTCTACGAAACTCA
TGCAATTAAAAATTCAAAAATTAGGTGCCTATGTCAGATAAGTAAAAAATTAGTTGATTA
TTATCAATTAATTTCTTCATTAGACGTAAATTATGAAAAGTTTTAGTTATGCTTTAGCTT
AAACATAATCATTCTTTTGTAAGTAAAATAAATCGCTTATTGGGCAAGAGTTTATTCATT
ACAAACTGGAATTAAGAGTGCAAAACAGCCTGATGAAAAAAGATTTCTTTTGAAAATTAT
GGATTGGTTAGAAGGATTCAAAAAAGCTAACAAAGATAATGAATCAATTACGAATGATAC
AGTTGCGCAAGCCTATCTCGAGAATTATGCTCATCGTCTCTTTACTTATGCTGATCAGCA
AGACAGAGCATCAAATTTTGGAAAAAATGTCGTTAAATCATTTTATACATCAGCAATGAT
TTATGACATTCTTACAGTTCTCGGAGAATTGAGTGAAGAAGCAAAGCAAAATCGAAAATA
CGCAAAGTGGAAAGCTGCTTATATTCATAATTGTTTGAAAAATGGTGAACAACCACATCC
CGGTCCACTTCCTAATGAAGAAGATGATGAATTACTCAATCTTGATGGATCTAATTCGAC
TCCAAGTGAGCCTGGTTCATCTTCATCTATGGGCTGGAATACTCAACCTAATCAACCTGA
AACTTCTCCTCAGCAACCATCACCTCCTTCAAATACAAACACATTTAATAATGATCCATT
CATGAACATTAGAGCTCCTTCTCCACCAAAAGATCCTGAAGAGAAAAATCCAGGTGGTTT
TGTTGCTTTTGATCCTGAACAATCAAATATTCCTGTGCCTCCACAATCGAAGGCAGCTAT
TTCCCCTGAAATGATGATAAAGGCGCAAAAGTATTGCAAATTTGCTGGCAGTGCTCTTAC
ATATGAAGATGTTCCTACTGCTATTGAAAATTTGCAAAAAGCATTAAGATTACTCACAAC
TGGACAAGATTCATAA

>g7654.t2 Gene=g7654 Length=245
MDWLEGFKKANKDNESITNDTVAQAYLENYAHRLFTYADQQDRASNFGKNVVKSFYTSAM
IYDILTVLGELSEEAKQNRKYAKWKAAYIHNCLKNGEQPHPGPLPNEEDDELLNLDGSNS
TPSEPGSSSSMGWNTQPNQPETSPQQPSPPSNTNTFNNDPFMNIRAPSPPKDPEEKNPGG
FVAFDPEQSNIPVPPQSKAAISPEMMIKAQKYCKFAGSALTYEDVPTAIENLQKALRLLT
TGQDS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g7654.t2 Gene3D G3DSA:1.25.40.270 - 1 99 9.3E-38
6 g7654.t2 Gene3D G3DSA:1.20.5.420 Immunoglobulin FC 203 241 5.4E-14
4 g7654.t2 MobiDBLite mobidb-lite consensus disorder prediction 118 141 -
5 g7654.t2 MobiDBLite mobidb-lite consensus disorder prediction 118 152 -
3 g7654.t2 PANTHER PTHR46009 VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN VTA1 HOMOLOG 1 242 1.0E-60
1 g7654.t2 Pfam PF04652 Vta1 like 1 95 4.5E-29
2 g7654.t2 Pfam PF18097 Vta1 C-terminal domain 203 240 4.0E-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. There were no conditions that were differentially expressed