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.t4 TSS g7654.t4 25092084 25092084
chr_2 g7654 g7654.t4 isoform g7654.t4 25092159 25093186
chr_2 g7654 g7654.t4 exon g7654.t4.exon1 25092159 25092240
chr_2 g7654 g7654.t4 exon g7654.t4.exon2 25092305 25092446
chr_2 g7654 g7654.t4 cds g7654.t4.CDS1 25092431 25092446
chr_2 g7654 g7654.t4 exon g7654.t4.exon3 25092501 25093186
chr_2 g7654 g7654.t4 cds g7654.t4.CDS2 25092501 25093186
chr_2 g7654 g7654.t4 TTS g7654.t4 25093267 25093267

Sequences

>g7654.t4 Gene=g7654 Length=910
ATGGCTGAAGCACCAACAGGTTTAAAACATATTCAAGCTTATTTGAAAATTGCAGCCGAT
CATGATCAAAGAGATGCTGTTGTCGCTTATTGGGCAAGAGTTTATTCATTACAAACTGGA
ATTAAGAGTGCAAAACAGCCTGATGAAAAAAGATTTCTTTTGAAAATTATGGATTGGTTA
GAAGGATTCAAAAAAGCTAACAAAGATAATGAATCAATTAGTGACGAATGATACAGTTGC
GCAAGCCTATCTCGAGAATTATGCTCATCGTCTCTTTACTTATGCTGATCAGCAAGACAG
AGCATCAAATTTTGGAAAAAATGTCGTTAAATCATTTTATACATCAGCAATGATTTATGA
CATTCTTACAGTTCTCGGAGAATTGAGTGAAGAAGCAAAGCAAAATCGAAAATACGCAAA
GTGGAAAGCTGCTTATATTCATAATTGTTTGAAAAATGGTGAACAACCACATCCCGGTCC
ACTTCCTAATGAAGAAGATGATGAATTACTCAATCTTGATGGATCTAATTCGACTCCAAG
TGAGCCTGGTTCATCTTCATCTATGGGCTGGAATACTCAACCTAATCAACCTGAAACTTC
TCCTCAGCAACCATCACCTCCTTCAAATACAAACACATTTAATAATGATCCATTCATGAA
CATTAGAGCTCCTTCTCCACCAAAAGATCCTGAAGAGAAAAATCCAGGTGGTTTTGTTGC
TTTTGATCCTGAACAATCAAATATTCCTGTGCCTCCACAATCGAAGGCAGCTATTTCCCC
TGAAATGATGATAAAGGCGCAAAAGTATTGCAAATTTGCTGGCAGTGCTCTTACATATGA
AGATGTTCCTACTGCTATTGAAAATTTGCAAAAAGCATTAAGATTACTCACAACTGGACA
AGATTCATAA

>g7654.t4 Gene=g7654 Length=233
MNQLVTNDTVAQAYLENYAHRLFTYADQQDRASNFGKNVVKSFYTSAMIYDILTVLGELS
EEAKQNRKYAKWKAAYIHNCLKNGEQPHPGPLPNEEDDELLNLDGSNSTPSEPGSSSSMG
WNTQPNQPETSPQQPSPPSNTNTFNNDPFMNIRAPSPPKDPEEKNPGGFVAFDPEQSNIP
VPPQSKAAISPEMMIKAQKYCKFAGSALTYEDVPTAIENLQKALRLLTTGQDS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g7654.t4 Gene3D G3DSA:1.25.40.270 - 1 87 3.1E-32
6 g7654.t4 Gene3D G3DSA:1.20.5.420 Immunoglobulin FC 191 229 5.0E-14
4 g7654.t4 MobiDBLite mobidb-lite consensus disorder prediction 106 140 -
5 g7654.t4 MobiDBLite mobidb-lite consensus disorder prediction 106 129 -
3 g7654.t4 PANTHER PTHR46009 VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN VTA1 HOMOLOG 2 230 1.9E-57
1 g7654.t4 Pfam PF04652 Vta1 like 2 83 1.0E-23
2 g7654.t4 Pfam PF18097 Vta1 C-terminal domain 191 228 3.7E-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