General information for g7654.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Vacuolar protein sorting-associated protein VTA1-like protein.
Parent gene
- The parent gene g7654 is located on chr_2: 25092501..25093186 (+ strand)
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.t6 | TSS | g7654.t6 | 25092084 | 25092084 |
| chr_2 | g7654 | g7654.t6 | isoform | g7654.t6 | 25092304 | 25093186 |
| chr_2 | g7654 | g7654.t6 | exon | g7654.t6.exon1 | 25092304 | 25092442 |
| chr_2 | g7654 | g7654.t6 | cds | g7654.t6.CDS1 | 25092391 | 25092442 |
| chr_2 | g7654 | g7654.t6 | exon | g7654.t6.exon2 | 25092501 | 25093186 |
| chr_2 | g7654 | g7654.t6 | cds | g7654.t6.CDS2 | 25092501 | 25093186 |
| chr_2 | g7654 | g7654.t6 | TTS | g7654.t6 | 25093267 | 25093267 |
Sequences
>g7654.t6 Gene=g7654 Length=825
GTCGCTTATTGGGCAAGAGTTTATTCATTACAAACTGGAATTAAGAGTGCAAAACAGCCT
GATGAAAAAAGATTTCTTTTGAAAATTATGGATTGGTTAGAAGGATTCAAAAAAGCTAAC
AAAGATAATGAATCAATTACGAATGATACAGTTGCGCAAGCCTATCTCGAGAATTATGCT
CATCGTCTCTTTACTTATGCTGATCAGCAAGACAGAGCATCAAATTTTGGAAAAAATGTC
GTTAAATCATTTTATACATCAGCAATGATTTATGACATTCTTACAGTTCTCGGAGAATTG
AGTGAAGAAGCAAAGCAAAATCGAAAATACGCAAAGTGGAAAGCTGCTTATATTCATAAT
TGTTTGAAAAATGGTGAACAACCACATCCCGGTCCACTTCCTAATGAAGAAGATGATGAA
TTACTCAATCTTGATGGATCTAATTCGACTCCAAGTGAGCCTGGTTCATCTTCATCTATG
GGCTGGAATACTCAACCTAATCAACCTGAAACTTCTCCTCAGCAACCATCACCTCCTTCA
AATACAAACACATTTAATAATGATCCATTCATGAACATTAGAGCTCCTTCTCCACCAAAA
GATCCTGAAGAGAAAAATCCAGGTGGTTTTGTTGCTTTTGATCCTGAACAATCAAATATT
CCTGTGCCTCCACAATCGAAGGCAGCTATTTCCCCTGAAATGATGATAAAGGCGCAAAAG
TATTGCAAATTTGCTGGCAGTGCTCTTACATATGAAGATGTTCCTACTGCTATTGAAAAT
TTGCAAAAAGCATTAAGATTACTCACAACTGGACAAGATTCATAA
>g7654.t6 Gene=g7654 Length=245
MDWLEGFKKANKDNESITNDTVAQAYLENYAHRLFTYADQQDRASNFGKNVVKSFYTSAM
IYDILTVLGELSEEAKQNRKYAKWKAAYIHNCLKNGEQPHPGPLPNEEDDELLNLDGSNS
TPSEPGSSSSMGWNTQPNQPETSPQQPSPPSNTNTFNNDPFMNIRAPSPPKDPEEKNPGG
FVAFDPEQSNIPVPPQSKAAISPEMMIKAQKYCKFAGSALTYEDVPTAIENLQKALRLLT
TGQDS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g7654.t6 | Gene3D | G3DSA:1.25.40.270 | - | 1 | 99 | 9.3E-38 |
| 6 | g7654.t6 | Gene3D | G3DSA:1.20.5.420 | Immunoglobulin FC | 203 | 241 | 5.4E-14 |
| 4 | g7654.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 118 | 141 | - |
| 5 | g7654.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 118 | 152 | - |
| 3 | g7654.t6 | PANTHER | PTHR46009 | VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN VTA1 HOMOLOG | 1 | 242 | 1.0E-60 |
| 1 | g7654.t6 | Pfam | PF04652 | Vta1 like | 1 | 95 | 4.5E-29 |
| 2 | g7654.t6 | 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
- This transcript has been annotated with K12199 (vacuolar protein sorting-associated protein VTA1)
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.
