General information for g8055.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Vacuolar protein sorting-associated protein 35.
Parent gene
- The parent gene g8055 is located on chr_2: 28279164..28281357 (+ 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 | g8055 | g8055.t4 | isoform | g8055.t4 | 28278180 | 28280310 |
| chr_2 | g8055 | g8055.t4 | exon | g8055.t4.exon1 | 28278180 | 28278182 |
| chr_2 | g8055 | g8055.t4 | cds | g8055.t4.CDS1 | 28278180 | 28278182 |
| chr_2 | g8055 | g8055.t4 | exon | g8055.t4.exon2 | 28278424 | 28280310 |
| chr_2 | g8055 | g8055.t4 | cds | g8055.t4.CDS2 | 28278424 | 28280310 |
| chr_2 | g8055 | g8055.t4 | TTS | g8055.t4 | 28281256 | 28281256 |
| chr_2 | g8055 | g8055.t4 | TSS | g8055.t4 | NA | NA |
Sequences
>g8055.t4 Gene=g8055 Length=1890
ATGCCTCAATCACCGACTCAGCTGGATGAGCAAGATAAGCTCTTAAGCGAGGCACTAGGT
GTCGTTCGCAATAATGCAATTCTTATGAAGCGAAATCTTGATAAAAATCGCCTAATGGAT
GGCCTTAAGTGTGCTAGTACAATGTTGGGTGAATTACGAACAAGTTTGTTATCACCAAAA
AGCTATTATGAGTTGTACATGGCGGTGACTGATGAATTGCGTTTTCTTGAAGTTTATTTA
CTGGATGAATTTCAAAAAGGTCATAAAATCACTGATTTGTATGAATTAGTACAATATGCG
GGCAATATTGTTCCACGCCTCTATTTGCTGATAACAGTTGGATTAGTTTACATCAAATCA
AATCCTATGACTAAAAAGAGCATTTTAAAAGATTTAGTTGAGATGTGTCGTGGAGTTCAA
AATCCATTGAGAGGATTATTTCTACGTAATTATCTTCTCACCCTACGCAACATTTTACCC
GATACTCCTGTTGGAAAAGATGACGAAACTGGCAACGTGCATGATTCGATTGACTTTATT
TTAACAAATTTCGCTGAAATGAACAAATTGTGGGTGAGAATGCAACATCAAGGACATTCA
AGTGAAAAATCAAGACGTGAAAAAGAAAGAGAAGAATTGAAAATTCTTGTTGGTACGAAT
TTAGTGCGTTTATCGCAACTGGACTCTGTCAATCTTGAAATTTATCAAAAAATCATTCTA
CCGAGTATTCTTGAACAAGTTGTAAGCTGTAGAGATGCCATCGCACAAGAATATTTAATG
GAATGCATTATTCAAGTGTTTCCAGATGAATTTCATTTACAGACGCTTGATCCATTCCTC
AAATCTTGTGCTCAACTACAATCAGGAGTGAATGTTAAATCAATTATAATTTCACTTATC
GACAGACTTGCTGCATATCATCAACGCAATGAAAAAGCTCACATTGATGCTGCTGATGGT
TCAATCATACCAATTGATGTACAGCTTTTTGATGTTTTTAGTATTCAGATTGCAAACATT
GTGCAGATCAGAACTGACATGCCGTTAGAAGACACAATCTCACTACAAGTTGCTCTCGTA
AATCTTGCACAAAAGGTTTATCCCGATCAAATCGATTATGTTGACAAAGTACTTGAGACA
ACAACACAAATTTTGGAGAATTTAAATATGTCAAGCATCAACCATTCATTGGCTGTTAAT
CAAGAACTTTCTCGATTATTGAGAGTTTGTATTGATTTCTATAATAACATTCTGACAATT
TTAGATCTGAAATTTTTCCCAAAATTGCTTTCAAAATTCGACTACACATCACGAAAAGCA
CTTGCTCTGTATTTGGTCATGAATATTTTAGATAATGAGACTTTTATTCCAACTGATGAG
CAAGTTGACGCTGTTCTTGAAATGTTATCACCATTGATTAAAGATCAAGAGGATCAGCCT
GCTGATACATTTGACCCAGAAGATTTTGCAGAAGAGCAAGGAATTGTTGGACGTTTTATA
CATTTGCTCAAGTCTGAACATCTTGATATGCAATATAAAATTTTAACTGTTGCGAAAAAA
CATTTTGCATCTGGCGGTACACAGAGAATCAAACATTGTTTGCCATCACTTGTTTTTCAA
GCATTCCAGCTGGCATATAAATATAAGGCAGTTGCAGCTGAGGATGAAAATTGGGACAAA
AAATGTCAAAAAATTATTCAGTTCTGTCACACTACAATAACTTCTATTGCACGTGCAGAA
TTGCCTGATTTGGCTCTAAGACTTTTCCTTCAAGGCGCTTTATGCATCGGTCAAATTGGT
CAAACCAATTATGAAGCTGTTGCATATGATTTTATGACACAAGCTTTTTCAATTTATGAA
GATGAAATTTCTGACTCAAAGTCACAACTT
>g8055.t4 Gene=g8055 Length=630
MPQSPTQLDEQDKLLSEALGVVRNNAILMKRNLDKNRLMDGLKCASTMLGELRTSLLSPK
SYYELYMAVTDELRFLEVYLLDEFQKGHKITDLYELVQYAGNIVPRLYLLITVGLVYIKS
NPMTKKSILKDLVEMCRGVQNPLRGLFLRNYLLTLRNILPDTPVGKDDETGNVHDSIDFI
LTNFAEMNKLWVRMQHQGHSSEKSRREKEREELKILVGTNLVRLSQLDSVNLEIYQKIIL
PSILEQVVSCRDAIAQEYLMECIIQVFPDEFHLQTLDPFLKSCAQLQSGVNVKSIIISLI
DRLAAYHQRNEKAHIDAADGSIIPIDVQLFDVFSIQIANIVQIRTDMPLEDTISLQVALV
NLAQKVYPDQIDYVDKVLETTTQILENLNMSSINHSLAVNQELSRLLRVCIDFYNNILTI
LDLKFFPKLLSKFDYTSRKALALYLVMNILDNETFIPTDEQVDAVLEMLSPLIKDQEDQP
ADTFDPEDFAEEQGIVGRFIHLLKSEHLDMQYKILTVAKKHFASGGTQRIKHCLPSLVFQ
AFQLAYKYKAVAAEDENWDKKCQKIIQFCHTTITSIARAELPDLALRLFLQGALCIGQIG
QTNYEAVAYDFMTQAFSIYEDEISDSKSQL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g8055.t4 | Gene3D | G3DSA:1.25.40.660 | - | 488 | 630 | 0 |
| 2 | g8055.t4 | PANTHER | PTHR11099 | VACUOLAR SORTING PROTEIN 35 | 3 | 630 | 0 |
| 3 | g8055.t4 | PANTHER | PTHR11099:SF0 | VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 35 | 3 | 630 | 0 |
| 5 | g8055.t4 | PIRSF | PIRSF009375 | Retromer_Vps35 | 4 | 630 | 0 |
| 1 | g8055.t4 | Pfam | PF03635 | Vacuolar protein sorting-associated protein 35 | 14 | 629 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0042147 | retrograde transport, endosome to Golgi | BP |
| GO:0030906 | retromer, cargo-selective complex | CC |
| GO:0015031 | protein transport | BP |
KEGG
Orthology
- This transcript has been annotated with K18468 (vacuolar protein sorting-associated protein 35)
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