General information for g8055.t1
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.t1 | isoform | g8055.t1 | 28278248 | 28280875 |
| chr_2 | g8055 | g8055.t1 | exon | g8055.t1.exon1 | 28278248 | 28278301 |
| chr_2 | g8055 | g8055.t1 | cds | g8055.t1.CDS1 | 28278248 | 28278301 |
| chr_2 | g8055 | g8055.t1 | exon | g8055.t1.exon2 | 28278424 | 28280661 |
| chr_2 | g8055 | g8055.t1 | cds | g8055.t1.CDS2 | 28278424 | 28280661 |
| chr_2 | g8055 | g8055.t1 | exon | g8055.t1.exon3 | 28280726 | 28280875 |
| chr_2 | g8055 | g8055.t1 | cds | g8055.t1.CDS3 | 28280726 | 28280875 |
| chr_2 | g8055 | g8055.t1 | TTS | g8055.t1 | 28281256 | 28281256 |
| chr_2 | g8055 | g8055.t1 | TSS | g8055.t1 | NA | NA |
Sequences
>g8055.t1 Gene=g8055 Length=2442
ATGTATATGTGGAATACGTCATCGTCAGCGACTCAAAGAACATTAAATTCGAATCCTCAA
TCACCGACTCAGCTGGATGAGCAAGATAAGCTCTTAAGCGAGGCACTAGGTGTCGTTCGC
AATAATGCAATTCTTATGAAGCGAAATCTTGATAAAAATCGCCTAATGGATGGCCTTAAG
TGTGCTAGTACAATGTTGGGTGAATTACGAACAAGTTTGTTATCACCAAAAAGCTATTAT
GAGTTGTACATGGCGGTGACTGATGAATTGCGTTTTCTTGAAGTTTATTTACTGGATGAA
TTTCAAAAAGGTCATAAAATCACTGATTTGTATGAATTAGTACAATATGCGGGCAATATT
GTTCCACGCCTCTATTTGCTGATAACAGTTGGATTAGTTTACATCAAATCAAATCCTATG
ACTAAAAAGAGCATTTTAAAAGATTTAGTTGAGATGTGTCGTGGAGTTCAAAATCCATTG
AGAGGATTATTTCTACGTAATTATCTTCTCACCCTACGCAACATTTTACCCGATACTCCT
GTTGGAAAAGATGACGAAACTGGCAACGTGCATGATTCGATTGACTTTATTTTAACAAAT
TTCGCTGAAATGAACAAATTGTGGGTGAGAATGCAACATCAAGGACATTCAAGTGAAAAA
TCAAGACGTGAAAAAGAAAGAGAAGAATTGAAAATTCTTGTTGGTACGAATTTAGTGCGT
TTATCGCAACTGGACTCTGTCAATCTTGAAATTTATCAAAAAATCATTCTACCGAGTATT
CTTGAACAAGTTGTAAGCTGTAGAGATGCCATCGCACAAGAATATTTAATGGAATGCATT
ATTCAAGTGTTTCCAGATGAATTTCATTTACAGACGCTTGATCCATTCCTCAAATCTTGT
GCTCAACTACAATCAGGAGTGAATGTTAAATCAATTATAATTTCACTTATCGACAGACTT
GCTGCATATCATCAACGCAATGAAAAAGCTCACATTGATGCTGCTGATGGTTCAATCATA
CCAATTGATGTACAGCTTTTTGATGTTTTTAGTATTCAGATTGCAAACATTGTGCAGATC
AGAACTGACATGCCGTTAGAAGACACAATCTCACTACAAGTTGCTCTCGTAAATCTTGCA
CAAAAGGTTTATCCCGATCAAATCGATTATGTTGACAAAGTACTTGAGACAACAACACAA
ATTTTGGAGAATTTAAATATGTCAAGCATCAACCATTCATTGGCTGTTAATCAAGAACTT
TCTCGATTATTGAGAGTTTGTATTGATTTCTATAATAACATTCTGACAATTTTAGATCTG
AAATTTTTCCCAAAATTGCTTTCAAAATTCGACTACACATCACGAAAAGCACTTGCTCTG
TATTTGGTCATGAATATTTTAGATAATGAGACTTTTATTCCAACTGATGAGCAAGTTGAC
GCTGTTCTTGAAATGTTATCACCATTGATTAAAGATCAAGAGGATCAGCCTGCTGATACA
TTTGACCCAGAAGATTTTGCAGAAGAGCAAGGAATTGTTGGACGTTTTATACATTTGCTC
AAGTCTGAACATCTTGATATGCAATATAAAATTTTAACTGTTGCGAAAAAACATTTTGCA
TCTGGCGGTACACAGAGAATCAAACATTGTTTGCCATCACTTGTTTTTCAAGCATTCCAG
CTGGCATATAAATATAAGGCAGTTGCAGCTGAGGATGAAAATTGGGACAAAAAATGTCAA
AAAATTATTCAGTTCTGTCACACTACAATAACTTCTATTGCACGTGCAGAATTGCCTGAT
TTGGCTCTAAGACTTTTCCTTCAAGGCGCTTTATGCATCGGTCAAATTGGTCAAACCAAT
TATGAAGCTGTTGCATATGATTTTATGACACAAGCTTTTTCAATTTATGAAGATGAAATT
TCTGACTCAAAGTCACAACTTGCAGCAATCACTCTAATTATTTCAACTGTAGAACAAATT
ACTTGTTTTAGTGAAGAAAATGCTGAGCCATTAAGGACAAATTGTGCGCTTGCTGCATCA
AAATTATTAAAGAAAGCTGATCAATGTCGTGCTGTTGTTGCATGCGCTAGTCTTTTCTGG
AGTGGAAAGAAAGACAATGAGGAAATGAAAGATGAGAAAAGAACACTCGAATGTTTGAAG
AAAGGCGTTAGAATTGCATCACAATGTTTAGATGTAAATGTTCAGGTTCAGTTGTATGTT
GAACTTTTAAACAGTTATCTTTACTATTTCGAAAGAGGAAATTCGCAAATAACTGTCTCA
ATGTTGAATCAGTTGATCGGCAAAATTAACGAGGAACTCCCAAATCTTGAAAAATCTGAA
GAAACAAAACAAATAGAAAGACATTTTAACAATACACTGGCACATATTAAAAGCAGAATA
GAGTCCAATTTGGAGGTGTCATTTGCTGGTATTTCAATATAA
>g8055.t1 Gene=g8055 Length=813
MYMWNTSSSATQRTLNSNPQSPTQLDEQDKLLSEALGVVRNNAILMKRNLDKNRLMDGLK
CASTMLGELRTSLLSPKSYYELYMAVTDELRFLEVYLLDEFQKGHKITDLYELVQYAGNI
VPRLYLLITVGLVYIKSNPMTKKSILKDLVEMCRGVQNPLRGLFLRNYLLTLRNILPDTP
VGKDDETGNVHDSIDFILTNFAEMNKLWVRMQHQGHSSEKSRREKEREELKILVGTNLVR
LSQLDSVNLEIYQKIILPSILEQVVSCRDAIAQEYLMECIIQVFPDEFHLQTLDPFLKSC
AQLQSGVNVKSIIISLIDRLAAYHQRNEKAHIDAADGSIIPIDVQLFDVFSIQIANIVQI
RTDMPLEDTISLQVALVNLAQKVYPDQIDYVDKVLETTTQILENLNMSSINHSLAVNQEL
SRLLRVCIDFYNNILTILDLKFFPKLLSKFDYTSRKALALYLVMNILDNETFIPTDEQVD
AVLEMLSPLIKDQEDQPADTFDPEDFAEEQGIVGRFIHLLKSEHLDMQYKILTVAKKHFA
SGGTQRIKHCLPSLVFQAFQLAYKYKAVAAEDENWDKKCQKIIQFCHTTITSIARAELPD
LALRLFLQGALCIGQIGQTNYEAVAYDFMTQAFSIYEDEISDSKSQLAAITLIISTVEQI
TCFSEENAEPLRTNCALAASKLLKKADQCRAVVACASLFWSGKKDNEEMKDEKRTLECLK
KGVRIASQCLDVNVQVQLYVELLNSYLYYFERGNSQITVSMLNQLIGKINEELPNLEKSE
ETKQIERHFNNTLAHIKSRIESNLEVSFAGISI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g8055.t1 | Gene3D | G3DSA:1.25.40.660 | - | 505 | 799 | 7.5E-118 |
| 4 | g8055.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 24 | - |
| 2 | g8055.t1 | PANTHER | PTHR11099 | VACUOLAR SORTING PROTEIN 35 | 21 | 802 | 0.0 |
| 3 | g8055.t1 | PANTHER | PTHR11099:SF0 | VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 35 | 21 | 802 | 0.0 |
| 6 | g8055.t1 | PIRSF | PIRSF009375 | Retromer_Vps35 | 21 | 812 | 1.9E-299 |
| 1 | g8055.t1 | Pfam | PF03635 | Vacuolar protein sorting-associated protein 35 | 31 | 771 | 8.7E-279 |
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.
