General information for g8055.t5
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.t5 | TSS | g8055.t5 | 28278423 | 28278423 |
| chr_2 | g8055 | g8055.t5 | isoform | g8055.t5 | 28278424 | 28281357 |
| chr_2 | g8055 | g8055.t5 | exon | g8055.t5.exon1 | 28278424 | 28280661 |
| chr_2 | g8055 | g8055.t5 | cds | g8055.t5.CDS1 | 28278505 | 28280661 |
| chr_2 | g8055 | g8055.t5 | exon | g8055.t5.exon2 | 28280726 | 28281357 |
| chr_2 | g8055 | g8055.t5 | cds | g8055.t5.CDS2 | 28280726 | 28280875 |
| chr_2 | g8055 | g8055.t5 | TTS | g8055.t5 | NA | NA |
Sequences
>g8055.t5 Gene=g8055 Length=2870
CCTCAATCACCGACTCAGCTGGATGAGCAAGATAAGCTCTTAAGCGAGGCACTAGGTGTC
GTTCGCAATAATGCAATTCTTATGAAGCGAAATCTTGATAAAAATCGCCTAATGGATGGC
CTTAAGTGTGCTAGTACAATGTTGGGTGAATTACGAACAAGTTTGTTATCACCAAAAAGC
TATTATGAGTTGTACATGGCGGTGACTGATGAATTGCGTTTTCTTGAAGTTTATTTACTG
GATGAATTTCAAAAAGGTCATAAAATCACTGATTTGTATGAATTAGTACAATATGCGGGC
AATATTGTTCCACGCCTCTATTTGCTGATAACAGTTGGATTAGTTTACATCAAATCAAAT
CCTATGACTAAAAAGAGCATTTTAAAAGATTTAGTTGAGATGTGTCGTGGAGTTCAAAAT
CCATTGAGAGGATTATTTCTACGTAATTATCTTCTCACCCTACGCAACATTTTACCCGAT
ACTCCTGTTGGAAAAGATGACGAAACTGGCAACGTGCATGATTCGATTGACTTTATTTTA
ACAAATTTCGCTGAAATGAACAAATTGTGGGTGAGAATGCAACATCAAGGACATTCAAGT
GAAAAATCAAGACGTGAAAAAGAAAGAGAAGAATTGAAAATTCTTGTTGGTACGAATTTA
GTGCGTTTATCGCAACTGGACTCTGTCAATCTTGAAATTTATCAAAAAATCATTCTACCG
AGTATTCTTGAACAAGTTGTAAGCTGTAGAGATGCCATCGCACAAGAATATTTAATGGAA
TGCATTATTCAAGTGTTTCCAGATGAATTTCATTTACAGACGCTTGATCCATTCCTCAAA
TCTTGTGCTCAACTACAATCAGGAGTGAATGTTAAATCAATTATAATTTCACTTATCGAC
AGACTTGCTGCATATCATCAACGCAATGAAAAAGCTCACATTGATGCTGCTGATGGTTCA
ATCATACCAATTGATGTACAGCTTTTTGATGTTTTTAGTATTCAGATTGCAAACATTGTG
CAGATCAGAACTGACATGCCGTTAGAAGACACAATCTCACTACAAGTTGCTCTCGTAAAT
CTTGCACAAAAGGTTTATCCCGATCAAATCGATTATGTTGACAAAGTACTTGAGACAACA
ACACAAATTTTGGAGAATTTAAATATGTCAAGCATCAACCATTCATTGGCTGTTAATCAA
GAACTTTCTCGATTATTGAGAGTTTGTATTGATTTCTATAATAACATTCTGACAATTTTA
GATCTGAAATTTTTCCCAAAATTGCTTTCAAAATTCGACTACACATCACGAAAAGCACTT
GCTCTGTATTTGGTCATGAATATTTTAGATAATGAGACTTTTATTCCAACTGATGAGCAA
GTTGACGCTGTTCTTGAAATGTTATCACCATTGATTAAAGATCAAGAGGATCAGCCTGCT
GATACATTTGACCCAGAAGATTTTGCAGAAGAGCAAGGAATTGTTGGACGTTTTATACAT
TTGCTCAAGTCTGAACATCTTGATATGCAATATAAAATTTTAACTGTTGCGAAAAAACAT
TTTGCATCTGGCGGTACACAGAGAATCAAACATTGTTTGCCATCACTTGTTTTTCAAGCA
TTCCAGCTGGCATATAAATATAAGGCAGTTGCAGCTGAGGATGAAAATTGGGACAAAAAA
TGTCAAAAAATTATTCAGTTCTGTCACACTACAATAACTTCTATTGCACGTGCAGAATTG
CCTGATTTGGCTCTAAGACTTTTCCTTCAAGGCGCTTTATGCATCGGTCAAATTGGTCAA
ACCAATTATGAAGCTGTTGCATATGATTTTATGACACAAGCTTTTTCAATTTATGAAGAT
GAAATTTCTGACTCAAAGTCACAACTTGCAGCAATCACTCTAATTATTTCAACTGTAGAA
CAAATTACTTGTTTTAGTGAAGAAAATGCTGAGCCATTAAGGACAAATTGTGCGCTTGCT
GCATCAAAATTATTAAAGAAAGCTGATCAATGTCGTGCTGTTGTTGCATGCGCTAGTCTT
TTCTGGAGTGGAAAGAAAGACAATGAGGAAATGAAAGATGAGAAAAGAACACTCGAATGT
TTGAAGAAAGGCGTTAGAATTGCATCACAATGTTTAGATGTAAATGTTCAGGTTCAGTTG
TATGTTGAACTTTTAAACAGTTATCTTTACTATTTCGAAAGAGGAAATTCGCAAATAACT
GTCTCAATGTTGAATCAGTTGATCGGCAAAATTAACGAGGAACTCCCAAATCTTGAAAAA
TCTGAAGAAACAAAACAAATAGAAAGACATTTTAACAATACACTGGCACATATTAAAAGC
AGAATAGAGTCCAATTTGGAGGTGTCATTTGCTGGTATTTCAATATAAAAGGAATTTTAT
GAATATTTTTATTAATTACCTTGTGAATATTGAATTAATTGGCTGGTATGGAATGTGACG
ATTTTTTTTAGTAAATCAAATGAGAAAATTGTGATTTATTGTTTATTATAATTTTCATAT
TGGATTGTTAAATTGTTTTGTAAATTTGACTATTGAAATTTAATTAAGCTAAAAAAATCA
TTTTGACCAATTTGCTCTTGTTAAACAAGAATAATGAAGAATTTAAAAATTTCCAATTAA
TTCCTAGCCAGCTAATTTATTTTCTTATATATATTTTTGTGTTAACAAATTCCGTATTAT
GTTATAATCTTTTTACTTATTACTAGAAAAATCAATAAAAAAAATGATTCTAGCATTTCT
AGAATGATTCAAAAATTCGTTTTTATTTTAACTCAAAAAATATTTTTGTTGGTTTATAAT
TTAATGTAAATTGAAGAGAAAAAAAAATAAAAAAATATTTCTAATACACA
>g8055.t5 Gene=g8055 Length=768
MKRNLDKNRLMDGLKCASTMLGELRTSLLSPKSYYELYMAVTDELRFLEVYLLDEFQKGH
KITDLYELVQYAGNIVPRLYLLITVGLVYIKSNPMTKKSILKDLVEMCRGVQNPLRGLFL
RNYLLTLRNILPDTPVGKDDETGNVHDSIDFILTNFAEMNKLWVRMQHQGHSSEKSRREK
EREELKILVGTNLVRLSQLDSVNLEIYQKIILPSILEQVVSCRDAIAQEYLMECIIQVFP
DEFHLQTLDPFLKSCAQLQSGVNVKSIIISLIDRLAAYHQRNEKAHIDAADGSIIPIDVQ
LFDVFSIQIANIVQIRTDMPLEDTISLQVALVNLAQKVYPDQIDYVDKVLETTTQILENL
NMSSINHSLAVNQELSRLLRVCIDFYNNILTILDLKFFPKLLSKFDYTSRKALALYLVMN
ILDNETFIPTDEQVDAVLEMLSPLIKDQEDQPADTFDPEDFAEEQGIVGRFIHLLKSEHL
DMQYKILTVAKKHFASGGTQRIKHCLPSLVFQAFQLAYKYKAVAAEDENWDKKCQKIIQF
CHTTITSIARAELPDLALRLFLQGALCIGQIGQTNYEAVAYDFMTQAFSIYEDEISDSKS
QLAAITLIISTVEQITCFSEENAEPLRTNCALAASKLLKKADQCRAVVACASLFWSGKKD
NEEMKDEKRTLECLKKGVRIASQCLDVNVQVQLYVELLNSYLYYFERGNSQITVSMLNQL
IGKINEELPNLEKSEETKQIERHFNNTLAHIKSRIESNLEVSFAGISI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g8055.t5 | Gene3D | G3DSA:1.25.40.660 | - | 460 | 754 | 6.7E-118 |
| 2 | g8055.t5 | PANTHER | PTHR11099 | VACUOLAR SORTING PROTEIN 35 | 1 | 757 | 0.0 |
| 3 | g8055.t5 | PANTHER | PTHR11099:SF0 | VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 35 | 1 | 757 | 0.0 |
| 8 | g8055.t5 | PIRSF | PIRSF009375 | Retromer_Vps35 | 1 | 767 | 1.3E-292 |
| 1 | g8055.t5 | Pfam | PF03635 | Vacuolar protein sorting-associated protein 35 | 1 | 726 | 1.9E-274 |
| 5 | g8055.t5 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 67 | - |
| 7 | g8055.t5 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 68 | 90 | - |
| 6 | g8055.t5 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 91 | 768 | - |
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.
