General information for g8967.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Vacuolar protein sorting-associated protein 11-like protein.
Parent gene
- The parent gene g8967 is located on chr_2: 34258768..34259937 (+ 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 | g8967 | g8967.t2 | isoform | g8967.t2 | 34258768 | 34259799 |
| chr_2 | g8967 | g8967.t2 | exon | g8967.t2.exon1 | 34258768 | 34259799 |
| chr_2 | g8967 | g8967.t2 | cds | g8967.t2.CDS1 | 34259009 | 34259797 |
| chr_2 | g8967 | g8967.t2 | TSS | g8967.t2 | NA | NA |
| chr_2 | g8967 | g8967.t2 | TTS | g8967.t2 | NA | NA |
Sequences
>g8967.t2 Gene=g8967 Length=1032
TTTAAATACAAAAGATTTTGGCAGTTTATATGGTTTATGCAAAAGATTAGGTCCAACAGA
TTCTTCAATTTGGCTTGCTACTCTTAATGGGCTAAAATCAAGTAATCAAGTTCCATCTTC
ATTTCTTCAAGAGATACTTCAAGTTATTGCAACAGAAAAGCTTCAGTCACCACTTCAAGT
GCTCAATATTTTAACATCTATCGATAATGGACCAAATTTGTCAACCGTTCGCAGTTATTT
CATGTCATCGTTTCAAAAGGAAGATGAAATCATTAAAAAGGATAGAGAGGCAGCAGAAAA
ATATCACAATGAAACAGAAGAGCTAAAAAATAATATTGAAACAATGAATAGAAAGCCAAT
CGAATTTCGTGGTAGTTTATGCGATGCATGTCATCAACCGCTCAACTTTCCGTCTCTTTT
CTTTCTCTGTAAGCATTCATTTCATCAGGATTGCATAAGAAGCTTCTCAGAAACTGAAAA
AGATTGCATGGTTTGTAGAAAGAAAAATACACAATTGCTTGATACGATGCATATTCAGAA
TGAAAGTCGTAATAAAAATCACATTTTTCAAGAGGAAATTGAAAAATCTCATGAACCTTT
TGGTGTAGTTGCTGAATATTTTTCGCGTAGTCTTTTCAATAAAATTGTTTTACTTTCTGA
TGACGATGATGAGAATAGAGAAAAGTTTGATGACATTAAATTATCAAGAAAACCACAACA
GAAACAATATGAGACAAAACCACTGCCAAATACTTCAGAAGGAAAAATTCGCTTAGAAGA
GACATTAGGAACAAATGTTCAACACAAACCACAATTGTCAGAGGGTAGATTAAGATTACA
AGAACAAAGTTATAATAAGAGTAAGCCTATTGAACGTTTTGCTACTCAATCGAAACCACA
ACAACAGCAATCAATTCGTAAAAAGCAAGAAGTTAAAGTAAACTATCCAATATCTTCTAA
TCCGTTTGATGACGATGATGATGATATTAAAAATGAAAATTATAATGAAGCATTAAATCC
ATTTGCTGATGA
>g8967.t2 Gene=g8967 Length=263
MSSFQKEDEIIKKDREAAEKYHNETEELKNNIETMNRKPIEFRGSLCDACHQPLNFPSLF
FLCKHSFHQDCIRSFSETEKDCMVCRKKNTQLLDTMHIQNESRNKNHIFQEEIEKSHEPF
GVVAEYFSRSLFNKIVLLSDDDDENREKFDDIKLSRKPQQKQYETKPLPNTSEGKIRLEE
TLGTNVQHKPQLSEGRLRLQEQSYNKSKPIERFATQSKPQQQQSIRKKQEVKVNYPISSN
PFDDDDDDIKNENYNEALNPFAD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g8967.t2 | CDD | cd16688 | RING-H2_Vps11 | 47 | 86 | 7.67228E-14 |
| 6 | g8967.t2 | Coils | Coil | Coil | 11 | 38 | - |
| 5 | g8967.t2 | Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain | 9 | 121 | 1.5E-8 |
| 8 | g8967.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 154 | 175 | - |
| 9 | g8967.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 210 | 236 | - |
| 10 | g8967.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 210 | 249 | - |
| 2 | g8967.t2 | PANTHER | PTHR23323:SF24 | VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 11 HOMOLOG | 3 | 141 | 9.8E-29 |
| 3 | g8967.t2 | PANTHER | PTHR23323 | VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN | 3 | 141 | 9.8E-29 |
| 1 | g8967.t2 | Pfam | PF12451 | Vacuolar protein sorting protein 11 C terminal | 92 | 133 | 4.0E-7 |
| 11 | g8967.t2 | ProSiteProfiles | PS50089 | Zinc finger RING-type profile. | 47 | 86 | 9.908 |
| 4 | g8967.t2 | SUPERFAMILY | SSF57850 | RING/U-box | 46 | 95 | 2.44E-8 |
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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
