General information for g12956.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Vacuolar protein sorting-associated protein 29.
Parent gene
- The parent gene g12956 is located on chr_1: 27155697..27156447 (- 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_1 | g12956 | g12956.t4 | TTS | g12956.t4 | 27154502 | 27154502 |
| chr_1 | g12956 | g12956.t4 | isoform | g12956.t4 | 27155317 | 27156447 |
| chr_1 | g12956 | g12956.t4 | exon | g12956.t4.exon1 | 27155317 | 27156059 |
| chr_1 | g12956 | g12956.t4 | cds | g12956.t4.CDS1 | 27155697 | 27156059 |
| chr_1 | g12956 | g12956.t4 | exon | g12956.t4.exon2 | 27156123 | 27156276 |
| chr_1 | g12956 | g12956.t4 | cds | g12956.t4.CDS2 | 27156123 | 27156266 |
| chr_1 | g12956 | g12956.t4 | exon | g12956.t4.exon3 | 27156340 | 27156377 |
| chr_1 | g12956 | g12956.t4 | exon | g12956.t4.exon4 | 27156441 | 27156447 |
| chr_1 | g12956 | g12956.t4 | TSS | g12956.t4 | 27156507 | 27156507 |
Sequences
>g12956.t4 Gene=g12956 Length=942
ATGGCAACTTGTTCTTGTGCTTGGAGATCTTCACATTCCATTTAGGAGTTCATGTATGCC
AAACAAGTTTAAAAAACTTCTCGTTCCTGGTCGCATTCATCATATTTTAGTAACGGGAAA
TTTATGTACTAAAGAATCTTATGATTATCTCAAGTCATTAGCGGGTGATGTTCATGTAGT
TAGAGGTGACTTTGATGATAATCCAAGTTATCCAGAACAAAAAGTCGTGACTGTAGGGCA
ATTTAGAATTGGTCTCTGTCACGGTCATCAAATCATTCCATGTGGTCAAACTGAAGCACT
TGCTGCCATTCAGAGACAACTTGATGTCGATATTCTCATAACTGGACACACTCACAAGTT
TGAAGCATATGAGCATGAGAACAAATTCTATATAAACCCAGGAAGTGCAACTGGCGCTTA
TACAACGCTTAATGAGACTAACAATGTCATTCCATCATTTATTCTTATGGACATTCAAGC
AACAACTGTAGTAACATACGTTTATCAACTCGATCTCGAAACACAGGAAGTTAAAGTTGA
GAGAATTGAATATAAAAAGTGAGAATTTTAAAATGTGTAGAGAGAGGGATTGCAATAATT
TAAGTAGTCACATGTCTGATATTAAAAACGAATTTATGAATCTCTTAAAATTGATAATCA
ATGAATATTTTAAAACCAGTATAAAATGCAATAATGCTCACAAAAGAATACGGAAATGTT
GAGTCCTTGATGTTGTTTTCTTTTTCAAAGATGAGCGATATTCAGTAGTTACAAAAAATT
TATTGTCATTGCTAAACTTAACAAATGATTCAAAGATGCCAAATTTTATTTTTCTTCATC
ACACAATTGGTTATAATGCATAAATACTGTAAAAAAATTCAAGGTAATCGACTGATTAGA
ATTGAATTCTTAAATATAAAATTTGAATAAGGAAAAATGCTT
>g12956.t4 Gene=g12956 Length=168
MPNKFKKLLVPGRIHHILVTGNLCTKESYDYLKSLAGDVHVVRGDFDDNPSYPEQKVVTV
GQFRIGLCHGHQIIPCGQTEALAAIQRQLDVDILITGHTHKFEAYEHENKFYINPGSATG
AYTTLNETNNVIPSFILMDIQATTVVTYVYQLDLETQEVKVERIEYKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g12956.t4 | CDD | cd07394 | MPP_Vps29 | 2 | 166 | 0 |
| 5 | g12956.t4 | Gene3D | G3DSA:3.60.21.10 | - | 1 | 168 | 0 |
| 2 | g12956.t4 | PANTHER | PTHR11124 | VACUOLAR SORTING PROTEIN VPS29 | 1 | 168 | 0 |
| 3 | g12956.t4 | PANTHER | PTHR11124:SF12 | VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 29 | 1 | 168 | 0 |
| 1 | g12956.t4 | Pfam | PF12850 | Calcineurin-like phosphoesterase superfamily domain | 13 | 141 | 0 |
| 4 | g12956.t4 | SUPERFAMILY | SSF56300 | Metallo-dependent phosphatases | 3 | 157 | 0 |
| 6 | g12956.t4 | TIGRFAM | TIGR00040 | yfcE: phosphodiesterase, MJ0936 family | 16 | 125 | 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:0030904 | retromer complex | CC |
| GO:0042147 | retrograde transport, endosome to Golgi | BP |
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.
