General information for g15522.t1
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 g15522 is located on chr_4: 5763028..5764145 (- 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_4 | g15522 | g15522.t1 | TTS | g15522.t1 | 5762011 | 5762011 |
| chr_4 | g15522 | g15522.t1 | isoform | g15522.t1 | 5762070 | 5763028 |
| chr_4 | g15522 | g15522.t1 | exon | g15522.t1.exon1 | 5762070 | 5762429 |
| chr_4 | g15522 | g15522.t1 | cds | g15522.t1.CDS1 | 5762070 | 5762429 |
| chr_4 | g15522 | g15522.t1 | exon | g15522.t1.exon2 | 5762494 | 5762647 |
| chr_4 | g15522 | g15522.t1 | cds | g15522.t1.CDS2 | 5762494 | 5762647 |
| chr_4 | g15522 | g15522.t1 | exon | g15522.t1.exon3 | 5762931 | 5762968 |
| chr_4 | g15522 | g15522.t1 | cds | g15522.t1.CDS3 | 5762931 | 5762968 |
| chr_4 | g15522 | g15522.t1 | exon | g15522.t1.exon4 | 5763026 | 5763028 |
| chr_4 | g15522 | g15522.t1 | cds | g15522.t1.CDS4 | 5763026 | 5763028 |
| chr_4 | g15522 | g15522.t1 | TSS | g15522.t1 | 5763117 | 5763117 |
Sequences
>g15522.t1 Gene=g15522 Length=555
ATGTTAGTTCTTGTGCTTGGAGATTTACATATTCCATTTAGGAGCTCCTGCCTACCAAGT
AAATTCAAGAAACTTCTCGTTCCTGGTCGCATTCATCATATTCTAGTCACTGGAAATTTA
TGCACAAAAGAATCCTACGATTACCTTAAATCGCTTGCTGGTGATGTTCATGTTGTTAAA
GGTGATTTTGACGATAACTTGAATTATCCAGAACAAAAAGTAGTAACAGTTGGACAATTT
AGAATTGGTCTCTGTCATGGTCATCAAATAGTTCCATGGGGAAACCCTGATGCACTTGCA
GTTGTTCAACGGCAACTTGATGTTGATATTCTCATTACTGGCCACACACATAAATTTGAA
GCTTACGAACATGAAAATAAATTTTACATAAATCCAGGAAGTGCAACAGGATCATTTAAT
GCCCTTGACAATGAACAAATTGTACCATCTTTTGTGTTGATGGATATTCAAGCTACAACT
GTCGTTACTTATGTTTATCAACTCGATCAGACAACACAGGAAGTTAAAGTTGAAAGAATT
GAATATAAAAAGTGA
>g15522.t1 Gene=g15522 Length=184
MLVLVLGDLHIPFRSSCLPSKFKKLLVPGRIHHILVTGNLCTKESYDYLKSLAGDVHVVK
GDFDDNLNYPEQKVVTVGQFRIGLCHGHQIVPWGNPDALAVVQRQLDVDILITGHTHKFE
AYEHENKFYINPGSATGSFNALDNEQIVPSFVLMDIQATTVVTYVYQLDQTTQEVKVERI
EYKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g15522.t1 | CDD | cd07394 | MPP_Vps29 | 2 | 182 | 0 |
| 5 | g15522.t1 | Gene3D | G3DSA:3.60.21.10 | - | 1 | 184 | 0 |
| 2 | g15522.t1 | PANTHER | PTHR11124 | VACUOLAR SORTING PROTEIN VPS29 | 1 | 184 | 0 |
| 3 | g15522.t1 | PANTHER | PTHR11124:SF12 | VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 29 | 1 | 184 | 0 |
| 1 | g15522.t1 | Pfam | PF12850 | Calcineurin-like phosphoesterase superfamily domain | 1 | 157 | 0 |
| 4 | g15522.t1 | SUPERFAMILY | SSF56300 | Metallo-dependent phosphatases | 1 | 170 | 0 |
| 6 | g15522.t1 | TIGRFAM | TIGR00040 | yfcE: phosphodiesterase, MJ0936 family | 1 | 141 | 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 transcript has been annotated with K18467 (vacuolar protein sorting-associated protein 29)
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.
