General information for g721.t28
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Vacuolar protein-sorting-associated protein 36.
Parent gene
- The parent gene g721 is located on chr_3: 5503187..5504024 (- 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_3 | g721 | g721.t28 | TTS | g721.t28 | 5502715 | 5502715 |
| chr_3 | g721 | g721.t28 | isoform | g721.t28 | 5502762 | 5504024 |
| chr_3 | g721 | g721.t28 | exon | g721.t28.exon1 | 5502762 | 5503133 |
| chr_3 | g721 | g721.t28 | cds | g721.t28.CDS1 | 5502762 | 5503133 |
| chr_3 | g721 | g721.t28 | exon | g721.t28.exon2 | 5503186 | 5504024 |
| chr_3 | g721 | g721.t28 | cds | g721.t28.CDS2 | 5503186 | 5503731 |
| chr_3 | g721 | g721.t28 | TSS | g721.t28 | 5504057 | 5504057 |
Sequences
>g721.t28 Gene=g721 Length=1211
ATGAATCGTTTTGAGTCTGTATCTGCAGCTTTAATTGAAGGTGAAACAATTGTGACAAAA
CATGATGGAGTTAAGATTTATAATGGACATGAGAAGGTAAAAAATTTAAATTAAAATATA
AAGAGAAAAATAAATAAAATGTTTTTTTACAGACAATTTTTGAAGATGGGGAGTTAACTT
TAACAACTCATAGACTTGTGTGGGCGAAAGAAGGAGAGTTTTCTAGAGGATCAAACGTTA
TTCAATTGCGATTAAAACTAATTAAATCACTCGATGAAGAAATTGGCAGTTCAATGTTCT
TTGGTAAAAAGAAAAGACTAATTATTCGCTTAAATGATATCACTGGAATTGAAAAATTGC
CCGGTCCAATGGATTATACTAATTACACTTTTATTAAACTGTCAGCGCCTCATGGAATCA
CTGCAAACTTCATTCAAGCTTTAAACGAAACTCTTATGGCTAGAGTTTTTGATATTGATA
GCTCAAACCCTAATTCTCCTAAAGTTCATAAAATCAAACAAAGAACAGGAATTTTAGGTA
TTGAAAAGAGCATTCAAGAGAAGCAAAAGCAAACAGATGAAAACATTTCTGTGGCATTTC
AAGACCTTAATAAACTAATTGTTATGGCAAAAGATATGGTTAACGTATCTAAAGCAATAA
GTCAAAAAATTCGAGACCGTCAATCTGATGCAACTGAAGATGAGACACAAAAATTCAAGA
GCTTGCTTATGAGCTTGGGTATAGATGATCCAGTAACGAAAGAAAATTTCACAAATAATA
CTGAGTATTTGCGTAGTCTTGGGAATGAAATTTGCCAGTCACTTTTAGATCAAATGACAG
AACAAGGTGGTATGATGACAATAACTGAAGTTTATTGCCGAATAAATCGTGCTCGTGGTT
TAGAATTGGTTTCACCAGAGGATGTTTTAAATGCTTGTAAATTACTCAATGGACCTATGA
AATTAAGACAATACCCTTCTGGTGCAATGATTCTTCAACTTGAAAATCACAATGATGATC
AAGTTGCTGAAGAAATTGAAAAGTTAGTAATTGAATCAGAATCAATGTCCATAGAAGAAT
GCGCACGATTAAAAAACATTAGTGTTCTTCTGGCTCATGAACGCTTCCTCATTTCTGAAA
ATGCTGGAAAAATTTGTAGAGATGAATCTGTTGAAGGTCTTAGATTCTATCCGAATAAAT
TTCTAGCATGA
>g721.t28 Gene=g721 Length=305
MFFGKKKRLIIRLNDITGIEKLPGPMDYTNYTFIKLSAPHGITANFIQALNETLMARVFD
IDSSNPNSPKVHKIKQRTGILGIEKSIQEKQKQTDENISVAFQDLNKLIVMAKDMVNVSK
AISQKIRDRQSDATEDETQKFKSLLMSLGIDDPVTKENFTNNTEYLRSLGNEICQSLLDQ
MTEQGGMMTITEVYCRINRARGLELVSPEDVLNACKLLNGPMKLRQYPSGAMILQLENHN
DDQVAEEIEKLVIESESMSIEECARLKNISVLLAHERFLISENAGKICRDESVEGLRFYP
NKFLA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g721.t28 | Gene3D | G3DSA:2.30.29.30 | - | 1 | 64 | 1.6e-05 |
| 7 | g721.t28 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 161 | 237 | 0.0e+00 |
| 6 | g721.t28 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 238 | 305 | 0.0e+00 |
| 2 | g721.t28 | PANTHER | PTHR13128 | VACUOLAR PROTEIN-SORTING-ASSOCIATED PROTEIN 36 | 20 | 304 | 0.0e+00 |
| 1 | g721.t28 | Pfam | PF04157 | EAP30/Vps36 family | 78 | 291 | 0.0e+00 |
| 3 | g721.t28 | SUPERFAMILY | SSF46785 | Winged helix DNA-binding domain | 99 | 228 | 0.0e+00 |
| 4 | g721.t28 | SUPERFAMILY | SSF46785 | Winged helix DNA-binding domain | 201 | 304 | 0.0e+00 |
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:0032509 | endosome transport via multivesicular body sorting pathway | BP |
| GO:0043130 | ubiquitin binding | MF |
| GO:0000814 | ESCRT II complex | CC |
KEGG
Orthology
- This transcript has been annotated with K12190 (ESCRT-II complex subunit VPS36)
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.
