General information for g3860.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g3860 is located on chr_3: 28401228..28404544 (- 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 | g3860 | g3860.t1 | TTS | g3860.t1 | 28401162 | 28401162 |
| chr_3 | g3860 | g3860.t1 | isoform | g3860.t1 | 28401228 | 28402139 |
| chr_3 | g3860 | g3860.t1 | exon | g3860.t1.exon1 | 28401228 | 28402139 |
| chr_3 | g3860 | g3860.t1 | cds | g3860.t1.CDS1 | 28401228 | 28402139 |
| chr_3 | g3860 | g3860.t1 | TSS | g3860.t1 | 28402249 | 28402249 |
Sequences
>g3860.t1 Gene=g3860 Length=912
ATGGAAAATTTAATAAATCTACTTCCTTCGAATAAGGCCATTAAAAGTATTGAATTAATC
GAAAACATAAATGACTTCTCACCAAATTTTTTGCCAATTACTAAGACCTATGACCAAGAT
TTAGATGCTGATATATTGAAAGAGAATATTTTATTTGGAAAACGAAATACAAGATATTTG
TGCATAAGTAAAACTGATGGTTTTGAATCTCATGTTGTGGAACAAATAAAAATTATTAAC
GCAAACGATAATTTGGCAAGAGAAGGATTTTTGTCCATAAAAAAGACTTCAGACACAAAA
CAAAAAGCTTGGAGGAAAAAACAGCTCGTTTATAAGCTAAGTAAAATTGAAAACTGTAAT
GAATACATCACAGATATTGTCATTTTATCAAAGTATCGACCTCCTGCACCCGAAGGATTT
AAATATTTAGGAGAGTTAGAAAAAGTACATATTTGTTTTAAAACATCATCATCATCATCA
AAAAATTCACAGACTGAATCAGAGATTATCGATTTCACAAAACAGATCGAAAATCTCAAA
ATGCAATCAAATCTATATCCAATAGTGAATAATAATGGTGATAAGCATTATTATGAATCA
TTAAAACTTAGCTATCAACTACCAATGCAAAATAAACCCGTGCCAATAAGAGCTGCTCCT
TTGCCACCAACAAAAGCAGTTAAAGCAAGTAATACAGGAACACTGAGTCACTATTATAAT
GACGATTTTATTGGAATTCCTTTTGTATTGCATCCAAAAATTATACAAAATAATATTAAT
TCTGATGATATACCCAAATGCAGCTCAAAAGCTTCCACAGAATTGGAATATGACTTCAAT
CTTGAACGACAAATTTTAGTAAGCACTAAAAGTGAGAATCGTAAATCAACATCGACAAAT
CCATTTTTTTAA
>g3860.t1 Gene=g3860 Length=303
MENLINLLPSNKAIKSIELIENINDFSPNFLPITKTYDQDLDADILKENILFGKRNTRYL
CISKTDGFESHVVEQIKIINANDNLAREGFLSIKKTSDTKQKAWRKKQLVYKLSKIENCN
EYITDIVILSKYRPPAPEGFKYLGELEKVHICFKTSSSSSKNSQTESEIIDFTKQIENLK
MQSNLYPIVNNNGDKHYYESLKLSYQLPMQNKPVPIRAAPLPPTKAVKASNTGTLSHYYN
DDFIGIPFVLHPKIIQNNINSDDIPKCSSKASTELEYDFNLERQILVSTKSENRKSTSTN
PFF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g3860.t1 | Coils | Coil | Coil | 162 | 182 | - |
| 3 | g3860.t1 | Gene3D | G3DSA:2.100.10.50 | - | 12 | 162 | 1.5E-38 |
| 2 | g3860.t1 | PANTHER | PTHR31612 | MULTIVESICULAR BODY SUBUNIT 12A | 3 | 292 | 4.0E-46 |
| 1 | g3860.t1 | Pfam | PF10240 | Multivesicular body subunit 12 | 14 | 282 | 1.7E-54 |
| 6 | g3860.t1 | ProSiteProfiles | PS51498 | MABP domain profile. | 11 | 157 | 15.365 |
| 5 | g3860.t1 | ProSiteProfiles | PS51497 | UMA domain profile. | 243 | 286 | 8.676 |
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:0000813 | ESCRT I complex | CC |
KEGG
Orthology
- This transcript has been annotated with K12186 (ESCRT-I complex subunit MVB12)
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.
