General information for g4652.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as STIP1 homology and U box-containing protein 1.
Parent gene
- The parent gene g4652 is located on chr_2: 3955994..3956553 (- 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 | g4652 | g4652.t3 | TTS | g4652.t3 | 3954904 | 3954904 |
| chr_2 | g4652 | g4652.t3 | isoform | g4652.t3 | 3955073 | 3955994 |
| chr_2 | g4652 | g4652.t3 | exon | g4652.t3.exon1 | 3955073 | 3955241 |
| chr_2 | g4652 | g4652.t3 | cds | g4652.t3.CDS1 | 3955073 | 3955241 |
| chr_2 | g4652 | g4652.t3 | exon | g4652.t3.exon2 | 3955297 | 3955427 |
| chr_2 | g4652 | g4652.t3 | cds | g4652.t3.CDS2 | 3955297 | 3955427 |
| chr_2 | g4652 | g4652.t3 | exon | g4652.t3.exon3 | 3955486 | 3955733 |
| chr_2 | g4652 | g4652.t3 | cds | g4652.t3.CDS3 | 3955486 | 3955733 |
| chr_2 | g4652 | g4652.t3 | exon | g4652.t3.exon4 | 3955796 | 3955994 |
| chr_2 | g4652 | g4652.t3 | cds | g4652.t3.CDS4 | 3955796 | 3955889 |
| chr_2 | g4652 | g4652.t3 | TSS | g4652.t3 | 3956712 | 3956712 |
Sequences
>g4652.t3 Gene=g4652 Length=747
ATCAAGAATCCCAATAATCCAACGTACTTTACAAATCGAGCATTATGCTATATCAAATTA
AAACGATATGAATCGAGTTCACAGGATTGTCGTCGTGCTTTGGATATGGATCAAAATTTG
ATTAAAGGACATTTCTTTTTGGGTATAAGCCTCTTGGAATTAGAATACTTTGATGAAGCA
ATTAAACATTTACAGCGAGCGCAAGATCTTGGTAAAGAGCAAAAATTAAATTTTGGAGAT
GATATTGCTTCACAATTGCGTTTAGCAAGAAAGAAACGATGGAATTTATTGGAAGAAAAA
AGAATTCAACAAGAAATTGAATTGCAATCTTATCTTACTCGCTTAATTCGTGAAGATATG
GAAAATCGAATAGCAAAATTGAAACTTGAAGATAATATGACTGAAGAAGAAAAGAAAGAT
GCAGCATCTGATGTTGAACAACAATGTGAAAATTATACAAACGAACTGAATGGACTTTTT
GCAAAGGTTGATGATAGACGACAAAAGCGTGAAGTTCCTGATTATCTCTGTGGCAAAATT
TCCTTTGAAATTTTGCAAGAACCTGTTATTACTCCAAGTGGCATCACATATGAACGGAAG
GACATCGAAGAACATCTACAGCGCGTTGGTCACTTTGATCCAGTGACTCGTGTTCCATTG
ACTGTCGATCAACTAATTCCTAACTTTTCAATGAAAGAAGTTGTCGATTCGTTTATTCAG
GAAAATGAATGGGCTCTTGAGTACTAA
>g4652.t3 Gene=g4652 Length=213
MDQNLIKGHFFLGISLLELEYFDEAIKHLQRAQDLGKEQKLNFGDDIASQLRLARKKRWN
LLEEKRIQQEIELQSYLTRLIREDMENRIAKLKLEDNMTEEEKKDAASDVEQQCENYTNE
LNGLFAKVDDRRQKREVPDYLCGKISFEILQEPVITPSGITYERKDIEEHLQRVGHFDPV
TRVPLTVDQLIPNFSMKEVVDSFIQENEWALEY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g4652.t3 | CDD | cd16654 | RING-Ubox_CHIP | 137 | 203 | 8.83122E-47 |
| 8 | g4652.t3 | Coils | Coil | Coil | 82 | 127 | - |
| 6 | g4652.t3 | Gene3D | G3DSA:1.25.40.10 | - | 1 | 66 | 2.7E-14 |
| 7 | g4652.t3 | Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain | 134 | 213 | 3.2E-24 |
| 3 | g4652.t3 | PANTHER | PTHR46803 | E3 UBIQUITIN-PROTEIN LIGASE CHIP | 1 | 211 | 5.3E-74 |
| 4 | g4652.t3 | PANTHER | PTHR46803:SF2 | E3 UBIQUITIN-PROTEIN LIGASE CHIP | 1 | 211 | 5.3E-74 |
| 2 | g4652.t3 | Pfam | PF18391 | CHIP N-terminal tetratricopeptide repeat domain | 54 | 135 | 4.0E-26 |
| 1 | g4652.t3 | Pfam | PF04564 | U-box domain | 137 | 209 | 9.5E-29 |
| 12 | g4652.t3 | ProSiteProfiles | PS50293 | TPR repeat region circular profile. | 1 | 39 | 8.823 |
| 11 | g4652.t3 | ProSiteProfiles | PS51698 | U-box domain profile. | 136 | 210 | 30.944 |
| 10 | g4652.t3 | SMART | SM00504 | Ubox_2 | 140 | 203 | 7.0E-23 |
| 5 | g4652.t3 | SUPERFAMILY | SSF57850 | RING/U-box | 131 | 210 | 1.32E-23 |
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:0005515 | protein binding | MF |
| GO:0016567 | protein ubiquitination | BP |
| GO:0004842 | ubiquitin-protein transferase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K09561 (STIP1 homology and U-box containing protein 1)
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.
