General information for g10905.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as E3 ubiquitin-protein ligase sina.
Parent gene
- The parent gene g10905 is located on chr_1: 12544487..12545090 (+ 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 | g10905 | g10905.t1 | TSS | g10905.t1 | 12544047 | 12544047 |
| chr_1 | g10905 | g10905.t1 | isoform | g10905.t1 | 12544487 | 12545090 |
| chr_1 | g10905 | g10905.t1 | exon | g10905.t1.exon1 | 12544487 | 12544861 |
| chr_1 | g10905 | g10905.t1 | cds | g10905.t1.CDS1 | 12544487 | 12544861 |
| chr_1 | g10905 | g10905.t1 | exon | g10905.t1.exon2 | 12544947 | 12545090 |
| chr_1 | g10905 | g10905.t1 | cds | g10905.t1.CDS2 | 12544947 | 12545090 |
| chr_1 | g10905 | g10905.t1 | TTS | g10905.t1 | NA | NA |
Sequences
>g10905.t1 Gene=g10905 Length=519
ATGTCTGGACACAAAATCCCTATTAAACGAAAAGACTTGAACGGTTCATCAACATCCTCT
AATTCATCGATTTCAGAAAGTGGAGGTGGTGCTGATTTAGCATCACTCTTTGAATGTCCA
GTGTGTTTTGATTACGTGCTACCACCGATTCTTCAATGTCAAATGGGCCATTTAGTTTGT
TCCAGCTGTCGCTCAAAATTAACTTGCTGTCCTACGTGCCGCGGTTCACTCGGAAATATT
AGAAACTTGGCAATGGAAAAAGTCGCATCGAATGTCAAATTTCCATGTAAACATTCAAAT
AATGGCTGTGCTGCATCATTAGTATACACAGAAAAAGTTGATCACGAAGAAGTGTGCGAG
TTTCGTCCTTATCAGTGTCCATGTCCAGGAGCAAGTTGTAAATGGCAGGGTTCATTAGAT
TCTGTAATGCCACACTTAATAATGCACCATAAAAGCATCACAACACTACAAGGCGAAGAT
ATAGTTTTTCTCGCGACTGATATAAATTTACCCGGGTAA
>g10905.t1 Gene=g10905 Length=172
MSGHKIPIKRKDLNGSSTSSNSSISESGGGADLASLFECPVCFDYVLPPILQCQMGHLVC
SSCRSKLTCCPTCRGSLGNIRNLAMEKVASNVKFPCKHSNNGCAASLVYTEKVDHEEVCE
FRPYQCPCPGASCKWQGSLDSVMPHLIMHHKSITTLQGEDIVFLATDINLPG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g10905.t1 | Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain | 25 | 125 | 5.2E-10 |
| 7 | g10905.t1 | Gene3D | G3DSA:3.30.160.60 | Classic Zinc Finger | 126 | 149 | 1.6E-18 |
| 9 | g10905.t1 | Gene3D | G3DSA:2.60.210.10 | Apoptosis | 150 | 172 | 7.6E-7 |
| 6 | g10905.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 23 | - |
| 2 | g10905.t1 | PANTHER | PTHR45877 | E3 UBIQUITIN-PROTEIN LIGASE SIAH2 | 27 | 172 | 4.4E-80 |
| 3 | g10905.t1 | PANTHER | PTHR45877:SF1 | E3 UBIQUITIN-PROTEIN LIGASE SIAH1 | 27 | 172 | 4.4E-80 |
| 1 | g10905.t1 | Pfam | PF03145 | Seven in absentia protein family | 80 | 169 | 1.3E-36 |
| 10 | g10905.t1 | ProSiteProfiles | PS50089 | Zinc finger RING-type profile. | 39 | 74 | 9.258 |
| 11 | g10905.t1 | ProSiteProfiles | PS51081 | Zinc finger SIAH-type profile. | 91 | 151 | 16.455 |
| 5 | g10905.t1 | SUPERFAMILY | SSF57850 | RING/U-box | 33 | 93 | 5.59E-6 |
| 4 | g10905.t1 | SUPERFAMILY | SSF49599 | TRAF domain-like | 92 | 172 | 7.19E-25 |
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:0006511 | ubiquitin-dependent protein catabolic process | BP |
| GO:0005515 | protein binding | MF |
| GO:0007275 | multicellular organism development | BP |
| GO:0008270 | zinc ion binding | MF |
| GO:0005737 | cytoplasm | CC |
KEGG
Orthology
- This transcript has been annotated with K04506 (E3 ubiquitin-protein ligase SIAH1)
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.
