General information for g17735.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Condensin complex subunit 3.
Parent gene
- The parent gene g17735 is located on HiC_scaffold_173: 1..989 (- 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 |
|---|---|---|---|---|---|---|
| HiC_scaffold_173 | g17735 | g17735.t1 | isoform | g17735.t1 | 1 | 989 |
| HiC_scaffold_173 | g17735 | g17735.t1 | exon | g17735.t1.exon1 | 1 | 381 |
| HiC_scaffold_173 | g17735 | g17735.t1 | cds | g17735.t1.CDS1 | 3 | 381 |
| HiC_scaffold_173 | g17735 | g17735.t1 | exon | g17735.t1.exon2 | 505 | 989 |
| HiC_scaffold_173 | g17735 | g17735.t1 | cds | g17735.t1.CDS2 | 505 | 989 |
| HiC_scaffold_173 | g17735 | g17735.t1 | TSS | g17735.t1 | NA | NA |
| HiC_scaffold_173 | g17735 | g17735.t1 | TTS | g17735.t1 | NA | NA |
Sequences
>g17735.t1 Gene=g17735 Length=866
ATGAAAGATATTTCGCCCTTGGTGAGAACTCAAGCAGTTTTTGCATTACAAAGATTACAA
GATCCAGACTCAAGTGAAGATCCAGTAACAAAATCTTTTATATATCACATGGAATCAGAT
CCAGCAGTGAAAGTTCGTCAAGCAACAATAACAGCAATTGCAAAGAAATTACAAAATATT
CCTGCTATACTTGATCGACTTCATGATGTTGATGAGAAAGTTCGTCGTCATACATACTTG
CAAATGTCAAGTTATTCAGTCAAAAGCTACAAAATTGCAGATCGAATTGCTATTCTTAGT
GCAGGCTTGAATGATCGTTCTGAAATTGTGAAAAAAGCAGTGACAAATTTACTTCTTTCA
AATTGGATTGGTGTTTATGATCATGATTATGCTGAATTTATTCGTGCTATTAAATTGGAC
TCTAGTGAAAAGGAATTGATTAAATTTCGTAGTCTTGCTGAAACGGCTTTGAGTGAAATT
TTTAAAAAGCGAAAACTTAATGATTTAATTGCATACCTCAATGCATCCGAAAGTAAAGAA
TACAAAAATTGTCTTCAATTGGAAAAAACAACTTTAGAAATGTTGGTTGTTTGGAAAATG
ATTACAAAATGCTATCAAGATTATTTAAATGGCAAAAATAGAAGTGAAATCAAAGATGAT
GTTGGAAGTGATGATGAAGAAGAATCGACTTTAGTTAATCAATCTGTTTCAAATCTTAAC
ATTTTTCCTGAAGTTTCTGTATTTTGTGACTACTTAGAAAATTTTGTCAATAACTTCAAC
TTTGGCACTGATTTGGATGAAAAATATCAAAAAATTTATTTCAGTCAATGTCTTGTAATG
CTTTTGCAAATTGTTCAACTTAATGA
>g17735.t1 Gene=g17735 Length=288
MKDISPLVRTQAVFALQRLQDPDSSEDPVTKSFIYHMESDPAVKVRQATITAIAKKLQNI
PAILDRLHDVDEKVRRHTYLQMSSYSVKSYKIADRIAILSAGLNDRSEIVKKAVTNLLLS
NWIGVYDHDYAEFIRAIKLDSSEKELIKFRSLAETALSEIFKKRKLNDLIAYLNASESKE
YKNCLQLEKTTLEMLVVWKMITKCYQDYLNGKNRSEIKDDVGSDDEEESTLVNQSVSNLN
IFPEVSVFCDYLENFVNNFNFGTDLDEKYQKIYFSQCLVMLLQIVQLN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g17735.t1 | Gene3D | G3DSA:1.25.10.10 | - | 1 | 195 | 1e-07 |
| 1 | g17735.t1 | PANTHER | PTHR14418:SF5 | CONDENSIN COMPLEX SUBUNIT 3 | 1 | 279 | 0e+00 |
| 2 | g17735.t1 | PANTHER | PTHR14418 | CONDENSIN COMPLEX SUBUNIT 3-RELATED | 1 | 279 | 0e+00 |
| 3 | g17735.t1 | SUPERFAMILY | SSF48371 | ARM repeat | 2 | 167 | 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:0000796 | condensin complex | CC |
| GO:0007076 | mitotic chromosome condensation | BP |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
