General information for g12990.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative DNA fragmentation factor subunit beta.
Parent gene
- The parent gene g12990 is located on chr_1: 27383238..27384253 (+ 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 | g12990 | g12990.t3 | TSS | g12990.t3 | 27382941 | 27382941 |
| chr_1 | g12990 | g12990.t3 | isoform | g12990.t3 | 27383238 | 27384253 |
| chr_1 | g12990 | g12990.t3 | exon | g12990.t3.exon1 | 27383238 | 27384253 |
| chr_1 | g12990 | g12990.t3 | cds | g12990.t3.CDS1 | 27383528 | 27384253 |
| chr_1 | g12990 | g12990.t3 | TTS | g12990.t3 | NA | NA |
Sequences
>g12990.t3 Gene=g12990 Length=1016
GGTATGTTATTGATTTAATGCATTTACAGTTTATTTTTCTAATTAACAAATTGTAATCTT
TTTTTCCTCTAGATTTTGATGTAGTTTTAGAGTTTTTTCGTAAAAGTCATCAAGAAATAT
TTCATGCAAGAGATCTCATCAAAGATTTTCTTAAAAATAATCAAAATCAAGACATAATCA
AGGCTGTGATAAAATTACATGATGAAATAGATGAACAAACAAAATATTCTAGTAAAGAAC
AACATCCAGAATGGTTTGAAAAAATAGAAAATAAATCGAAAGAAGAAGTAATGAGGATGA
AGGCAAAAGATCGAATAAAAGGTTATTTTTATAAAACAAAAGATGAGCTTACAAAATCGC
CACTTTATCGCTGCAACATTCAAGCTCGAAAAATAATAGAAAACTTGTTAAATGATTTTT
TCTTGTTTTTGAATGGAGTTGAATACTTTGAGTGTTTATTTGATCGAACACACGATAAAA
AATTTCACATAGTGACAAATGATGATGAAATTGATGCTAAACCTTTTAAGAAAAGAAGAA
GGATAGGTTCTGATACAAAACAAAAAATTAAAGAAAGCAATATTTTTGAAGACTGTCGAG
TTGCACTTTGCAATGATCTTGGTGTTTTTAATTGTCATGGAGCTTATACAACTGACAGAT
GCGGTTATGAGCATAAAATAAATCCTTATTCAAGTCGTGAGTCTCTCATTCTCTTTCAAA
TTTTCAATCTTGATCATCAAATTGAAATTTCGAGAAGTATATTTCCGTCTATATTAAAAA
ATGTTGAGAAATTATGTGAAGGAAAGGAAATAATTTGTGAAAAACACAAGAAAGAATGTA
CAGAATTGTCGACATTAACATATTTCTTTGAAATATTCACAATTAGAAATTTAAAACTAG
TTCATATCATCTGTCACGATAAAGGTTCACATGATTTAAATACTAAAGCAAAATTACTCT
GCAGTGATTGCAAAGAAGCTAAAATGATAAGAAAACTCAATATTAAAATTTCTTAA
>g12990.t3 Gene=g12990 Length=241
MRMKAKDRIKGYFYKTKDELTKSPLYRCNIQARKIIENLLNDFFLFLNGVEYFECLFDRT
HDKKFHIVTNDDEIDAKPFKKRRRIGSDTKQKIKESNIFEDCRVALCNDLGVFNCHGAYT
TDRCGYEHKINPYSSRESLILFQIFNLDHQIEISRSIFPSILKNVEKLCEGKEIICEKHK
KECTELSTLTYFFEIFTIRNLKLVHIICHDKGSHDLNTKAKLLCSDCKEAKMIRKLNIKI
S
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g12990.t3 | PANTHER | PTHR13067 | CASPASE-ACTIVATED DNASE | 1 | 234 | 0 |
| 1 | g12990.t3 | Pfam | PF09230 | DNA fragmentation factor 40 kDa | 1 | 229 | 0 |
| 3 | g12990.t3 | SUPERFAMILY | SSF54060 | His-Me finger endonucleases | 1 | 233 | 0 |
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:0005634 | nucleus | CC |
| GO:0016787 | hydrolase activity | MF |
| GO:0004536 | deoxyribonuclease activity | MF |
| GO:0005737 | cytoplasm | CC |
| GO:0006309 | apoptotic DNA fragmentation | 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.
