General information for g12990.t1
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.t1 | TSS | g12990.t1 | 27382941 | 27382941 |
| chr_1 | g12990 | g12990.t1 | isoform | g12990.t1 | 27382989 | 27384253 |
| chr_1 | g12990 | g12990.t1 | exon | g12990.t1.exon1 | 27382989 | 27383238 |
| chr_1 | g12990 | g12990.t1 | cds | g12990.t1.CDS1 | 27382989 | 27383238 |
| chr_1 | g12990 | g12990.t1 | exon | g12990.t1.exon2 | 27383310 | 27384253 |
| chr_1 | g12990 | g12990.t1 | cds | g12990.t1.CDS2 | 27383310 | 27384253 |
| chr_1 | g12990 | g12990.t1 | TTS | g12990.t1 | NA | NA |
Sequences
>g12990.t1 Gene=g12990 Length=1194
ATGTTTAATTTCTTTAAAAATAAGACTGATTTAAAAGGTTTTAAAGTGTGTTCAAACACA
GAACGTAATAAAAAGTATGGGATTGCTGCCGATTCATTAAAATCTTTAACACAAAAGATC
AAAGACAAGTTTAATATTGACAATTTTGATCTCTTCTTTGATGGTATGCTTATTTCTGAT
GAATTCTTTAAAACTTTACCAAATAATTCACAAATTGTCATTGTAAAGAATGGAGAAGAA
TACAAGACTGATTTTGATGTAGTTTTAGAGTTTTTTCGTAAAAGTCATCAAGAAATATTT
CATGCAAGAGATCTCATCAAAGATTTTCTTAAAAATAATCAAAATCAAGACATAATCAAG
GCTGTGATAAAATTACATGATGAAATAGATGAACAAACAAAATATTCTAGTAAAGAACAA
CATCCAGAATGGTTTGAAAAAATAGAAAATAAATCGAAAGAAGAAGTAATGAGGATGAAG
GCAAAAGATCGAATAAAAGGTTATTTTTATAAAACAAAAGATGAGCTTACAAAATCGCCA
CTTTATCGCTGCAACATTCAAGCTCGAAAAATAATAGAAAACTTGTTAAATGATTTTTTC
TTGTTTTTGAATGGAGTTGAATACTTTGAGTGTTTATTTGATCGAACACACGATAAAAAA
TTTCACATAGTGACAAATGATGATGAAATTGATGCTAAACCTTTTAAGAAAAGAAGAAGG
ATAGGTTCTGATACAAAACAAAAAATTAAAGAAAGCAATATTTTTGAAGACTGTCGAGTT
GCACTTTGCAATGATCTTGGTGTTTTTAATTGTCATGGAGCTTATACAACTGACAGATGC
GGTTATGAGCATAAAATAAATCCTTATTCAAGTCGTGAGTCTCTCATTCTCTTTCAAATT
TTCAATCTTGATCATCAAATTGAAATTTCGAGAAGTATATTTCCGTCTATATTAAAAAAT
GTTGAGAAATTATGTGAAGGAAAGGAAATAATTTGTGAAAAACACAAGAAAGAATGTACA
GAATTGTCGACATTAACATATTTCTTTGAAATATTCACAATTAGAAATTTAAAACTAGTT
CATATCATCTGTCACGATAAAGGTTCACATGATTTAAATACTAAAGCAAAATTACTCTGC
AGTGATTGCAAAGAAGCTAAAATGATAAGAAAACTCAATATTAAAATTTCTTAA
>g12990.t1 Gene=g12990 Length=397
MFNFFKNKTDLKGFKVCSNTERNKKYGIAADSLKSLTQKIKDKFNIDNFDLFFDGMLISD
EFFKTLPNNSQIVIVKNGEEYKTDFDVVLEFFRKSHQEIFHARDLIKDFLKNNQNQDIIK
AVIKLHDEIDEQTKYSSKEQHPEWFEKIENKSKEEVMRMKAKDRIKGYFYKTKDELTKSP
LYRCNIQARKIIENLLNDFFLFLNGVEYFECLFDRTHDKKFHIVTNDDEIDAKPFKKRRR
IGSDTKQKIKESNIFEDCRVALCNDLGVFNCHGAYTTDRCGYEHKINPYSSRESLILFQI
FNLDHQIEISRSIFPSILKNVEKLCEGKEIICEKHKKECTELSTLTYFFEIFTIRNLKLV
HIICHDKGSHDLNTKAKLLCSDCKEAKMIRKLNIKIS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g12990.t1 | Gene3D | G3DSA:3.10.20.10 | - | 5 | 86 | 0.000000 |
| 3 | g12990.t1 | PANTHER | PTHR13067 | CASPASE-ACTIVATED DNASE | 8 | 390 | 0.000000 |
| 2 | g12990.t1 | Pfam | PF02017 | CIDE-N domain | 12 | 81 | 0.000000 |
| 1 | g12990.t1 | Pfam | PF09230 | DNA fragmentation factor 40 kDa | 105 | 385 | 0.000000 |
| 8 | g12990.t1 | ProSiteProfiles | PS51135 | CIDE-N domain profile. | 10 | 83 | 17.375000 |
| 6 | g12990.t1 | SMART | SM00266 | CAD_1 | 12 | 81 | 0.000046 |
| 5 | g12990.t1 | SUPERFAMILY | SSF54277 | CAD & PB1 domains | 9 | 90 | 0.000000 |
| 4 | g12990.t1 | SUPERFAMILY | SSF54060 | His-Me finger endonucleases | 84 | 389 | 0.000000 |
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:0006915 | apoptotic process | BP |
| GO:0006309 | apoptotic DNA fragmentation | BP |
KEGG
Orthology
- This transcript has been annotated with K02311 (DNA fragmentation factor, 40 kD, beta subunit [EC:3.-.-.-])
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.
