General information for g1108.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Histone H2AX.
Parent gene
- The parent gene g1108 is located on chr_3: 8212811..8213255 (- 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_3 | g1108 | g1108.t1 | TTS | g1108.t1 | 8212688 | 8212688 |
| chr_3 | g1108 | g1108.t1 | isoform | g1108.t1 | 8212811 | 8213255 |
| chr_3 | g1108 | g1108.t1 | exon | g1108.t1.exon1 | 8212811 | 8213061 |
| chr_3 | g1108 | g1108.t1 | cds | g1108.t1.CDS1 | 8212811 | 8213061 |
| chr_3 | g1108 | g1108.t1 | exon | g1108.t1.exon2 | 8213126 | 8213255 |
| chr_3 | g1108 | g1108.t1 | cds | g1108.t1.CDS2 | 8213126 | 8213255 |
| chr_3 | g1108 | g1108.t1 | TSS | g1108.t1 | 8213356 | 8213356 |
Sequences
>g1108.t1 Gene=g1108 Length=381
ATGGCAAACACCGGAGGAAAAATAAATACTAAAAAAGTAAGCCGTTCATCAAAGGCAGGA
TTGACATTTCCAGTTGGTCGAATTCATCGTCATTTGCGTAGAGGCCATTATGCTGAACGA
ATTGGTGCAGGTGCTCCTGTATACTTGGCTGCTGTCATTGAATATCTCACTGCTGAAATA
TTGGAATTGGCTGGAAATGCTGCTCGTGATAATAAAAAATCTCGTGTTATACCTCGTCAC
TTGAAATTGGCAATAGCAAATGATGAAGAATTGAATAAACTCTTATCTAATGTCACAATT
TCTCAAGGAGGCGTTATACCAAACATTCATGCTGTACTTTTGCCAAAGAAGACCACTAAA
AAATCATCTGAAGACCATTAA
>g1108.t1 Gene=g1108 Length=126
MANTGGKINTKKVSRSSKAGLTFPVGRIHRHLRRGHYAERIGAGAPVYLAAVIEYLTAEI
LELAGNAARDNKKSRVIPRHLKLAIANDEELNKLLSNVTISQGGVIPNIHAVLLPKKTTK
KSSEDH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g1108.t1 | CDD | cd00074 | H2A | 4 | 117 | 3.0365E-70 |
| 11 | g1108.t1 | Gene3D | G3DSA:1.10.20.10 | Histone | 1 | 125 | 4.8E-62 |
| 3 | g1108.t1 | PANTHER | PTHR23430:SF222 | HISTONE H2A | 4 | 123 | 4.3E-63 |
| 4 | g1108.t1 | PANTHER | PTHR23430 | HISTONE H2A | 4 | 123 | 4.3E-63 |
| 5 | g1108.t1 | PRINTS | PR00620 | Histone H2A signature | 11 | 33 | 2.2E-52 |
| 7 | g1108.t1 | PRINTS | PR00620 | Histone H2A signature | 40 | 55 | 2.2E-52 |
| 9 | g1108.t1 | PRINTS | PR00620 | Histone H2A signature | 55 | 68 | 2.2E-52 |
| 6 | g1108.t1 | PRINTS | PR00620 | Histone H2A signature | 69 | 83 | 2.2E-52 |
| 8 | g1108.t1 | PRINTS | PR00620 | Histone H2A signature | 97 | 115 | 2.2E-52 |
| 2 | g1108.t1 | Pfam | PF00125 | Core histone H2A/H2B/H3/H4 | 10 | 85 | 4.3E-14 |
| 1 | g1108.t1 | Pfam | PF16211 | C-terminus of histone H2A | 89 | 122 | 3.4E-21 |
| 13 | g1108.t1 | ProSitePatterns | PS00046 | Histone H2A signature. | 19 | 25 | - |
| 14 | g1108.t1 | SMART | SM00414 | h2a4 | 1 | 120 | 4.3E-77 |
| 10 | g1108.t1 | SUPERFAMILY | SSF47113 | Histone-fold | 12 | 117 | 5.54E-45 |
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:0003677 | DNA binding | MF |
| GO:0046982 | protein heterodimerization activity | MF |
| GO:0000786 | nucleosome | CC |
KEGG
Orthology
- This transcript has been annotated with K11251 (histone H2A)
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. There were no conditions that were differentially expressed