General information for g1109.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Histone H2AX.
Parent gene
- The parent gene g1109 is located on chr_3: 8213962..8214198 (+ 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 | g1109 | g1109.t1 | TSS | g1109.t1 | 8213656 | 8213656 |
| chr_3 | g1109 | g1109.t1 | isoform | g1109.t1 | 8213754 | 8214198 |
| chr_3 | g1109 | g1109.t1 | exon | g1109.t1.exon1 | 8213754 | 8213883 |
| chr_3 | g1109 | g1109.t1 | cds | g1109.t1.CDS1 | 8213754 | 8213883 |
| chr_3 | g1109 | g1109.t1 | exon | g1109.t1.exon2 | 8213948 | 8214198 |
| chr_3 | g1109 | g1109.t1 | cds | g1109.t1.CDS2 | 8213948 | 8214198 |
| chr_3 | g1109 | g1109.t1 | TTS | g1109.t1 | 8214336 | 8214336 |
Sequences
>g1109.t1 Gene=g1109 Length=381
ATGTCTAGCACCGGAGGAAAAATTCACGCTAAAGCAGTAAGCCGTTCATCAAAGGCAGGA
TTGACATTTCCAGTTGGTCGAATTCATCGCCATTTGCGTAAAGGCCATTATGCTGAACGA
ATTGGTGCAGGTGCTCCTGTATACTTGGCTGCTATTTTAGAATATCTCTCTGCTGAAATA
TTGGAATTGGCTGGAAATGCTGCTCGTGATAATAAAAAATCTCGCATTTTGCCTCGTCAC
TTGAAATTGGCTATAGCAAATGACGAAGAGTTGAATAAGCTCTTATCTAATGTCACAATT
TCTCAAGGAGGCGTTATGCCAAACATTCATGCTGTACTTTTGCCTAAGAAGACCACTAAA
AAATCAGCTGAAGACCATTAA
>g1109.t1 Gene=g1109 Length=126
MSSTGGKIHAKAVSRSSKAGLTFPVGRIHRHLRKGHYAERIGAGAPVYLAAILEYLSAEI
LELAGNAARDNKKSRILPRHLKLAIANDEELNKLLSNVTISQGGVMPNIHAVLLPKKTTK
KSAEDH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g1109.t1 | CDD | cd00074 | H2A | 4 | 117 | 6.77338E-69 |
| 11 | g1109.t1 | Gene3D | G3DSA:1.10.20.10 | Histone | 1 | 126 | 2.1E-62 |
| 3 | g1109.t1 | PANTHER | PTHR23430:SF199 | HISTONE H2AX | 3 | 121 | 5.6E-64 |
| 4 | g1109.t1 | PANTHER | PTHR23430 | HISTONE H2A | 3 | 121 | 5.6E-64 |
| 5 | g1109.t1 | PRINTS | PR00620 | Histone H2A signature | 11 | 33 | 1.3E-52 |
| 7 | g1109.t1 | PRINTS | PR00620 | Histone H2A signature | 40 | 55 | 1.3E-52 |
| 9 | g1109.t1 | PRINTS | PR00620 | Histone H2A signature | 55 | 68 | 1.3E-52 |
| 6 | g1109.t1 | PRINTS | PR00620 | Histone H2A signature | 69 | 83 | 1.3E-52 |
| 8 | g1109.t1 | PRINTS | PR00620 | Histone H2A signature | 97 | 115 | 1.3E-52 |
| 2 | g1109.t1 | Pfam | PF00125 | Core histone H2A/H2B/H3/H4 | 11 | 85 | 1.7E-14 |
| 1 | g1109.t1 | Pfam | PF16211 | C-terminus of histone H2A | 89 | 122 | 8.0E-22 |
| 13 | g1109.t1 | ProSitePatterns | PS00046 | Histone H2A signature. | 19 | 25 | - |
| 14 | g1109.t1 | SMART | SM00414 | h2a4 | 1 | 120 | 2.2E-77 |
| 10 | g1109.t1 | SUPERFAMILY | SSF47113 | Histone-fold | 14 | 117 | 6.52E-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