Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Histone H2AX.

Parent gene

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.t2 TSS g1109.t2 8213656 8213656
chr_3 g1109 g1109.t2 isoform g1109.t2 8213754 8214198
chr_3 g1109 g1109.t2 exon g1109.t2.exon1 8213754 8213877
chr_3 g1109 g1109.t2 cds g1109.t2.CDS1 8213754 8213877
chr_3 g1109 g1109.t2 exon g1109.t2.exon2 8213942 8214198
chr_3 g1109 g1109.t2 cds g1109.t2.CDS2 8213942 8214198
chr_3 g1109 g1109.t2 TTS g1109.t2 8214336 8214336

Sequences

>g1109.t2 Gene=g1109 Length=381
ATGTCTAGCACCGGAGGAAAAATTCACGCTAAAGCAGTAAGCCGTTCATCAAAGGCAGGA
TTGACATTTCCAGTTGGTCGAATTCATCGCCATTTGCGTAAAGGCCATTATGCTGAACGA
ATTGAATTAGGTGCTCCTGTATACTTGGCTGCTATTTTAGAATATCTCTCTGCTGAAATA
TTGGAATTGGCTGGAAATGCTGCTCGTGATAATAAAAAATCTCGCATTTTGCCTCGTCAC
TTGAAATTGGCTATAGCAAATGACGAAGAGTTGAATAAGCTCTTATCTAATGTCACAATT
TCTCAAGGAGGCGTTATGCCAAACATTCATGCTGTACTTTTGCCTAAGAAGACCACTAAA
AAATCAGCTGAAGACCATTAA

>g1109.t2 Gene=g1109 Length=126
MSSTGGKIHAKAVSRSSKAGLTFPVGRIHRHLRKGHYAERIELGAPVYLAAILEYLSAEI
LELAGNAARDNKKSRILPRHLKLAIANDEELNKLLSNVTISQGGVMPNIHAVLLPKKTTK
KSAEDH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g1109.t2 CDD cd00074 H2A 4 117 5.69662E-67
11 g1109.t2 Gene3D G3DSA:1.10.20.10 Histone 1 126 6.1E-61
3 g1109.t2 PANTHER PTHR23430:SF199 HISTONE H2AX 3 121 4.8E-62
4 g1109.t2 PANTHER PTHR23430 HISTONE H2A 3 121 4.8E-62
5 g1109.t2 PRINTS PR00620 Histone H2A signature 11 33 1.6E-50
7 g1109.t2 PRINTS PR00620 Histone H2A signature 40 55 1.6E-50
9 g1109.t2 PRINTS PR00620 Histone H2A signature 55 68 1.6E-50
6 g1109.t2 PRINTS PR00620 Histone H2A signature 69 83 1.6E-50
8 g1109.t2 PRINTS PR00620 Histone H2A signature 97 115 1.6E-50
2 g1109.t2 Pfam PF00125 Core histone H2A/H2B/H3/H4 11 85 2.4E-13
1 g1109.t2 Pfam PF16211 C-terminus of histone H2A 89 122 8.0E-22
13 g1109.t2 ProSitePatterns PS00046 Histone H2A signature. 19 25 -
14 g1109.t2 SMART SM00414 h2a4 1 120 7.8E-75
10 g1109.t2 SUPERFAMILY SSF47113 Histone-fold 14 117 1.79E-43

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

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