Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Histone H2A.J.

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_1 g14173 g14173.t2 TSS g14173.t2 35225001 35225001
chr_1 g14173 g14173.t2 isoform g14173.t2 35225094 35225701
chr_1 g14173 g14173.t2 exon g14173.t2.exon1 35225094 35225256
chr_1 g14173 g14173.t2 cds g14173.t2.CDS1 35225094 35225256
chr_1 g14173 g14173.t2 exon g14173.t2.exon2 35225321 35225494
chr_1 g14173 g14173.t2 cds g14173.t2.CDS2 35225321 35225494
chr_1 g14173 g14173.t2 exon g14173.t2.exon3 35225552 35225701
chr_1 g14173 g14173.t2 cds g14173.t2.CDS3 35225552 35225553
chr_1 g14173 g14173.t2 TTS g14173.t2 35225852 35225852

Sequences

>g14173.t2 Gene=g14173 Length=487
ATGTCTGCAGAATTAAAAAAATCAGAAAGTAAAGTATCTCTTCGTTCAAACAAAGATAAC
AAACTAGGACCAACATATGGAGCAAAAGAAAAAAAAATTAAAGCTCCAGCAATTTCGCGC
TCAAAACGTGCTGGTTTAACTTTTCCTGTTAGTCGCGTTCATCGATATCTTCGCAAAGGA
TCTTTTGAACGTATTGGTACTGGTGCTGCAGTTTACATTACTGCTGTTTTAGAATATTTG
ACAGCAGAAATGTTAGAATTAGCTGGCGATGTTTCACGTGATTTAAAGAAAACTCGTATA
ATTCCTCGTCATATTCAGCTTGCTGTTCGTCATGTATGATGATGAACTTGGTAAACTTTT
GCAACAAGTTACAATTGCTGAAGGCGGTGTTTTGCCATTTATTCATGCCGTTTTACAACC
AAAGAAGACACAAGCTAAGCTAGCAGAAATAGCAGCAGTTAATTCTATAAAATCTAATTC
ACCATAA

>g14173.t2 Gene=g14173 Length=112
MSAELKKSESKVSLRSNKDNKLGPTYGAKEKKIKAPAISRSKRAGLTFPVSRVHRYLRKG
SFERIGTGAAVYITAVLEYLTAEMLELAGDVSRDLKKTRIIPRHIQLAVRHV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g14173.t2 Gene3D G3DSA:1.10.20.10 Histone 25 111 2.2E-34
11 g14173.t2 MobiDBLite mobidb-lite consensus disorder prediction 1 16 -
12 g14173.t2 MobiDBLite mobidb-lite consensus disorder prediction 1 27 -
2 g14173.t2 PANTHER PTHR23430:SF59 HISTONE H2A.J 27 111 4.6E-33
3 g14173.t2 PANTHER PTHR23430 HISTONE H2A 27 111 4.6E-33
5 g14173.t2 PRINTS PR00620 Histone H2A signature 36 58 2.0E-23
4 g14173.t2 PRINTS PR00620 Histone H2A signature 79 92 2.0E-23
6 g14173.t2 PRINTS PR00620 Histone H2A signature 93 107 2.0E-23
1 g14173.t2 Pfam PF00125 Core histone H2A/H2B/H3/H4 24 110 2.1E-14
9 g14173.t2 ProSitePatterns PS00046 Histone H2A signature. 44 50 -
10 g14173.t2 SMART SM00414 h2a4 25 111 3.7E-26
7 g14173.t2 SUPERFAMILY SSF47113 Histone-fold 25 110 7.45E-33

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 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. There were no conditions that were differentially expressed