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.t1 TSS g14173.t1 35225001 35225001
chr_1 g14173 g14173.t1 isoform g14173.t1 35225094 35225701
chr_1 g14173 g14173.t1 exon g14173.t1.exon1 35225094 35225256
chr_1 g14173 g14173.t1 cds g14173.t1.CDS1 35225094 35225256
chr_1 g14173 g14173.t1 exon g14173.t1.exon2 35225321 35225490
chr_1 g14173 g14173.t1 cds g14173.t1.CDS2 35225321 35225490
chr_1 g14173 g14173.t1 exon g14173.t1.exon3 35225552 35225701
chr_1 g14173 g14173.t1 cds g14173.t1.CDS3 35225552 35225701
chr_1 g14173 g14173.t1 TTS g14173.t1 35225852 35225852

Sequences

>g14173.t1 Gene=g14173 Length=483
ATGTCTGCAGAATTAAAAAAATCAGAAAGTAAAGTATCTCTTCGTTCAAACAAAGATAAC
AAACTAGGACCAACATATGGAGCAAAAGAAAAAAAAATTAAAGCTCCAGCAATTTCGCGC
TCAAAACGTGCTGGTTTAACTTTTCCTGTTAGTCGCGTTCATCGATATCTTCGCAAAGGA
TCTTTTGAACGTATTGGTACTGGTGCTGCAGTTTACATTACTGCTGTTTTAGAATATTTG
ACAGCAGAAATGTTAGAATTAGCTGGCGATGTTTCACGTGATTTAAAGAAAACTCGTATA
ATTCCTCGTCATATTCAGCTTGCTGTTCGTCATGATGATGAACTTGGTAAACTTTTGCAA
CAAGTTACAATTGCTGAAGGCGGTGTTTTGCCATTTATTCATGCCGTTTTACAACCAAAG
AAGACACAAGCTAAGCTAGCAGAAATAGCAGCAGTTAATTCTATAAAATCTAATTCACCA
TAA

>g14173.t1 Gene=g14173 Length=160
MSAELKKSESKVSLRSNKDNKLGPTYGAKEKKIKAPAISRSKRAGLTFPVSRVHRYLRKG
SFERIGTGAAVYITAVLEYLTAEMLELAGDVSRDLKKTRIIPRHIQLAVRHDDELGKLLQ
QVTIAEGGVLPFIHAVLQPKKTQAKLAEIAAVNSIKSNSP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g14173.t1 CDD cd00074 H2A 32 141 3.33902E-56
10 g14173.t1 Gene3D G3DSA:1.10.20.10 Histone 25 149 7.1E-51
14 g14173.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 16 -
15 g14173.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 29 -
3 g14173.t1 PANTHER PTHR23430:SF72 HISTONE H2A TYPE 2-B 29 145 1.7E-50
4 g14173.t1 PANTHER PTHR23430 HISTONE H2A 29 145 1.7E-50
6 g14173.t1 PRINTS PR00620 Histone H2A signature 36 58 1.3E-33
5 g14173.t1 PRINTS PR00620 Histone H2A signature 79 92 1.3E-33
8 g14173.t1 PRINTS PR00620 Histone H2A signature 93 107 1.3E-33
7 g14173.t1 PRINTS PR00620 Histone H2A signature 121 139 1.3E-33
2 g14173.t1 Pfam PF00125 Core histone H2A/H2B/H3/H4 26 111 5.2E-14
1 g14173.t1 Pfam PF16211 C-terminus of histone H2A 113 145 1.1E-15
12 g14173.t1 ProSitePatterns PS00046 Histone H2A signature. 44 50 -
13 g14173.t1 SMART SM00414 h2a4 25 144 2.3E-62
9 g14173.t1 SUPERFAMILY SSF47113 Histone-fold 36 143 2.62E-36

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