Gene loci information

Transcript annotation

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

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 g1647 g1647.t6 isoform g1647.t6 12286701 12287963
chr_3 g1647 g1647.t6 exon g1647.t6.exon1 12286701 12287520
chr_3 g1647 g1647.t6 TTS g1647.t6 12286709 12286709
chr_3 g1647 g1647.t6 cds g1647.t6.CDS1 12287335 12287520
chr_3 g1647 g1647.t6 exon g1647.t6.exon2 12287848 12287963
chr_3 g1647 g1647.t6 cds g1647.t6.CDS2 12287848 12287961
chr_3 g1647 g1647.t6 TSS g1647.t6 12288402 12288402

Sequences

>g1647.t6 Gene=g1647 Length=936
AGTTCCCAGTTGGACGTATCCACAGACATTTAAAGAACCGCACAACAAGTCATGGTCGCG
TCGGAGCAACCGCTGCTGTTTACTCTGCTGCTATCTTGGAATATTTGACTGCTGAAGTTC
TTGAGTTAGCTGGTAATGCATCAAAGGACTTGAAAGTCAAACGTATCACACCACGTCATT
TACAATTGGCCATTCGCGGAGATGAGGAACTCGATTCATTGATTAAAGCAACAATTGCCG
GTGGTGGTGTTATTCCTCATATTCACAAATCACTCATTGGCAAGAAAGGCGGTCCTGAAT
AATCTTGAAATTTAACATTATTTCAAACAGCGTCTACAACAATTTTCAGTTTTTTATTGT
TCTAATTTTCCTACAACTATCTACCTACTTTTCTTATTTTTAATTTTTGTTTAAGATGAG
ACACATACATACATACATACAAATATTATAATTATGCTCTTAAAATTTAACACGAGAGAG
ATGATTAGCAAAACTTAGATTTACATACATTTATTTTCTTCATATTAATTATATATCGAT
GAGGCGATGGAATCAGAGAAACGATAAGACAAAAAATGAACCTGATTAATATATAACTTT
AAAAACACATAATGGACTTAATCTTTTCTTTGATTCTTTTGGCAATTTGAAAAATATTTT
TAAACGGATGCATTTTAATGAGAGAATTCTATAAAATTGAGGTTTTACAATCACCAAACA
ACTTTTTTAAATGAAACGACATTCTTTTTTTTTTGTAGATCATTAAGGTTTTTGATTTTG
TCACAGAGAGTTTTCCTATTTCCTTTCCTCTTTTTTCCAAGTTGTATGAGTTTTCACCAG
AGAGATATAAAAATATAAACATTTTAGCTAATGATAAATGATAAAAACGATGTAAAAACT
AAATAAAAAAATTTAAAAGTAAGGAAAACTATATGA

>g1647.t6 Gene=g1647 Length=99
FPVGRIHRHLKNRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHL
QLAIRGDEELDSLIKATIAGGGVIPHIHKSLIGKKGGPE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g1647.t6 CDD cd00074 H2A 1 95 0
11 g1647.t6 Gene3D G3DSA:1.10.20.10 Histone 1 99 0
3 g1647.t6 PANTHER PTHR23430:SF280 HISTONE H2A.V 1 97 0
4 g1647.t6 PANTHER PTHR23430 HISTONE H2A 1 97 0
8 g1647.t6 PRINTS PR00620 Histone H2A signature 19 34 0
7 g1647.t6 PRINTS PR00620 Histone H2A signature 34 47 0
5 g1647.t6 PRINTS PR00620 Histone H2A signature 48 62 0
6 g1647.t6 PRINTS PR00620 Histone H2A signature 75 93 0
2 g1647.t6 Pfam PF00125 Core histone H2A/H2B/H3/H4 1 67 0
1 g1647.t6 Pfam PF16211 C-terminus of histone H2A 68 97 0
10 g1647.t6 SMART SM00414 h2a4 1 98 0
9 g1647.t6 SUPERFAMILY SSF47113 Histone-fold 1 75 0

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