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.t19 TTS g1647.t19 12286709 12286709
chr_3 g1647 g1647.t19 isoform g1647.t19 12286928 12288326
chr_3 g1647 g1647.t19 exon g1647.t19.exon1 12286928 12287520
chr_3 g1647 g1647.t19 cds g1647.t19.CDS1 12287335 12287520
chr_3 g1647 g1647.t19 exon g1647.t19.exon2 12287848 12287961
chr_3 g1647 g1647.t19 cds g1647.t19.CDS2 12287848 12287961
chr_3 g1647 g1647.t19 exon g1647.t19.exon3 12288067 12288137
chr_3 g1647 g1647.t19 cds g1647.t19.CDS3 12288067 12288137
chr_3 g1647 g1647.t19 exon g1647.t19.exon4 12288324 12288326
chr_3 g1647 g1647.t19 cds g1647.t19.CDS4 12288324 12288324
chr_3 g1647 g1647.t19 TSS g1647.t19 12288402 12288402

Sequences

>g1647.t19 Gene=g1647 Length=781
ATGGCAAAGCTGGAAAGGATTCAGGAAAAGCAAAGGCTAAGGCTGTCTCACGTTCTGCAC
GTGCTGGCTTACAGTTCCCAGTTGGACGTATCCACAGACATTTAAAGAACCGCACAACAA
GTCATGGTCGCGTCGGAGCAACCGCTGCTGTTTACTCTGCTGCTATCTTGGAATATTTGA
CTGCTGAAGTTCTTGAGTTAGCTGGTAATGCATCAAAGGACTTGAAAGTCAAACGTATCA
CACCACGTCATTTACAATTGGCCATTCGCGGAGATGAGGAACTCGATTCATTGATTAAAG
CAACAATTGCCGGTGGTGGTGTTATTCCTCATATTCACAAATCACTCATTGGCAAGAAAG
GCGGTCCTGAATAATCTTGAAATTTAACATTATTTCAAACAGCGTCTACAACAATTTTCA
GTTTTTTATTGTTCTAATTTTCCTACAACTATCTACCTACTTTTCTTATTTTTAATTTTT
GTTTAAGATGAGACACATACATACATACATACAAATATTATAATTATGCTCTTAAAATTT
AACACGAGAGAGATGATTAGCAAAACTTAGATTTACATACATTTATTTTCTTCATATTAA
TTATATATCGATGAGGCGATGGAATCAGAGAAACGATAAGACAAAAAATGAACCTGATTA
ATATATAACTTTAAAAACACATAATGGACTTAATCTTTTCTTTGATTCTTTTGGCAATTT
GAAAAATATTTTTAAACGGATGCATTTTAATGAGAGAATTCTATAAAATTGAGGTTTTAC
A

>g1647.t19 Gene=g1647 Length=123
GKAGKDSGKAKAKAVSRSARAGLQFPVGRIHRHLKNRTTSHGRVGATAAVYSAAILEYLT
AEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDSLIKATIAGGGVIPHIHKSLIGKKG
GPE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g1647.t19 CDD cd00074 H2A 5 119 6.6007E-61
11 g1647.t19 Gene3D G3DSA:1.10.20.10 Histone 1 122 6.4E-55
3 g1647.t19 PANTHER PTHR23430:SF280 HISTONE H2A.V 1 121 6.8E-70
4 g1647.t19 PANTHER PTHR23430 HISTONE H2A 1 121 6.8E-70
7 g1647.t19 PRINTS PR00620 Histone H2A signature 13 35 6.0E-44
6 g1647.t19 PRINTS PR00620 Histone H2A signature 43 58 6.0E-44
5 g1647.t19 PRINTS PR00620 Histone H2A signature 58 71 6.0E-44
9 g1647.t19 PRINTS PR00620 Histone H2A signature 72 86 6.0E-44
8 g1647.t19 PRINTS PR00620 Histone H2A signature 99 117 6.0E-44
2 g1647.t19 Pfam PF00125 Core histone H2A/H2B/H3/H4 4 91 3.2E-19
1 g1647.t19 Pfam PF16211 C-terminus of histone H2A 92 121 1.2E-12
13 g1647.t19 ProSitePatterns PS00046 Histone H2A signature. 21 27 -
14 g1647.t19 SMART SM00414 h2a4 2 122 6.7E-73
10 g1647.t19 SUPERFAMILY SSF47113 Histone-fold 3 99 1.77E-42

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.

Raw TPM values