Gene loci information

Transcript annotation

  • This transcript has been annotated as Histone H2A.

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_2 g6759 g6759.t1 isoform g6759.t1 18503439 18505683
chr_2 g6759 g6759.t1 exon g6759.t1.exon1 18503439 18503824
chr_2 g6759 g6759.t1 cds g6759.t1.CDS1 18503439 18503824
chr_2 g6759 g6759.t1 exon g6759.t1.exon2 18505527 18505683
chr_2 g6759 g6759.t1 cds g6759.t1.CDS2 18505527 18505683
chr_2 g6759 g6759.t1 TSS g6759.t1 18505725 18505725
chr_2 g6759 g6759.t1 TTS g6759.t1 NA NA

Sequences

>g6759.t1 Gene=g6759 Length=543
ATGGCACCACCAAAAACAAGCGGTAAAGCAGCAAAGAAAGCCGGAAAGGCACAGAAAAAT
ATCTCAAAGGATGACAAGAAGAAGAAGCGTCATCGTCGTAAGGAGTCATATGCAATTTAC
ATCTTCAAAGTCTTGAAACAAGTTCATCCTGATACTGCAAAAATGTCAGGACGAGGCAAA
GGAGGCAAAGTTAAGGCAAAGGCAAAGTCACGATCAAGCCGTGCTGGACTTCAATTCCCA
GTCGGTCGTATTCATCGTCTTCTCCGCAAAGGAAACTATGGTGAACGTGTTGGTGCTGGT
GCTCCAGTATATTTGGCTGCTGTCATGGAATATTTGGCTGCTGAAGTTCTTGAATTGGCA
GGAAATGCTGCTCGTGATAACAAAAAGACAAGAATCATCCCACGTCACTTGCAATTGGCC
ATCCGTAATGACGAAGAATTGAATAAACTTCTCTCAGGCGTCACAATCGCTCAAGGTGGT
GTTTTGCCAAACATTCAAGCAGTCTTGTTGCCAAAGAAGACTGAAACCAAGAAAACAGCT
TAA

>g6759.t1 Gene=g6759 Length=180
MAPPKTSGKAAKKAGKAQKNISKDDKKKKRHRRKESYAIYIFKVLKQVHPDTAKMSGRGK
GGKVKAKAKSRSSRAGLQFPVGRIHRLLRKGNYGERVGAGAPVYLAAVMEYLAAEVLELA
GNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKTETKKTA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g6759.t1 CDD cd00074 H2A 70 173 6.48341E-69
12 g6759.t1 Gene3D G3DSA:1.10.20.10 Histone 1 58 1.7E-12
11 g6759.t1 Gene3D G3DSA:1.10.20.10 Histone 59 180 2.9E-66
17 g6759.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 35 -
16 g6759.t1 MobiDBLite mobidb-lite consensus disorder prediction 52 72 -
3 g6759.t1 PANTHER PTHR23430:SF222 HISTONE H2A 56 177 1.2E-73
4 g6759.t1 PANTHER PTHR23430 HISTONE H2A 56 177 1.2E-73
5 g6759.t1 PRINTS PR00620 Histone H2A signature 67 89 4.0E-55
8 g6759.t1 PRINTS PR00620 Histone H2A signature 96 111 4.0E-55
9 g6759.t1 PRINTS PR00620 Histone H2A signature 111 124 4.0E-55
7 g6759.t1 PRINTS PR00620 Histone H2A signature 125 139 4.0E-55
6 g6759.t1 PRINTS PR00620 Histone H2A signature 153 171 4.0E-55
2 g6759.t1 Pfam PF00125 Core histone H2A/H2B/H3/H4 65 142 2.2E-15
1 g6759.t1 Pfam PF16211 C-terminus of histone H2A 145 178 1.4E-20
14 g6759.t1 ProSitePatterns PS00046 Histone H2A signature. 75 81 -
15 g6759.t1 SMART SM00414 h2a4 57 176 2.6E-80
10 g6759.t1 SUPERFAMILY SSF47113 Histone-fold 28 151 1.05E-48

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