Gene loci information

Transcript annotation

  • This transcript has been annotated as Histone H3.3.

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 g13236 g13236.t25 TTS g13236.t25 28728090 28728090
chr_1 g13236 g13236.t25 isoform g13236.t25 28728458 28729366
chr_1 g13236 g13236.t25 exon g13236.t25.exon1 28728458 28728857
chr_1 g13236 g13236.t25 cds g13236.t25.CDS1 28728816 28728857
chr_1 g13236 g13236.t25 exon g13236.t25.exon2 28728924 28729084
chr_1 g13236 g13236.t25 cds g13236.t25.CDS2 28728924 28729084
chr_1 g13236 g13236.t25 exon g13236.t25.exon3 28729166 28729277
chr_1 g13236 g13236.t25 cds g13236.t25.CDS3 28729166 28729277
chr_1 g13236 g13236.t25 exon g13236.t25.exon4 28729352 28729366
chr_1 g13236 g13236.t25 cds g13236.t25.CDS4 28729352 28729366
chr_1 g13236 g13236.t25 TSS g13236.t25 28730099 28730099

Sequences

>g13236.t25 Gene=g13236 Length=688
ATGGCACGTACAAAGCAAACTGCCCGTAAATCAACTGGAGGTAAGGCACCACGTAAGCAA
TTGGCAACTAAAGCCGCTCGTAAATCAGCACCATCAACCGGAGGTGTTAAGAAACCACAT
CGTTATCGTTTGGTTCGTGAAATTGCTCAGGATTTCAAAACCGATTTACGTTTCCAGTCG
GCTGCCATCGGCGCTCTTCAGGAAGCATCAGAAGCTTACTTGGTCGGACTGTTCGAAGAT
ACAAACTTGTGCGCTATCCACGCTAAGCGCGTCACAATTATGCCCAAGGATATCCAACTC
GCTCGTCGTATTCGTGGCGAACGTGCTTAAGAAGGAGGAATTAAATTATTAATTGACGTC
AGGAAATTAATACAAAATCTCCTAGATAATTTACTTTCATACAATTACTTCACATTTTTC
ATCAAAAAAAAAGAGTGTTTAAGGGAAGCAGATTGGAAGCGGACAATGGCCGTTTATAGA
ATTTAAGAGATATCATTATTATCAGTATAGTAATAATTTTTTCTTCACAACACCATTATT
ATTACTATTTTATGTGAAATTCAATTTTCTAAACATTAGTGCATCAACGATTTCTTTAAT
TTTTTCTTTTTTTCTTGAGACATTTATACATTACATTTTATGGATAAATATATTAGTTAT
AATTTTTATCTTCATTAGTTCAACATAA

>g13236.t25 Gene=g13236 Length=109
MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRLVREIAQDFKTDLRFQS
AAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g13236.t25 Gene3D G3DSA:1.10.20.10 Histone 2 39 1.5E-12
10 g13236.t25 Gene3D G3DSA:1.10.20.10 Histone 40 109 1.5E-40
14 g13236.t25 MobiDBLite mobidb-lite consensus disorder prediction 1 39 -
3 g13236.t25 PANTHER PTHR11426 HISTONE H3 1 43 1.5E-64
5 g13236.t25 PANTHER PTHR11426:SF198 - 1 43 1.5E-64
2 g13236.t25 PANTHER PTHR11426 HISTONE H3 43 109 1.5E-64
4 g13236.t25 PANTHER PTHR11426:SF198 - 43 109 1.5E-64
6 g13236.t25 PRINTS PR00622 Histone H3 signature 3 17 1.0E-22
7 g13236.t25 PRINTS PR00622 Histone H3 signature 17 31 1.0E-22
8 g13236.t25 PRINTS PR00622 Histone H3 signature 34 55 1.0E-22
1 g13236.t25 Pfam PF00125 Core histone H2A/H2B/H3/H4 42 105 3.4E-29
12 g13236.t25 ProSitePatterns PS00322 Histone H3 signature 1. 15 21 -
13 g13236.t25 SMART SM00428 h35 8 109 1.2E-44
9 g13236.t25 SUPERFAMILY SSF47113 Histone-fold 2 106 7.38E-40

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.

Raw TPM values