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.t24 TTS g13236.t24 28728090 28728090
chr_1 g13236 g13236.t24 isoform g13236.t24 28728390 28729366
chr_1 g13236 g13236.t24 exon g13236.t24.exon1 28728390 28728857
chr_1 g13236 g13236.t24 cds g13236.t24.CDS1 28728816 28728857
chr_1 g13236 g13236.t24 exon g13236.t24.exon2 28728942 28729277
chr_1 g13236 g13236.t24 cds g13236.t24.CDS2 28728942 28729277
chr_1 g13236 g13236.t24 exon g13236.t24.exon3 28729352 28729366
chr_1 g13236 g13236.t24 cds g13236.t24.CDS3 28729352 28729366
chr_1 g13236 g13236.t24 TSS g13236.t24 28730099 28730099

Sequences

>g13236.t24 Gene=g13236 Length=819
ATGGCACGTACAAAGCAAACTGCCCGTAAATCAACTGGAGGTAAGGCACCACGTAAGCAA
TTGGCAACTAAAGCCGCTCGTAAATCAGCACCATCAACCGGAGGTGTTAAGAAACCACAT
CGTTATCGTCCCGGTACAGTCGCTCTTCGTGAGATCCGTCGTTATCAGAAATCAACAGAA
TTGTTGATCCGCAAACTGCCATTCCAACGTTTGGTTCGTGAAATTGCTCAGGATTTCAAA
ACCGATTTACGTTTCCAGTCGGCTGCCATCGGCGCTCTTCAGGAAGCATCAGAAGCTTAC
TTGGTCGGACTGTTCGAAGATACAAACTTGTGCGCTATCCACGCTAAGCGCGATATCCAA
CTCGCTCGTCGTATTCGTGGCGAACGTGCTTAAGAAGGAGGAATTAAATTATTAATTGAC
GTCAGGAAATTAATACAAAATCTCCTAGATAATTTACTTTCATACAATTACTTCACATTT
TTCATCAAAAAAAAAGAGTGTTTAAGGGAAGCAGATTGGAAGCGGACAATGGCCGTTTAT
AGAATTTAAGAGATATCATTATTATCAGTATAGTAATAATTTTTTCTTCACAACACCATT
ATTATTACTATTTTATGTGAAATTCAATTTTCTAAACATTAGTGCATCAACGATTTCTTT
AATTTTTTCTTTTTTTCTTGAGACATTTATACATTACATTTTATGGATAAATATATTAGT
TATAATTTTTATCTTCATTAGTTCAACATAACTTTGTAATCTTATTTTTTTTGGAAAAAT
AATAGTAACTTAAGATTTTTAAATGTTTTCTTCAGTACA

>g13236.t24 Gene=g13236 Length=130
MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRDIQ
LARRIRGERA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g13236.t24 Gene3D G3DSA:1.10.20.10 Histone 2 130 6.0E-71
16 g13236.t24 MobiDBLite mobidb-lite consensus disorder prediction 1 43 -
2 g13236.t24 PANTHER PTHR11426 HISTONE H3 1 130 2.5E-85
3 g13236.t24 PANTHER PTHR11426:SF198 - 1 130 2.5E-85
5 g13236.t24 PRINTS PR00622 Histone H3 signature 3 17 5.3E-71
8 g13236.t24 PRINTS PR00622 Histone H3 signature 17 31 5.3E-71
10 g13236.t24 PRINTS PR00622 Histone H3 signature 34 55 5.3E-71
4 g13236.t24 PRINTS PR00622 Histone H3 signature 58 75 5.3E-71
7 g13236.t24 PRINTS PR00622 Histone H3 signature 80 98 5.3E-71
9 g13236.t24 PRINTS PR00622 Histone H3 signature 98 114 5.3E-71
6 g13236.t24 PRINTS PR00622 Histone H3 signature 114 130 5.3E-71
1 g13236.t24 Pfam PF00125 Core histone H2A/H2B/H3/H4 1 126 2.1E-44
14 g13236.t24 ProSitePatterns PS00322 Histone H3 signature 1. 15 21 -
13 g13236.t24 ProSitePatterns PS00959 Histone H3 signature 2. 67 75 -
15 g13236.t24 SMART SM00428 h35 34 130 3.2E-63
11 g13236.t24 SUPERFAMILY SSF47113 Histone-fold 2 127 1.89E-49

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