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.t4 isoform g13236.t4 28728069 28730099
chr_1 g13236 g13236.t4 exon g13236.t4.exon1 28728069 28728857
chr_1 g13236 g13236.t4 TTS g13236.t4 28728090 28728090
chr_1 g13236 g13236.t4 cds g13236.t4.CDS1 28728816 28728857
chr_1 g13236 g13236.t4 exon g13236.t4.exon2 28728924 28729277
chr_1 g13236 g13236.t4 cds g13236.t4.CDS2 28728924 28729277
chr_1 g13236 g13236.t4 exon g13236.t4.exon3 28729352 28729404
chr_1 g13236 g13236.t4 cds g13236.t4.CDS3 28729352 28729366
chr_1 g13236 g13236.t4 exon g13236.t4.exon4 28730020 28730099
chr_1 g13236 g13236.t4 TSS g13236.t4 28730099 28730099

Sequences

>g13236.t4 Gene=g13236 Length=1276
AATTCATTTCGAGGTCTTCATTTGTCAAGTCGGGAGATTTTTAAAATAAATTAATTTAAA
TAAATTTCAACTTTCAAAAGTTTAACACAGCTCAGCAAAAAGAAGAAAAAAATAAAAGAT
GGCACGTACAAAGCAAACTGCCCGTAAATCAACTGGAGGTAAGGCACCACGTAAGCAATT
GGCAACTAAAGCCGCTCGTAAATCAGCACCATCAACCGGAGGTGTTAAGAAACCACATCG
TTATCGTCCCGGTACAGTCGCTCTTCGTGAGATCCGTCGTTATCAGAAATCAACAGAATT
GTTGATCCGCAAACTGCCATTCCAACGTTTGGTTCGTGAAATTGCTCAGGATTTCAAAAC
CGATTTACGTTTCCAGTCGGCTGCCATCGGCGCTCTTCAGGAAGCATCAGAAGCTTACTT
GGTCGGACTGTTCGAAGATACAAACTTGTGCGCTATCCACGCTAAGCGCGTCACAATTAT
GCCCAAGGATATCCAACTCGCTCGTCGTATTCGTGGCGAACGTGCTTAAGAAGGAGGAAT
TAAATTATTAATTGACGTCAGGAAATTAATACAAAATCTCCTAGATAATTTACTTTCATA
CAATTACTTCACATTTTTCATCAAAAAAAAAGAGTGTTTAAGGGAAGCAGATTGGAAGCG
GACAATGGCCGTTTATAGAATTTAAGAGATATCATTATTATCAGTATAGTAATAATTTTT
TCTTCACAACACCATTATTATTACTATTTTATGTGAAATTCAATTTTCTAAACATTAGTG
CATCAACGATTTCTTTAATTTTTTCTTTTTTTCTTGAGACATTTATACATTACATTTTAT
GGATAAATATATTAGTTATAATTTTTATCTTCATTAGTTCAACATAACTTTGTAATCTTA
TTTTTTTTGGAAAAATAATAGTAACTTAAGATTTTTAAATGTTTTCTTCAGTACAGACAT
TTTCTTTTTATACAAAACCAATTAATCACATTTGGATTAATTAATAATTTAATGAGTATG
ACATACCTATAAAAAAATAATTTAGGCGATACGCATAAAAATTGGAAAAAATGGGAGCTA
TCTTTTTACAGAAGCAAGCGACAGTGAAAATATAATTACACATTACATAGAAATAACAAT
GAAAGGAGAACTTTTAATTACAAAATATTGCAAGAGACATTTCATTTCAATATTCTGATG
TAATAATTTATGAAGAATTTTTTTAAATAAAGGTAAAAGAGAAGCACCCAACAAAAAAAA
CAAGAAATGACGTTTT

>g13236.t4 Gene=g13236 Length=136
MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g13236.t4 Gene3D G3DSA:1.10.20.10 Histone 2 136 1.8E-79
16 g13236.t4 MobiDBLite mobidb-lite consensus disorder prediction 1 43 -
2 g13236.t4 PANTHER PTHR11426 HISTONE H3 1 136 9.5E-95
3 g13236.t4 PANTHER PTHR11426:SF198 - 1 136 9.5E-95
5 g13236.t4 PRINTS PR00622 Histone H3 signature 3 17 2.9E-85
7 g13236.t4 PRINTS PR00622 Histone H3 signature 17 31 2.9E-85
10 g13236.t4 PRINTS PR00622 Histone H3 signature 34 55 2.9E-85
4 g13236.t4 PRINTS PR00622 Histone H3 signature 58 75 2.9E-85
6 g13236.t4 PRINTS PR00622 Histone H3 signature 80 98 2.9E-85
9 g13236.t4 PRINTS PR00622 Histone H3 signature 98 114 2.9E-85
8 g13236.t4 PRINTS PR00622 Histone H3 signature 114 135 2.9E-85
1 g13236.t4 Pfam PF00125 Core histone H2A/H2B/H3/H4 1 132 8.5E-54
14 g13236.t4 ProSitePatterns PS00322 Histone H3 signature 1. 15 21 -
13 g13236.t4 ProSitePatterns PS00959 Histone H3 signature 2. 67 75 -
15 g13236.t4 SMART SM00428 h35 34 136 5.4E-74
11 g13236.t4 SUPERFAMILY SSF47113 Histone-fold 2 133 6.54E-57

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