Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Histone H2B.

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
HiC_scaffold_226 g17755 g17755.t1 isoform g17755.t1 1 583
HiC_scaffold_226 g17755 g17755.t1 exon g17755.t1.exon1 275 583
HiC_scaffold_226 g17755 g17755.t1 cds g17755.t1.CDS1 275 583
HiC_scaffold_226 g17755 g17755.t1 TTS g17755.t1 674 674
HiC_scaffold_226 g17755 g17755.t1 TSS g17755.t1 NA NA

Sequences

>g17755.t1 Gene=g17755 Length=309
GATGACAAGAAGAAGAAGCGTCATCGTCGTAAGGAGTCATATGCAATTTACATCTTCAAA
GTCTTGAAACAAGTTCATCCTGATACTGGTATTTCATCAAAAGCCATGAGCATCATGAAC
TCATTTGTAAACGACATTTTCGAACGTATTGCTGCTGAGGCATCACGCTTGGCTCACTAC
AACAAGCGCTCAACAATCACATCACGAGAGATTCAAACAGCAGTTCGTCTTCTCTTACCT
GGTGAATTGGCTAAGCATGCTGTCTCAGAAGGCACAAAAGCTGTCACCAAATACACATCA
TCAAAATAA

>g17755.t1 Gene=g17755 Length=102
DDKKKKRHRRKESYAIYIFKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASRLAHY
NKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g17755.t1 Gene3D G3DSA:1.10.20.10 Histone 1 102 1.2E-63
2 g17755.t1 PANTHER PTHR23428:SF266 HISTONE H2B 2 102 1.4E-60
3 g17755.t1 PANTHER PTHR23428 HISTONE H2B 2 102 1.4E-60
5 g17755.t1 PRINTS PR00621 Histone H2B signature 14 32 1.1E-52
8 g17755.t1 PRINTS PR00621 Histone H2B signature 33 53 1.1E-52
7 g17755.t1 PRINTS PR00621 Histone H2B signature 55 72 1.1E-52
6 g17755.t1 PRINTS PR00621 Histone H2B signature 72 85 1.1E-52
4 g17755.t1 PRINTS PR00621 Histone H2B signature 85 98 1.1E-52
1 g17755.t1 Pfam PF00125 Core histone H2A/H2B/H3/H4 3 77 2.5E-22
11 g17755.t1 ProSitePatterns PS00357 Histone H2B signature. 69 91 -
10 g17755.t1 SMART SM00427 h2b3 4 100 2.7E-74
9 g17755.t1 SUPERFAMILY SSF47113 Histone-fold 2 102 1.24E-55

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