Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Histone H2B.1/H2B.2.

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 g7425 g7425.t4 TTS g7425.t4 23634025 23634025
chr_2 g7425 g7425.t4 isoform g7425.t4 23634215 23637750
chr_2 g7425 g7425.t4 exon g7425.t4.exon1 23634215 23634502
chr_2 g7425 g7425.t4 cds g7425.t4.CDS1 23634217 23634502
chr_2 g7425 g7425.t4 exon g7425.t4.exon2 23637444 23637750
chr_2 g7425 g7425.t4 cds g7425.t4.CDS2 23637444 23637481
chr_2 g7425 g7425.t4 TSS g7425.t4 NA NA

Sequences

>g7425.t4 Gene=g7425 Length=595
TTACTTTGATGATGTGTATTTGGTGACAGCTTTTGTGCCTTCTGAGACAGCGTGCTTAGC
CAATTCACCAGGCAAGAGAAGACGGACGGCTGTTTGGATTTCTCGTGATGTGATTGTTGA
GCGTTTATTGTAATGAGCCAAGCGTGATGCTTCAGCTGCGATACGTTCAAAGATATCATT
GACGAATGAGTTCATGATGCTCATGGCCTTTGAAGAAATACCAGTATCAGGATGAACTTG
TTTCAAGACTTTGAAGATGTAAATTGCATATGATTCCTTACGACGATGACGCTTCTTCTT
CTTGTCAATTTCGTAAAAAATGGNAATCATATGCAATTTACATCTTCAAAGTCTTGAAAC
AAGTTCATCCTGATACTGGTATTTCTTCAAAGGCCATGAGCATCATGAACTCATTCGTCA
ATGATATCTTTGAACGTATCGCAGCTGAAGCATCACGCTTGGCTCATTACAACAAGCGCT
CAACAATCACATCACGAGAAATCCAAACAGCCGTCCGTCTTCTCTTGCCTGGTGAATTGG
CTAAGCACGCTGTCTCAGAAGGCACAAAAGCTGTCACCAAATACACATCATCAAA

>g7425.t4 Gene=g7425 Length=108
MIPYDDDASSSCQFRKKWXSYAIYIFKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAE
ASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g7425.t4 Gene3D G3DSA:1.10.20.10 Histone 5 108 2.1E-59
2 g7425.t4 PANTHER PTHR23428:SF266 HISTONE H2B 15 108 4.8E-56
3 g7425.t4 PANTHER PTHR23428 HISTONE H2B 15 108 4.8E-56
8 g7425.t4 PRINTS PR00621 Histone H2B signature 21 39 1.3E-52
6 g7425.t4 PRINTS PR00621 Histone H2B signature 40 60 1.3E-52
5 g7425.t4 PRINTS PR00621 Histone H2B signature 62 79 1.3E-52
4 g7425.t4 PRINTS PR00621 Histone H2B signature 79 92 1.3E-52
7 g7425.t4 PRINTS PR00621 Histone H2B signature 92 105 1.3E-52
1 g7425.t4 Pfam PF00125 Core histone H2A/H2B/H3/H4 11 84 5.4E-21
11 g7425.t4 ProSitePatterns PS00357 Histone H2B signature. 76 98 -
10 g7425.t4 SMART SM00427 h2b3 13 107 3.3E-70
9 g7425.t4 SUPERFAMILY SSF47113 Histone-fold 12 108 1.05E-52

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