Gene loci information

Transcript annotation

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

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_3 g1946 g1946.t3 TTS g1946.t3 14012456 14012456
chr_3 g1946 g1946.t3 isoform g1946.t3 14012577 14013648
chr_3 g1946 g1946.t3 exon g1946.t3.exon1 14012577 14012729
chr_3 g1946 g1946.t3 cds g1946.t3.CDS1 14012577 14012729
chr_3 g1946 g1946.t3 exon g1946.t3.exon2 14012785 14012913
chr_3 g1946 g1946.t3 cds g1946.t3.CDS2 14012785 14012913
chr_3 g1946 g1946.t3 exon g1946.t3.exon3 14012973 14013317
chr_3 g1946 g1946.t3 cds g1946.t3.CDS3 14012973 14013260
chr_3 g1946 g1946.t3 exon g1946.t3.exon4 14013602 14013648
chr_3 g1946 g1946.t3 TSS g1946.t3 NA NA

Sequences

>g1946.t3 Gene=g1946 Length=674
CCCTAAACTTTTATTTACCTGAATACCCCTAAAAATGTTTCTTTCAGGAAAGTAAAGTAT
TGAAGAAAAAAGCAAAAAAGACAAAATCTCATTTAAAGACTGCTATGAATAAAAGTCAAA
AAAATGTAAAATCAACTCTTCAACTATCTGATGATGAAAATTCTGAGAAAGACGATGAAA
TCATTAGAAGAGTTAATGTGCGAATTGCTGAGTATTCTTTTCCTTCTCAACTTATTCAAT
CAGTCAATAAAATGGAGGATGTTGAGTTAGAATCTGAAATGATACATGCTGAAGCAGAAG
CGAATAACAAAAATGCTGTACATTCAATATCAAAATCAAAAAGAAAATATAAGAAAAGTA
GAAATGAGAACTTTTCAAGGTTCATTCATAAAGTATTAAAGAATACATATCCTGAAATCT
CTATTTCAAAGAAAGCAATGGATATAATGAATTCTTTTGTTCACGACATAATTGAAAGGC
TTGTTAATGAAGTATCAAAACTTATTGGATACAGTGGAAGAAAAACTTTATTATCTCGTG
ATATGCAAACTGCATGTAAATTTCTTTTATCTGGAGAATTGCAAGTAATCGCGATAAGTG
AAGCATCAAGGGCTTTAAATAAATATCTAAATTCGCTCCATTCAGACAATGCAAATGAAA
GTGGTGAATCGTAA

>g1946.t3 Gene=g1946 Length=189
MNKSQKNVKSTLQLSDDENSEKDDEIIRRVNVRIAEYSFPSQLIQSVNKMEDVELESEMI
HAEAEANNKNAVHSISKSKRKYKKSRNENFSRFIHKVLKNTYPEISISKKAMDIMNSFVH
DIIERLVNEVSKLIGYSGRKTLLSRDMQTACKFLLSGELQVIAISEASRALNKYLNSLHS
DNANESGES

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g1946.t3 Gene3D G3DSA:1.10.20.10 Histone 53 177 8.0E-36
11 g1946.t3 MobiDBLite mobidb-lite consensus disorder prediction 1 22 -
2 g1946.t3 PANTHER PTHR23428:SF252 HISTONE H2B 62 177 5.0E-30
3 g1946.t3 PANTHER PTHR23428 HISTONE H2B 62 177 5.0E-30
8 g1946.t3 PRINTS PR00621 Histone H2B signature 90 108 1.1E-22
7 g1946.t3 PRINTS PR00621 Histone H2B signature 109 129 1.1E-22
6 g1946.t3 PRINTS PR00621 Histone H2B signature 131 148 1.1E-22
5 g1946.t3 PRINTS PR00621 Histone H2B signature 148 161 1.1E-22
4 g1946.t3 PRINTS PR00621 Histone H2B signature 161 174 1.1E-22
1 g1946.t3 Pfam PF00125 Core histone H2A/H2B/H3/H4 59 152 8.2E-12
10 g1946.t3 SMART SM00427 h2b3 80 176 2.1E-28
9 g1946.t3 SUPERFAMILY SSF47113 Histone-fold 64 176 1.53E-32

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. There were no conditions that were differentially expressed