Gene loci information

Transcript annotation

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

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 g738 g738.t1 TSS g738.t1 5625975 5625975
chr_3 g738 g738.t1 isoform g738.t1 5626067 5626862
chr_3 g738 g738.t1 exon g738.t1.exon1 5626067 5626304
chr_3 g738 g738.t1 cds g738.t1.CDS1 5626067 5626304
chr_3 g738 g738.t1 exon g738.t1.exon2 5626359 5626498
chr_3 g738 g738.t1 cds g738.t1.CDS2 5626359 5626498
chr_3 g738 g738.t1 exon g738.t1.exon3 5626551 5626862
chr_3 g738 g738.t1 cds g738.t1.CDS3 5626551 5626862
chr_3 g738 g738.t1 TTS g738.t1 5626834 5626834

Sequences

>g738.t1 Gene=g738 Length=690
ATGCCACCTAAAGCTGCCAAAGCAAGATCAAAAACTCCAAAACCAACAAAAAAAGAACCA
GAGCCAAAGAAACCTGCAGCAGCAGTTGTTGAAGAAGAAGATGAAGATGAATCCGGTAGC
GAGGATGAAGAAATGGAAGAATCAGTTCCAGCTCAAAATGCCAATAATAAAGGCGAAGAC
GAGTCTAATAGTGAAGAAGACGAAGAGGATGATGATGAAGATGAAGAAGAAGAAGAAGAT
CCACCTGCGCAAAACAATGTTCAAAAGGATGTAGCATCAGAGAAAAAAACACGTGGTCGA
CCTAAAGTAGTTCATTCAGATTCTATGAAGAAGAAAAAGAAAATTAATAGGATCTCATAT
TCACATTTTATTTATAAGGTTTTAAAGCAAATTCATCCTGAAATGCGAATTTCTGGTAAA
TCGATGAATATTATGAACGATTTTGTTCAGGATATTTTTGAACGAATCGCTTCTGAAGGT
TCCAATTTGTCACATAGAGGTAGAAAACAAACAATGACATCACGTGAAATTGATACTGCA
ACAAAATTGATTCTACCTGGTGAATTAGCTCGACATGCAGAAAATGAAGGAAAGAAAAGT
ATTGCTAATTATCTTCGAGTGACAGAAGAAGAAAAAGTTTCAAAATCAACTAAAAATGTA
CCAAAAAAAAGTAGTAAAGAAACTTCTTAA

>g738.t1 Gene=g738 Length=229
MPPKAAKARSKTPKPTKKEPEPKKPAAAVVEEEDEDESGSEDEEMEESVPAQNANNKGED
ESNSEEDEEDDDEDEEEEEDPPAQNNVQKDVASEKKTRGRPKVVHSDSMKKKKKINRISY
SHFIYKVLKQIHPEMRISGKSMNIMNDFVQDIFERIASEGSNLSHRGRKQTMTSREIDTA
TKLILPGELARHAENEGKKSIANYLRVTEEEKVSKSTKNVPKKSSKETS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g738.t1 Gene3D G3DSA:1.10.20.10 Histone 80 207 2.8E-40
14 g738.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 112 -
13 g738.t1 MobiDBLite mobidb-lite consensus disorder prediction 12 30 -
12 g738.t1 MobiDBLite mobidb-lite consensus disorder prediction 31 48 -
15 g738.t1 MobiDBLite mobidb-lite consensus disorder prediction 61 81 -
11 g738.t1 MobiDBLite mobidb-lite consensus disorder prediction 204 229 -
2 g738.t1 PANTHER PTHR23428:SF248 HISTONE H2B TYPE 1-J 98 204 5.7E-35
3 g738.t1 PANTHER PTHR23428 HISTONE H2B 98 204 5.7E-35
7 g738.t1 PRINTS PR00621 Histone H2B signature 120 138 1.3E-31
4 g738.t1 PRINTS PR00621 Histone H2B signature 139 159 1.3E-31
8 g738.t1 PRINTS PR00621 Histone H2B signature 161 178 1.3E-31
5 g738.t1 PRINTS PR00621 Histone H2B signature 178 191 1.3E-31
6 g738.t1 PRINTS PR00621 Histone H2B signature 191 204 1.3E-31
1 g738.t1 Pfam PF00125 Core histone H2A/H2B/H3/H4 69 183 6.1E-14
10 g738.t1 SMART SM00427 h2b3 110 206 3.5E-43
9 g738.t1 SUPERFAMILY SSF47113 Histone-fold 93 205 2.55E-37

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