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.t1 TTS g1946.t1 14012456 14012456
chr_3 g1946 g1946.t1 isoform g1946.t1 14012577 14013329
chr_3 g1946 g1946.t1 exon g1946.t1.exon1 14012577 14012729
chr_3 g1946 g1946.t1 cds g1946.t1.CDS1 14012577 14012729
chr_3 g1946 g1946.t1 exon g1946.t1.exon2 14012785 14012913
chr_3 g1946 g1946.t1 cds g1946.t1.CDS2 14012785 14012913
chr_3 g1946 g1946.t1 exon g1946.t1.exon3 14012973 14013329
chr_3 g1946 g1946.t1 cds g1946.t1.CDS3 14012973 14013329
chr_3 g1946 g1946.t1 TSS g1946.t1 14013455 14013455

Sequences

>g1946.t1 Gene=g1946 Length=639
ATGAAAAAACAGGAAAGTAAAGTATTGAAGAAAAAAGCAAAAAAGACAAAATCTCATTTA
AAGACTGCTATGAATAAAAGTCAAAAAAATGTAAAATCAACTCTTCAACTATCTGATGAT
GAAAATTCTGAGAAAGACGATGAAATCATTAGAAGAGTTAATGTGCGAATTGCTGAGTAT
TCTTTTCCTTCTCAACTTATTCAATCAGTCAATAAAATGGAGGATGTTGAGTTAGAATCT
GAAATGATACATGCTGAAGCAGAAGCGAATAACAAAAATGCTGTACATTCAATATCAAAA
TCAAAAAGAAAATATAAGAAAAGTAGAAATGAGAACTTTTCAAGGTTCATTCATAAAGTA
TTAAAGAATACATATCCTGAAATCTCTATTTCAAAGAAAGCAATGGATATAATGAATTCT
TTTGTTCACGACATAATTGAAAGGCTTGTTAATGAAGTATCAAAACTTATTGGATACAGT
GGAAGAAAAACTTTATTATCTCGTGATATGCAAACTGCATGTAAATTTCTTTTATCTGGA
GAATTGCAAGTAATCGCGATAAGTGAAGCATCAAGGGCTTTAAATAAATATCTAAATTCG
CTCCATTCAGACAATGCAAATGAAAGTGGTGAATCGTAA

>g1946.t1 Gene=g1946 Length=212
MKKQESKVLKKKAKKTKSHLKTAMNKSQKNVKSTLQLSDDENSEKDDEIIRRVNVRIAEY
SFPSQLIQSVNKMEDVELESEMIHAEAEANNKNAVHSISKSKRKYKKSRNENFSRFIHKV
LKNTYPEISISKKAMDIMNSFVHDIIERLVNEVSKLIGYSGRKTLLSRDMQTACKFLLSG
ELQVIAISEASRALNKYLNSLHSDNANESGES

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g1946.t1 Gene3D G3DSA:1.10.20.10 Histone 76 200 1.1E-35
14 g1946.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 46 -
15 g1946.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 22 -
13 g1946.t1 MobiDBLite mobidb-lite consensus disorder prediction 23 37 -
2 g1946.t1 PANTHER PTHR23428:SF252 HISTONE H2B 85 200 1.1E-29
3 g1946.t1 PANTHER PTHR23428 HISTONE H2B 85 200 1.1E-29
8 g1946.t1 PRINTS PR00621 Histone H2B signature 113 131 1.6E-22
7 g1946.t1 PRINTS PR00621 Histone H2B signature 132 152 1.6E-22
6 g1946.t1 PRINTS PR00621 Histone H2B signature 154 171 1.6E-22
4 g1946.t1 PRINTS PR00621 Histone H2B signature 171 184 1.6E-22
5 g1946.t1 PRINTS PR00621 Histone H2B signature 184 197 1.6E-22
1 g1946.t1 Pfam PF00125 Core histone H2A/H2B/H3/H4 82 175 1.2E-11
12 g1946.t1 SMART SM00427 h2b3 103 199 2.1E-28
9 g1946.t1 SUPERFAMILY SSF47113 Histone-fold 87 199 2.18E-32
10 g1946.t1 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 11 -

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.

Raw TPM values