Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Histone H4.

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 g7409 g7409.t1 TTS g7409.t1 23606078 23606078
chr_2 g7409 g7409.t1 isoform g7409.t1 23606126 23606437
chr_2 g7409 g7409.t1 exon g7409.t1.exon1 23606126 23606437
chr_2 g7409 g7409.t1 cds g7409.t1.CDS1 23606126 23606437
chr_2 g7409 g7409.t1 TSS g7409.t1 23606497 23606497

Sequences

>g7409.t1 Gene=g7409 Length=312
ATGACTGGCCGTGGTAAAGGAGGCAAAGGTTTGGGAAAAGGAGGTGCAAAGCGTCATCGT
AAAGTTCTTCGTGATAATATCCAAGGTATCACAAAGCCAGCCATTCGTCGTTTGGCTCGT
CGTGGTGGTGTCAAGCGTATTTCAGGCTTGATCTACGAAGAAACTCGAGGTGTTTTGAAA
GTTTTCTTGGAAAATGTCATTCGTGATGCAGTCACATACACTGAACACGCCAAACGCAAG
ACTGTTACAGCTATGGATGTCGTCTATGCTTTGAAACGTCAGGGACGCACTCTCTATGGT
TTCGGAGGTTAA

>g7409.t1 Gene=g7409 Length=103
MTGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g7409.t1 CDD cd00076 H4 18 101 1.49589E-43
11 g7409.t1 Gene3D G3DSA:1.10.20.10 Histone 2 103 2.2E-60
16 g7409.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 20 -
2 g7409.t1 PANTHER PTHR10484 HISTONE H4 1 103 1.1E-68
3 g7409.t1 PANTHER PTHR10484:SF185 HISTONE H4 1 103 1.1E-68
4 g7409.t1 PRINTS PR00623 Histone H4 signature 5 16 1.4E-63
7 g7409.t1 PRINTS PR00623 Histone H4 signature 20 39 1.4E-63
5 g7409.t1 PRINTS PR00623 Histone H4 signature 40 60 1.4E-63
9 g7409.t1 PRINTS PR00623 Histone H4 signature 62 76 1.4E-63
6 g7409.t1 PRINTS PR00623 Histone H4 signature 77 89 1.4E-63
8 g7409.t1 PRINTS PR00623 Histone H4 signature 89 100 1.4E-63
1 g7409.t1 Pfam PF15511 Centromere kinetochore component CENP-T histone fold 35 96 2.2E-8
13 g7409.t1 ProSitePatterns PS00047 Histone H4 signature. 15 19 -
15 g7409.t1 SMART SM00417 h44 16 90 2.9E-29
14 g7409.t1 SMART SM00803 TAF_cls 28 93 0.0086
10 g7409.t1 SUPERFAMILY SSF47113 Histone-fold 3 102 8.38E-33

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:0006352 DNA-templated transcription, initiation BP
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