Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Histone H2A.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_3 g663 g663.t2 TTS g663.t2 5046656 5046656
chr_3 g663 g663.t2 isoform g663.t2 5046788 5047687
chr_3 g663 g663.t2 exon g663.t2.exon1 5046788 5047044
chr_3 g663 g663.t2 cds g663.t2.CDS1 5046788 5047044
chr_3 g663 g663.t2 exon g663.t2.exon2 5047110 5047250
chr_3 g663 g663.t2 cds g663.t2.CDS2 5047110 5047239
chr_3 g663 g663.t2 exon g663.t2.exon3 5047383 5047461
chr_3 g663 g663.t2 exon g663.t2.exon4 5047527 5047687
chr_3 g663 g663.t2 TSS g663.t2 NA NA

Sequences

>g663.t2 Gene=g663 Length=638
GACAGTGTTTGTTTCTTTGTGATAAATACCGTTTATTACCGTGATGTAAAAGAATCTCAT
AATAAAATGCTATCTCAGATTTCATTTTATCCTTCTCTTTCACAATAAACACATTTTATC
TCATCTTTTCTTTCATTCCTCAATTTCAAAGTGTTTAAATGATCACATTTCAACTGTGAC
ATCAACTTATCGTTCAAAAAAAATTTTTTGTAACCTCATTTTGTGCTTGTCTTTCATCGT
AATTGTAGAAAATGTCTTCTAAAAAAGATGGCCATAAAAAGGTTCCAGTATCACGGTCTT
CAAAGGCCGGTTTAACTTTTCCTGTGGCTAGAATTCATAGAAATTTAAGAAAAGGTGGTT
ATTGTGAGAGAGTTGGTACAGGAGCTGCCATTTATCTTACTGCTGTTTTAGAATATTTAA
CAGCTGAAATTTTGGAATTAGCAGGAAATGCAGCAAGAGATAACAAGAAAGGTCGAATTT
TACCGCGTCATATTCAATTGGCAATAAGAAATGATGAAGAACTCAATCGTTTATTACAAA
ACACTACAATCTCTGATGGAGGTGTCTTACCAAATATTCACGCAATTTTATTACCAAAGA
AGACAGTTAAAGGAACAAGAAGAGATGATGATGAATAA

>g663.t2 Gene=g663 Length=128
MSSKKDGHKKVPVSRSSKAGLTFPVARIHRNLRKGGYCERVGTGAAIYLTAVLEYLTAEI
LELAGNAARDNKKGRILPRHIQLAIRNDEELNRLLQNTTISDGGVLPNIHAILLPKKTVK
GTRRDDDE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g663.t2 CDD cd00074 H2A 9 117 5.73112E-64
11 g663.t2 Gene3D G3DSA:1.10.20.10 Histone 1 124 7.9E-57
3 g663.t2 PANTHER PTHR23430:SF72 HISTONE H2A TYPE 2-B 8 121 1.4E-56
4 g663.t2 PANTHER PTHR23430 HISTONE H2A 8 121 1.4E-56
5 g663.t2 PRINTS PR00620 Histone H2A signature 11 33 2.3E-46
7 g663.t2 PRINTS PR00620 Histone H2A signature 40 55 2.3E-46
9 g663.t2 PRINTS PR00620 Histone H2A signature 55 68 2.3E-46
6 g663.t2 PRINTS PR00620 Histone H2A signature 69 83 2.3E-46
8 g663.t2 PRINTS PR00620 Histone H2A signature 97 115 2.3E-46
2 g663.t2 Pfam PF00125 Core histone H2A/H2B/H3/H4 9 86 5.6E-15
1 g663.t2 Pfam PF16211 C-terminus of histone H2A 89 121 2.8E-17
13 g663.t2 ProSitePatterns PS00046 Histone H2A signature. 19 25 -
14 g663.t2 SMART SM00414 h2a4 1 120 1.0E-71
10 g663.t2 SUPERFAMILY SSF47113 Histone-fold 14 117 1.95E-42

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. There were no conditions that were differentially expressed