Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Histone H2A.V .

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 g1647 g1647.t1 TTS g1647.t1 12286709 12286709
chr_3 g1647 g1647.t1 isoform g1647.t1 12287335 12288326
chr_3 g1647 g1647.t1 exon g1647.t1.exon1 12287335 12287520
chr_3 g1647 g1647.t1 cds g1647.t1.CDS1 12287335 12287520
chr_3 g1647 g1647.t1 exon g1647.t1.exon2 12287848 12287961
chr_3 g1647 g1647.t1 cds g1647.t1.CDS2 12287848 12287961
chr_3 g1647 g1647.t1 exon g1647.t1.exon3 12288067 12288144
chr_3 g1647 g1647.t1 cds g1647.t1.CDS3 12288067 12288144
chr_3 g1647 g1647.t1 exon g1647.t1.exon4 12288324 12288326
chr_3 g1647 g1647.t1 cds g1647.t1.CDS4 12288324 12288326
chr_3 g1647 g1647.t1 TSS g1647.t1 12288402 12288402

Sequences

>g1647.t1 Gene=g1647 Length=381
ATGGCTGGAGGCAAAGCTGGAAAGGATTCAGGAAAAGCAAAGGCTAAGGCTGTCTCACGT
TCTGCACGTGCTGGCTTACAGTTCCCAGTTGGACGTATCCACAGACATTTAAAGAACCGC
ACAACAAGTCATGGTCGCGTCGGAGCAACCGCTGCTGTTTACTCTGCTGCTATCTTGGAA
TATTTGACTGCTGAAGTTCTTGAGTTAGCTGGTAATGCATCAAAGGACTTGAAAGTCAAA
CGTATCACACCACGTCATTTACAATTGGCCATTCGCGGAGATGAGGAACTCGATTCATTG
ATTAAAGCAACAATTGCCGGTGGTGGTGTTATTCCTCATATTCACAAATCACTCATTGGC
AAGAAAGGCGGTCCTGAATAA

>g1647.t1 Gene=g1647 Length=126
MAGGKAGKDSGKAKAKAVSRSARAGLQFPVGRIHRHLKNRTTSHGRVGATAAVYSAAILE
YLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDSLIKATIAGGGVIPHIHKSLIG
KKGGPE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g1647.t1 CDD cd00074 H2A 8 122 5.59594E-61
11 g1647.t1 Gene3D G3DSA:1.10.20.10 Histone 4 125 7.0E-55
15 g1647.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 22 -
3 g1647.t1 PANTHER PTHR23430:SF280 HISTONE H2A.V 2 124 2.2E-71
4 g1647.t1 PANTHER PTHR23430 HISTONE H2A 2 124 2.2E-71
7 g1647.t1 PRINTS PR00620 Histone H2A signature 16 38 6.4E-44
8 g1647.t1 PRINTS PR00620 Histone H2A signature 46 61 6.4E-44
6 g1647.t1 PRINTS PR00620 Histone H2A signature 61 74 6.4E-44
9 g1647.t1 PRINTS PR00620 Histone H2A signature 75 89 6.4E-44
5 g1647.t1 PRINTS PR00620 Histone H2A signature 102 120 6.4E-44
2 g1647.t1 Pfam PF00125 Core histone H2A/H2B/H3/H4 7 94 3.2E-19
1 g1647.t1 Pfam PF16211 C-terminus of histone H2A 95 124 1.2E-12
13 g1647.t1 ProSitePatterns PS00046 Histone H2A signature. 24 30 -
14 g1647.t1 SMART SM00414 h2a4 5 125 6.7E-73
10 g1647.t1 SUPERFAMILY SSF47113 Histone-fold 3 102 6.01E-43

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.

Raw TPM values