General information for g6808.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Histone H2A.
Parent gene
- The parent gene g6808 is located on chr_2: 18836705..18837145 (+ strand)
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 | g6808 | g6808.t1 | TSS | g6808.t1 | 18500430 | 18500430 |
| chr_2 | g6808 | g6808.t1 | isoform | g6808.t1 | 18836705 | 18837145 |
| chr_2 | g6808 | g6808.t1 | exon | g6808.t1.exon1 | 18836705 | 18837145 |
| chr_2 | g6808 | g6808.t1 | cds | g6808.t1.CDS1 | 18836705 | 18837145 |
| chr_2 | g6808 | g6808.t1 | TTS | g6808.t1 | NA | NA |
Sequences
>g6808.t1 Gene=g6808 Length=441
ATGTCAGGACGAGGCAAAGGAGGCAAAGTTAAGGCAAAGGCAAAGTCACGATCAAGCGTG
CTGGACTCAATTCCCAGTCGGTCGTATTCATCGTCTTCTCCGCAAGGAAACTATGGTGAA
CGTGTTGGTGCTGGTGCTCCAGTATATTTGGCTGCTGTCATGGAATATTTGGCTGCTGAA
GTTCTTGAATTGGCAGGAAATGCTGCTCGTGATAACAAAAAGACAAGAATCATCCCACGT
CACTTGCAATTGGCCATCCGTAATGACGAAGAATTGAATAAACTTCTCTCAGGCGTCACA
ATCGCTCAAGGTGGTGTTTTGCCAAACATTCAAGCCGTCTTGTTGCCAAAGAAGACTGAA
ACAAGAAAACAGCCTAAATCAAACCAACTGCAAAATAACATCTCAAAACCGTCCTTTTTA
GGACGAAAAATTTTAATTTAG
>g6808.t1 Gene=g6808 Length=146
MSGRGKGGKVKAKAKSRSSVLDSIPSRSYSSSSPQGNYGERVGAGAPVYLAAVMEYLAAE
VLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKTE
TRKQPKSNQLQNNISKPSFLGRKILI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g6808.t1 | CDD | cd00074 | H2A | 36 | 118 | 2.44514E-53 |
| 10 | g6808.t1 | Gene3D | G3DSA:1.10.20.10 | Histone | 2 | 123 | 1.4E-49 |
| 14 | g6808.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 38 | - |
| 13 | g6808.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 19 | 38 | - |
| 3 | g6808.t1 | PANTHER | PTHR23430:SF222 | HISTONE H2A | 2 | 124 | 8.3E-60 |
| 4 | g6808.t1 | PANTHER | PTHR23430 | HISTONE H2A | 2 | 124 | 8.3E-60 |
| 8 | g6808.t1 | PRINTS | PR00620 | Histone H2A signature | 41 | 56 | 3.1E-39 |
| 6 | g6808.t1 | PRINTS | PR00620 | Histone H2A signature | 56 | 69 | 3.1E-39 |
| 7 | g6808.t1 | PRINTS | PR00620 | Histone H2A signature | 70 | 84 | 3.1E-39 |
| 5 | g6808.t1 | PRINTS | PR00620 | Histone H2A signature | 98 | 116 | 3.1E-39 |
| 2 | g6808.t1 | Pfam | PF00125 | Core histone H2A/H2B/H3/H4 | 39 | 87 | 6.4E-10 |
| 1 | g6808.t1 | Pfam | PF16211 | C-terminus of histone H2A | 90 | 123 | 1.1E-20 |
| 12 | g6808.t1 | SMART | SM00414 | h2a4 | 3 | 121 | 4.7E-57 |
| 9 | g6808.t1 | SUPERFAMILY | SSF47113 | Histone-fold | 35 | 118 | 9.95E-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: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.
