General information for g2449.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 g2449 is located on chr_3: 18026222..18026646 (- 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_3 | g2449 | g2449.t1 | TTS | g2449.t1 | 18026215 | 18026215 |
| chr_3 | g2449 | g2449.t1 | isoform | g2449.t1 | 18026222 | 18026646 |
| chr_3 | g2449 | g2449.t1 | exon | g2449.t1.exon1 | 18026222 | 18026472 |
| chr_3 | g2449 | g2449.t1 | cds | g2449.t1.CDS1 | 18026222 | 18026472 |
| chr_3 | g2449 | g2449.t1 | exon | g2449.t1.exon2 | 18026529 | 18026646 |
| chr_3 | g2449 | g2449.t1 | cds | g2449.t1.CDS2 | 18026529 | 18026646 |
| chr_3 | g2449 | g2449.t1 | TSS | g2449.t1 | NA | NA |
Sequences
>g2449.t1 Gene=g2449 Length=369
ATGTCAGGACGTGGAAAAGGAGGCAAAGTTAAGGCAAAGGCAAAGTCACGATCAAGCCGT
GCTGGACTTCAGTTCCCAGTTGGTCGTATTCATCGACTTCTCCGCAAAGGAAACTATGCT
GCTGAAGTTCTTGAATTGGCAGGAAATGCTGCTCGTGATAACAAAAAGACAAGAATTATT
CCACGTCACTTGCAATTGGCCATTCGTAATGACGAAGAATTGAATAAACTTCTCTCAGGA
GTCACAATCGCTCAAGGTGGTGTATTGCCAAACATTCAGGCTGTCTTGTTACCAAAAGAA
GACCGAAACAAAGAAAACTGCTTAAATTCATCAAAAGCAAAGATCATCATCTTAAAACCG
TCCTTTTAA
>g2449.t1 Gene=g2449 Length=122
MSGRGKGGKVKAKAKSRSSRAGLQFPVGRIHRLLRKGNYAAEVLELAGNAARDNKKTRII
PRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKEDRNKENCLNSSKAKIIILKP
SF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g2449.t1 | CDD | cd00074 | H2A | 16 | 99 | 1.91045E-50 |
| 8 | g2449.t1 | Gene3D | G3DSA:1.10.20.10 | Histone | 2 | 40 | 1.7E-12 |
| 7 | g2449.t1 | Gene3D | G3DSA:1.10.20.10 | Histone | 41 | 107 | 2.1E-32 |
| 12 | g2449.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 21 | - |
| 3 | g2449.t1 | PANTHER | PTHR23430:SF222 | HISTONE H2A | 2 | 40 | 1.4E-52 |
| 5 | g2449.t1 | PANTHER | PTHR23430 | HISTONE H2A | 2 | 40 | 1.4E-52 |
| 2 | g2449.t1 | PANTHER | PTHR23430:SF222 | HISTONE H2A | 40 | 104 | 1.4E-52 |
| 4 | g2449.t1 | PANTHER | PTHR23430 | HISTONE H2A | 40 | 104 | 1.4E-52 |
| 1 | g2449.t1 | Pfam | PF16211 | C-terminus of histone H2A | 72 | 104 | 4.9E-19 |
| 10 | g2449.t1 | ProSitePatterns | PS00046 | Histone H2A signature. | 21 | 27 | - |
| 11 | g2449.t1 | SMART | SM00414 | h2a4 | 3 | 103 | 6.6E-52 |
| 6 | g2449.t1 | SUPERFAMILY | SSF47113 | Histone-fold | 4 | 100 | 3.49E-32 |
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.
