General information for g9501.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Probable histone H2A.2.
Parent gene
- The parent gene g9501 is located on chr_1: 3801608..3802238 (- 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_1 | g9501 | g9501.t1 | TTS | g9501.t1 | 3801407 | 3801407 |
| chr_1 | g9501 | g9501.t1 | isoform | g9501.t1 | 3801608 | 3802126 |
| chr_1 | g9501 | g9501.t1 | exon | g9501.t1.exon1 | 3801608 | 3802126 |
| chr_1 | g9501 | g9501.t1 | cds | g9501.t1.CDS1 | 3801608 | 3802126 |
| chr_1 | g9501 | g9501.t1 | TSS | g9501.t1 | NA | NA |
Sequences
>g9501.t1 Gene=g9501 Length=519
ATGTCTCAAGTATTAATTACGTCAACACCTCTTATTACAAATTCAGCTTTGCCTTCAGTT
TTTTCATCTGAAAACGAAGATGAAAGCTCTATGGAAATCAGCGATAATAATAACATCACT
CCAGTAGTAGAATTCGGCCGAAATACATCAAATCGAAAGAAAAATGTAACACTTGCTTCT
CGAAGTGGTTTGGTATTTCCTACTGGTCGCATAAAAAGATATCTAAAGAATAGTAAAATT
GCAAATAGAGTATCTGTTGGATCTGCTGTTTATTGTAGTGCTATTTTGGAATATCTTGTT
GCTGAAATATTGGAACTGGCTTCAAATGCTGCTCGCGAAAATAATCGAACTCGTATCACT
CCACGTCATTTGAATTTAGCTATTCGCAATGATGAAGAGTTGTCGAGATTAGTTGGAAAT
CAAACTGTAATTGCTGGAGGTGGCGTAATGCCACATATTCATGAAGTGCTTTTGCCTAAA
AATTCATCTCAAAATCGTGCTTCTAAACATAATAAATAA
>g9501.t1 Gene=g9501 Length=172
MSQVLITSTPLITNSALPSVFSSENEDESSMEISDNNNITPVVEFGRNTSNRKKNVTLAS
RSGLVFPTGRIKRYLKNSKIANRVSVGSAVYCSAILEYLVAEILELASNAARENNRTRIT
PRHLNLAIRNDEELSRLVGNQTVIAGGGVMPHIHEVLLPKNSSQNRASKHNK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g9501.t1 | CDD | cd00074 | H2A | 50 | 160 | 0 |
| 12 | g9501.t1 | Gene3D | G3DSA:1.10.20.10 | Histone | 46 | 170 | 0 |
| 3 | g9501.t1 | PANTHER | PTHR23430:SF95 | HISTONE H2A.1-RELATED | 49 | 171 | 0 |
| 4 | g9501.t1 | PANTHER | PTHR23430 | HISTONE H2A | 49 | 171 | 0 |
| 6 | g9501.t1 | PRINTS | PR00620 | Histone H2A signature | 54 | 76 | 0 |
| 7 | g9501.t1 | PRINTS | PR00620 | Histone H2A signature | 83 | 98 | 0 |
| 8 | g9501.t1 | PRINTS | PR00620 | Histone H2A signature | 98 | 111 | 0 |
| 9 | g9501.t1 | PRINTS | PR00620 | Histone H2A signature | 112 | 126 | 0 |
| 5 | g9501.t1 | PRINTS | PR00620 | Histone H2A signature | 141 | 159 | 0 |
| 2 | g9501.t1 | Pfam | PF00125 | Core histone H2A/H2B/H3/H4 | 27 | 129 | 0 |
| 1 | g9501.t1 | Pfam | PF16211 | C-terminus of histone H2A | 132 | 164 | 0 |
| 11 | g9501.t1 | SMART | SM00414 | h2a4 | 46 | 164 | 0 |
| 10 | g9501.t1 | SUPERFAMILY | SSF47113 | Histone-fold | 45 | 165 | 0 |
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. There were no conditions that were differentially expressed