General information for g2445.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Histone H2A.
Parent gene
- The parent gene g2445 is located on chr_3: 18013928..18014335 (+ 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 | g2445 | g2445.t1 | isoform | g2445.t1 | 18013928 | 18014335 |
| chr_3 | g2445 | g2445.t1 | exon | g2445.t1.exon1 | 18013928 | 18014335 |
| chr_3 | g2445 | g2445.t1 | cds | g2445.t1.CDS1 | 18013928 | 18014335 |
| chr_3 | g2445 | g2445.t1 | TTS | g2445.t1 | 18014477 | 18014477 |
| chr_3 | g2445 | g2445.t1 | TSS | g2445.t1 | NA | NA |
Sequences
>g2445.t1 Gene=g2445 Length=408
ATGTCAGGACGTGGAAAAGGAGGCAAAGTTAAGGCAAAGGCAAAGTCACGATCAAGCCGT
GCTGGACTTCAGTTCCCAGTTGGTCGTATTCATCGACTTCTCCGCAAAGGAAACTATGGT
GAACGCGTTGGCGCTGGTGCTCCAGTTTATTTGGCTGCCGTTATGGAATATTTAGCTGCT
GAAGTTCTTGAATTGGCAGGAAATGCTGCTCGTGATAACAAAAAGACAAGAATTATTCCA
CGTCACTTGCAATTGGCCATTCGTAATGACGAAGAATTGAATAAACTTCTCTCAGGAGTC
ACAATCGCTCAAGGTGGTGTATTGCCAAACATTCAGGCTGTCTTGTTACCAAAGAAGACC
GAACAAAAGAAACTGCTTAAATTCATCAAGCAAAGATCATCATCTTAA
>g2445.t1 Gene=g2445 Length=135
MSGRGKGGKVKAKAKSRSSRAGLQFPVGRIHRLLRKGNYGERVGAGAPVYLAAVMEYLAA
EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKT
EQKKLLKFIKQRSSS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g2445.t1 | CDD | cd00074 | H2A | 16 | 119 | 3.8313E-68 |
| 11 | g2445.t1 | Gene3D | G3DSA:1.10.20.10 | Histone | 2 | 124 | 1.2E-66 |
| 15 | g2445.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 20 | - |
| 3 | g2445.t1 | PANTHER | PTHR23430:SF222 | HISTONE H2A | 2 | 124 | 1.6E-74 |
| 4 | g2445.t1 | PANTHER | PTHR23430 | HISTONE H2A | 2 | 124 | 1.6E-74 |
| 5 | g2445.t1 | PRINTS | PR00620 | Histone H2A signature | 13 | 35 | 1.8E-55 |
| 7 | g2445.t1 | PRINTS | PR00620 | Histone H2A signature | 42 | 57 | 1.8E-55 |
| 6 | g2445.t1 | PRINTS | PR00620 | Histone H2A signature | 57 | 70 | 1.8E-55 |
| 8 | g2445.t1 | PRINTS | PR00620 | Histone H2A signature | 71 | 85 | 1.8E-55 |
| 9 | g2445.t1 | PRINTS | PR00620 | Histone H2A signature | 99 | 117 | 1.8E-55 |
| 2 | g2445.t1 | Pfam | PF00125 | Core histone H2A/H2B/H3/H4 | 11 | 88 | 1.1E-15 |
| 1 | g2445.t1 | Pfam | PF16211 | C-terminus of histone H2A | 91 | 124 | 1.2E-20 |
| 13 | g2445.t1 | ProSitePatterns | PS00046 | Histone H2A signature. | 21 | 27 | - |
| 14 | g2445.t1 | SMART | SM00414 | h2a4 | 3 | 122 | 2.3E-80 |
| 10 | g2445.t1 | SUPERFAMILY | SSF47113 | Histone-fold | 15 | 119 | 6.44E-46 |
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 transcript has been annotated with K11251 (histone H2A)
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.
