General information for g6804.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Histone H2A.
Parent gene
- The parent gene g6804 is located on chr_2: 18830938..18838123 (+ 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 | g6804 | g6804.t1 | TSS | g6804.t1 | 18829151 | 18829151 |
| chr_2 | g6804 | g6804.t1 | isoform | g6804.t1 | 18829950 | 18830938 |
| chr_2 | g6804 | g6804.t1 | exon | g6804.t1.exon1 | 18829950 | 18829982 |
| chr_2 | g6804 | g6804.t1 | cds | g6804.t1.CDS1 | 18829950 | 18829982 |
| chr_2 | g6804 | g6804.t1 | exon | g6804.t1.exon2 | 18830552 | 18830938 |
| chr_2 | g6804 | g6804.t1 | cds | g6804.t1.CDS2 | 18830552 | 18830938 |
| chr_2 | g6804 | g6804.t1 | TTS | g6804.t1 | 18830917 | 18830917 |
Sequences
>g6804.t1 Gene=g6804 Length=420
ATGATTGAAATTTCTTCATATAAAATACTAGTCCAAAAATGTCAGGACGAGGCAAAAGGA
GGAAAAGTTAAGGCAAAGGCAAAGTCACGATCAAGTCGTGCTGGACTTCAATTCCCAGTC
GGTCGTATTCATCGTCTTCTACGCAAAGGAAACTATGGTGAACGTGTTGGTGCTGGTGCT
CCAGTATATTTGGCTGCTGTCATGGAATATTTGGCTGCTGAAGTTCTTGAATTGGCAGGA
AATGCTGCTCGTGATAACAAAAAGACAAGAATCATCCCACGTCACTTGCAATTGGCCATC
CGTAATGACGAAGAATTGAATAAACTTCTCTCAGGCGTCACAATCGCTCAAGGTGGTGTT
TTGCCAAACATTCAGGCCGTCTTGTTGCCAAAGAAGACCGAAACAAAGAAAACAGCTTAA
>g6804.t1 Gene=g6804 Length=139
MIEISSYKILVQKCQDEAKGGKVKAKAKSRSSRAGLQFPVGRIHRLLRKGNYGERVGAGA
PVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGV
LPNIQAVLLPKKTETKKTA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g6804.t1 | CDD | cd00074 | H2A | 29 | 132 | 8.95674E-70 |
| 11 | g6804.t1 | Gene3D | G3DSA:1.10.20.10 | Histone | 15 | 139 | 1.0E-66 |
| 3 | g6804.t1 | PANTHER | PTHR23430:SF222 | HISTONE H2A | 17 | 136 | 2.7E-72 |
| 4 | g6804.t1 | PANTHER | PTHR23430 | HISTONE H2A | 17 | 136 | 2.7E-72 |
| 9 | g6804.t1 | PRINTS | PR00620 | Histone H2A signature | 26 | 48 | 2.0E-55 |
| 5 | g6804.t1 | PRINTS | PR00620 | Histone H2A signature | 55 | 70 | 2.0E-55 |
| 6 | g6804.t1 | PRINTS | PR00620 | Histone H2A signature | 70 | 83 | 2.0E-55 |
| 8 | g6804.t1 | PRINTS | PR00620 | Histone H2A signature | 84 | 98 | 2.0E-55 |
| 7 | g6804.t1 | PRINTS | PR00620 | Histone H2A signature | 112 | 130 | 2.0E-55 |
| 2 | g6804.t1 | Pfam | PF00125 | Core histone H2A/H2B/H3/H4 | 21 | 101 | 6.6E-16 |
| 1 | g6804.t1 | Pfam | PF16211 | C-terminus of histone H2A | 104 | 137 | 8.8E-21 |
| 13 | g6804.t1 | ProSitePatterns | PS00046 | Histone H2A signature. | 34 | 40 | - |
| 14 | g6804.t1 | SMART | SM00414 | h2a4 | 15 | 135 | 3.6E-80 |
| 10 | g6804.t1 | SUPERFAMILY | SSF47113 | Histone-fold | 28 | 132 | 7.19E-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.
