General information for g8248.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Histone H3.
Parent gene
- The parent gene g8248 is located on chr_2: 29274989..29275400 (+ 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 | g8248 | g8248.t1 | TSS | g8248.t1 | 29274936 | 29274936 |
| chr_2 | g8248 | g8248.t1 | isoform | g8248.t1 | 29274989 | 29275400 |
| chr_2 | g8248 | g8248.t1 | exon | g8248.t1.exon1 | 29274989 | 29275067 |
| chr_2 | g8248 | g8248.t1 | cds | g8248.t1.CDS1 | 29274989 | 29275067 |
| chr_2 | g8248 | g8248.t1 | exon | g8248.t1.exon2 | 29275123 | 29275400 |
| chr_2 | g8248 | g8248.t1 | cds | g8248.t1.CDS2 | 29275123 | 29275400 |
| chr_2 | g8248 | g8248.t1 | TTS | g8248.t1 | 29275451 | 29275451 |
Sequences
>g8248.t1 Gene=g8248 Length=357
ATGGCTCGTACAAAGCAGACCGCTCGTAAATCAACTGGAGGTAAAGCACCTCGTAAGCAA
TTGGCCACAAAGGCTGCTCGAACAGTCGCTCTTCGTGAAATTCGTCGTTACCAAAAATCA
ACTGAATTGCTCATCCGCAAATTGCCTTTCCAACGCTTAGTTCGTGAAATTGCTCAAGAT
TTCAAAACTGATTTGCGTTTCCAATCATCAGCAGTTATGGCATTGCAAGAAGCATCAGAA
GCTTATTTGGTTGGTCTTTTTGAAGATACAAACTTGTGCGCCATTCATGCTAAGCGTGTA
ACAATCATGCCAAAAGATATTCAACTCGCTCGTCGTATTCGTGGTGAACGTGCTTAA
>g8248.t1 Gene=g8248 Length=118
MARTKQTARKSTGGKAPRKQLATKAARTVALREIRRYQKSTELLIRKLPFQRLVREIAQD
FKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g8248.t1 | Gene3D | G3DSA:1.10.20.10 | Histone | 2 | 118 | 4.1E-60 |
| 16 | g8248.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 24 | - |
| 3 | g8248.t1 | PANTHER | PTHR11426 | HISTONE H3 | 1 | 29 | 7.9E-72 |
| 5 | g8248.t1 | PANTHER | PTHR11426:SF198 | - | 1 | 29 | 7.9E-72 |
| 2 | g8248.t1 | PANTHER | PTHR11426 | HISTONE H3 | 28 | 118 | 7.9E-72 |
| 4 | g8248.t1 | PANTHER | PTHR11426:SF198 | - | 28 | 118 | 7.9E-72 |
| 10 | g8248.t1 | PRINTS | PR00622 | Histone H3 signature | 16 | 37 | 2.9E-52 |
| 7 | g8248.t1 | PRINTS | PR00622 | Histone H3 signature | 40 | 57 | 2.9E-52 |
| 9 | g8248.t1 | PRINTS | PR00622 | Histone H3 signature | 62 | 80 | 2.9E-52 |
| 6 | g8248.t1 | PRINTS | PR00622 | Histone H3 signature | 80 | 96 | 2.9E-52 |
| 8 | g8248.t1 | PRINTS | PR00622 | Histone H3 signature | 96 | 117 | 2.9E-52 |
| 1 | g8248.t1 | Pfam | PF00125 | Core histone H2A/H2B/H3/H4 | 1 | 114 | 1.4E-45 |
| 14 | g8248.t1 | ProSitePatterns | PS00322 | Histone H3 signature 1. | 15 | 21 | - |
| 13 | g8248.t1 | ProSitePatterns | PS00959 | Histone H3 signature 2. | 49 | 57 | - |
| 15 | g8248.t1 | SMART | SM00428 | h35 | 17 | 118 | 1.7E-67 |
| 11 | g8248.t1 | SUPERFAMILY | SSF47113 | Histone-fold | 2 | 115 | 1.37E-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 K11253 (histone H3)
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.
