General information for g4523.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Histone H3.3.
Parent gene
- The parent gene g4523 is located on chr_2: 3052824..3058147 (+ 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 | g4523 | g4523.t1 | TSS | g4523.t1 | 3052000 | 3052000 |
| chr_2 | g4523 | g4523.t1 | isoform | g4523.t1 | 3052361 | 3052893 |
| chr_2 | g4523 | g4523.t1 | exon | g4523.t1.exon1 | 3052361 | 3052752 |
| chr_2 | g4523 | g4523.t1 | cds | g4523.t1.CDS1 | 3052361 | 3052752 |
| chr_2 | g4523 | g4523.t1 | exon | g4523.t1.exon2 | 3052824 | 3052893 |
| chr_2 | g4523 | g4523.t1 | cds | g4523.t1.CDS2 | 3052824 | 3052893 |
| chr_2 | g4523 | g4523.t1 | TTS | g4523.t1 | 3053343 | 3053343 |
Sequences
>g4523.t1 Gene=g4523 Length=462
ATGGTTCGAACTAAACAAACCGCACGTAAGTCAACTGCAACAAGAGGCTCGATCAAGTTG
CAAAGAATATTGGAAACAAAAAGAAAAGAACCGAAGCAACATAAGCAATTCATACCAGTC
GGGAGGAAGCATGTTAAGGACACCAATCATGAGAGAAAGAGAAGATATCGTCCTGGAACT
CTTGCGTTGAAGGAAATAAGACGCTATCAAAAGACAACTGAATTATTGCTACGCGTTGCA
CCGTTTCAAAGACTTGTCAGAGAAATAAGTGAATCATTTAAATCTGATTTTCGTTATCAA
GCAGGAGCTTTGCATGCATTACAAGAGGCAGCAGAATCTTATATCATCGGATTGTTTGAG
GACACAAATTTGTGTGCAATACACGCCAAGCGAGTTACAATTATGCCTAACGACATTCGA
TTGGCTATGCGCATCCGAGGTGAAGGAAGATGGGCCAAATAA
>g4523.t1 Gene=g4523 Length=153
MVRTKQTARKSTATRGSIKLQRILETKRKEPKQHKQFIPVGRKHVKDTNHERKRRYRPGT
LALKEIRRYQKTTELLLRVAPFQRLVREISESFKSDFRYQAGALHALQEAAESYIIGLFE
DTNLCAIHAKRVTIMPNDIRLAMRIRGEGRWAK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g4523.t1 | Gene3D | G3DSA:1.10.20.10 | Histone | 2 | 149 | 1.9E-54 |
| 2 | g4523.t1 | PANTHER | PTHR11426 | HISTONE H3 | 1 | 148 | 1.9E-51 |
| 3 | g4523.t1 | PANTHER | PTHR11426:SF194 | HISTONE H3 | 1 | 148 | 1.9E-51 |
| 5 | g4523.t1 | PRINTS | PR00622 | Histone H3 signature | 3 | 17 | 2.1E-24 |
| 4 | g4523.t1 | PRINTS | PR00622 | Histone H3 signature | 112 | 128 | 2.1E-24 |
| 6 | g4523.t1 | PRINTS | PR00622 | Histone H3 signature | 128 | 149 | 2.1E-24 |
| 1 | g4523.t1 | Pfam | PF00125 | Core histone H2A/H2B/H3/H4 | 29 | 146 | 8.8E-41 |
| 9 | g4523.t1 | ProSitePatterns | PS00959 | Histone H3 signature 2. | 81 | 89 | - |
| 8 | g4523.t1 | SMART | SM00428 | h35 | 48 | 150 | 7.9E-59 |
| 7 | g4523.t1 | SUPERFAMILY | SSF47113 | Histone-fold | 30 | 148 | 1.8E-39 |
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.
