General information for g7425.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Histone H2B.
Parent gene
- The parent gene g7425 is located on chr_2: 23634215..23637750 (- 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 | g7425 | g7425.t1 | isoform | g7425.t1 | 23632066 | 23634405 |
| chr_2 | g7425 | g7425.t1 | exon | g7425.t1.exon1 | 23632066 | 23632231 |
| chr_2 | g7425 | g7425.t1 | cds | g7425.t1.CDS1 | 23632066 | 23632231 |
| chr_2 | g7425 | g7425.t1 | exon | g7425.t1.exon2 | 23634215 | 23634405 |
| chr_2 | g7425 | g7425.t1 | cds | g7425.t1.CDS2 | 23634215 | 23634405 |
| chr_2 | g7425 | g7425.t1 | TSS | g7425.t1 | NA | NA |
| chr_2 | g7425 | g7425.t1 | TTS | g7425.t1 | NA | NA |
Sequences
>g7425.t1 Gene=g7425 Length=357
ATGAACTCATTCGTCAATGATATCTTTGAACGTATCGCAGCTGAAGCATCACGCTTGGCT
CATTACAACAAGCGCTCAACAATCACATCACGAGAAATCCAAACAGCCGTCCGTCTTCTC
TTGCCTGGTGAATTGGCTAAGCACGCTGTCTCAGAAGGCACAAAAGCTGTCACCAAATAC
ACATCATCAAATATTGATAAGACAAGATGCTATGAATTTTCTGATGTCTGCCTTTTGAAA
GCAAATCCACAATCACTTTACTGCATGATGACTCGAAGTAAAAATCATCAATTACATACA
AGAAAACCTTATCAGTTTCATTTATCAGATGAGATTCTAGGTAAACTTGATTCATGA
>g7425.t1 Gene=g7425 Length=118
MNSFVNDIFERIAAEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKY
TSSNIDKTRCYEFSDVCLLKANPQSLYCMMTRSKNHQLHTRKPYQFHLSDEILGKLDS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g7425.t1 | Gene3D | G3DSA:1.10.20.10 | Histone | 1 | 64 | 6.2E-38 |
| 2 | g7425.t1 | PANTHER | PTHR23428:SF266 | HISTONE H2B | 1 | 68 | 3.8E-37 |
| 3 | g7425.t1 | PANTHER | PTHR23428 | HISTONE H2B | 1 | 68 | 3.8E-37 |
| 5 | g7425.t1 | PRINTS | PR00621 | Histone H2B signature | 17 | 34 | 9.2E-26 |
| 6 | g7425.t1 | PRINTS | PR00621 | Histone H2B signature | 34 | 47 | 9.2E-26 |
| 4 | g7425.t1 | PRINTS | PR00621 | Histone H2B signature | 47 | 60 | 9.2E-26 |
| 1 | g7425.t1 | Pfam | PF00125 | Core histone H2A/H2B/H3/H4 | 1 | 39 | 9.9E-11 |
| 9 | g7425.t1 | ProSitePatterns | PS00357 | Histone H2B signature. | 31 | 53 | - |
| 8 | g7425.t1 | SMART | SM00427 | h2b3 | 1 | 62 | 3.7E-33 |
| 7 | g7425.t1 | SUPERFAMILY | SSF47113 | Histone-fold | 1 | 63 | 1.54E-34 |
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.
