General information for g2444.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 g2444 is located on chr_3: 18013312..18013620 (- 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 | g2444 | g2444.t1 | TTS | g2444.t1 | 18013170 | 18013170 |
| chr_3 | g2444 | g2444.t1 | isoform | g2444.t1 | 18013312 | 18013620 |
| chr_3 | g2444 | g2444.t1 | exon | g2444.t1.exon1 | 18013312 | 18013620 |
| chr_3 | g2444 | g2444.t1 | cds | g2444.t1.CDS1 | 18013312 | 18013620 |
| chr_3 | g2444 | g2444.t1 | TSS | g2444.t1 | NA | NA |
Sequences
>g2444.t1 Gene=g2444 Length=309
ATGACAAGAAAAGAAGCGTCATCGTCGCAAGGAATCATATGCAATTTACATTTTCAAAGT
CTTGAAGCAAGTCCATCCCGATACTGGTATCTCATCAAAAGCTATGAGCATCATGAATTC
TCGTTTGTTAATGATATTTTCGAACGCATTGCTGCTGAGGCATCACGCTTGGCTCATTAC
AACAAACGTTCAACAATCACATCACGAGAAATTCAAACAGCAGTTCGTCTTCTCTTGCCT
GGTGAATTGGCTAAGCACGCTGTCTCAGAAGGCACAAAAGCTGTCACTAAATACACATCA
TCAAAATAA
>g2444.t1 Gene=g2444 Length=102
MTRKEASSSQGIICNLHFQSLEASPSRYWYLIKSYEHHEFSFVNDIFERIAAEASRLAHY
NKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g2444.t1 | Gene3D | G3DSA:1.10.20.10 | Histone | 40 | 102 | 1.6E-36 |
| 2 | g2444.t1 | PANTHER | PTHR23428:SF266 | HISTONE H2B | 41 | 102 | 1.8E-35 |
| 3 | g2444.t1 | PANTHER | PTHR23428 | HISTONE H2B | 41 | 102 | 1.8E-35 |
| 7 | g2444.t1 | PRINTS | PR00621 | Histone H2B signature | 33 | 53 | 4.5E-32 |
| 6 | g2444.t1 | PRINTS | PR00621 | Histone H2B signature | 55 | 72 | 4.5E-32 |
| 5 | g2444.t1 | PRINTS | PR00621 | Histone H2B signature | 72 | 85 | 4.5E-32 |
| 4 | g2444.t1 | PRINTS | PR00621 | Histone H2B signature | 85 | 98 | 4.5E-32 |
| 1 | g2444.t1 | Pfam | PF00125 | Core histone H2A/H2B/H3/H4 | 41 | 77 | 8.5E-10 |
| 10 | g2444.t1 | ProSitePatterns | PS00357 | Histone H2B signature. | 69 | 91 | - |
| 9 | g2444.t1 | SMART | SM00427 | h2b3 | 2 | 100 | 1.9E-33 |
| 8 | g2444.t1 | SUPERFAMILY | SSF47113 | Histone-fold | 41 | 102 | 1.24E-33 |
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.
