General information for g8900.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 g8900 is located on chr_2: 33754765..33755142 (- 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 | g8900 | g8900.t1 | TSS | g8900.t1 | 29272243 | 29272243 |
| chr_2 | g8900 | g8900.t1 | isoform | g8900.t1 | 33754765 | 33755142 |
| chr_2 | g8900 | g8900.t1 | exon | g8900.t1.exon1 | 33754765 | 33755142 |
| chr_2 | g8900 | g8900.t1 | cds | g8900.t1.CDS1 | 33754765 | 33755142 |
| chr_2 | g8900 | g8900.t1 | TTS | g8900.t1 | NA | NA |
Sequences
>g8900.t1 Gene=g8900 Length=378
ATGGCACCACCAAAAACAAGCGGTAAAGCAGCAAAAAAAGCCGGAAAGGCACAGAAAAAT
ATTTCAAAAGATGACAAGAAAAAGAAGCGTCATCGTCGTAAGGAATCATATACAATTTAC
ATCTTCAAAGTCTTGAAACAAGTCCATCCTGATACTGGTATTTCATCAAAAGCAATGAGC
ATCATGAACTCATTTGTTAACGACATTTTCGAGCGTATTGCTGCTGAGGCATCACGCTTG
GCTCACTACAACAAACGCTCAACAATCACATCACGAGAAATTCAAACAGCAGTTCGTCTT
CTCTTGCCTGGTGAATTGGCTAAGCATGCTGTCTCAGAAGGCACAAAAGCTGTCACCAAA
TACACATCATCAAAATAA
>g8900.t1 Gene=g8900 Length=125
MAPPKTSGKAAKKAGKAQKNISKDDKKKKRHRRKESYTIYIFKVLKQVHPDTGISSKAMS
IMNSFVNDIFERIAAEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTK
YTSSK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g8900.t1 | Gene3D | G3DSA:1.10.20.10 | Histone | 1 | 125 | 7.2E-66 |
| 13 | g8900.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 33 | - |
| 2 | g8900.t1 | PANTHER | PTHR23428:SF125 | HISTONE H2B 3-RELATED | 1 | 125 | 1.6E-63 |
| 3 | g8900.t1 | PANTHER | PTHR23428 | HISTONE H2B | 1 | 125 | 1.6E-63 |
| 8 | g8900.t1 | PRINTS | PR00621 | Histone H2B signature | 37 | 55 | 2.8E-52 |
| 7 | g8900.t1 | PRINTS | PR00621 | Histone H2B signature | 56 | 76 | 2.8E-52 |
| 6 | g8900.t1 | PRINTS | PR00621 | Histone H2B signature | 78 | 95 | 2.8E-52 |
| 4 | g8900.t1 | PRINTS | PR00621 | Histone H2B signature | 95 | 108 | 2.8E-52 |
| 5 | g8900.t1 | PRINTS | PR00621 | Histone H2B signature | 108 | 121 | 2.8E-52 |
| 1 | g8900.t1 | Pfam | PF00125 | Core histone H2A/H2B/H3/H4 | 6 | 100 | 7.7E-24 |
| 11 | g8900.t1 | ProSitePatterns | PS00357 | Histone H2B signature. | 92 | 114 | - |
| 12 | g8900.t1 | SMART | SM00427 | h2b3 | 27 | 123 | 8.7E-74 |
| 9 | g8900.t1 | SUPERFAMILY | SSF47113 | Histone-fold | 9 | 125 | 1.08E-57 |
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 K11252 (histone H2B)
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.
