General information for g5224.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Histone H2B type 1-A.
Parent gene
- The parent gene g5224 is located on chr_2: 7919070..7919610 (- 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 | g5224 | g5224.t1 | TTS | g5224.t1 | 7918921 | 7918921 |
| chr_2 | g5224 | g5224.t1 | isoform | g5224.t1 | 7919070 | 7919610 |
| chr_2 | g5224 | g5224.t1 | exon | g5224.t1.exon1 | 7919070 | 7919330 |
| chr_2 | g5224 | g5224.t1 | cds | g5224.t1.CDS1 | 7919070 | 7919330 |
| chr_2 | g5224 | g5224.t1 | exon | g5224.t1.exon2 | 7919443 | 7919610 |
| chr_2 | g5224 | g5224.t1 | cds | g5224.t1.CDS2 | 7919443 | 7919610 |
| chr_2 | g5224 | g5224.t1 | TSS | g5224.t1 | 7919709 | 7919709 |
Sequences
>g5224.t1 Gene=g5224 Length=429
ATGGCTAAATCAAAGAAAGCAGCTAAAATAAGTAAGATGGCAGCAAAAGCAAAACGAGTC
ATTGAAAAGACTCTAGTTGGATCTACAGAAGCTGGAAAAGTTGCTAGCGGTGAAAAGAAA
GCTCGTAAAAAGAGCAAGAAAGAATCCTTCTCTACTTACATCTTTAAAGTATTGCGCCAA
GTTCATCCTGATGCTGGAATTTCATCCAAGGCAATGATAACCATGAACTCGTTTGTTTTC
GATATTTTTGAACGTATCGTTTCCGAATGCACAAAATTGGTTAAATATAGCAATAGCAAG
ACACTCACTTCACGCGATGTTCAATCTGCAGTTCGTTTCCTCCTACCAGGCGAATTGGCT
AAACATGCTGTCTCTGAAGGCACAAAAGCCGTAACTAAATACACAACCTCTATTGCTAAG
AAAGATTAA
>g5224.t1 Gene=g5224 Length=142
MAKSKKAAKISKMAAKAKRVIEKTLVGSTEAGKVASGEKKARKKSKKESFSTYIFKVLRQ
VHPDAGISSKAMITMNSFVFDIFERIVSECTKLVKYSNSKTLTSRDVQSAVRFLLPGELA
KHAVSEGTKAVTKYTTSIAKKD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g5224.t1 | Gene3D | G3DSA:1.10.20.10 | Histone | 2 | 137 | 5.0E-49 |
| 11 | g5224.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 29 | 48 | - |
| 2 | g5224.t1 | PANTHER | PTHR23428:SF252 | HISTONE H2B | 30 | 137 | 9.1E-46 |
| 3 | g5224.t1 | PANTHER | PTHR23428 | HISTONE H2B | 30 | 137 | 9.1E-46 |
| 8 | g5224.t1 | PRINTS | PR00621 | Histone H2B signature | 50 | 68 | 3.3E-39 |
| 4 | g5224.t1 | PRINTS | PR00621 | Histone H2B signature | 69 | 89 | 3.3E-39 |
| 7 | g5224.t1 | PRINTS | PR00621 | Histone H2B signature | 91 | 108 | 3.3E-39 |
| 6 | g5224.t1 | PRINTS | PR00621 | Histone H2B signature | 108 | 121 | 3.3E-39 |
| 5 | g5224.t1 | PRINTS | PR00621 | Histone H2B signature | 121 | 134 | 3.3E-39 |
| 1 | g5224.t1 | Pfam | PF00125 | Core histone H2A/H2B/H3/H4 | 28 | 112 | 2.1E-16 |
| 10 | g5224.t1 | SMART | SM00427 | h2b3 | 40 | 136 | 2.3E-51 |
| 9 | g5224.t1 | SUPERFAMILY | SSF47113 | Histone-fold | 32 | 137 | 1.51E-44 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5224/g5224.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5224.t1.fa.iupred3.txt does not exist
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. There were no conditions that were differentially expressed