General information for g11868.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Histone H3.
Parent gene
- The parent gene g11868 is located on chr_1: 18840566..18854095 (- 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_1 | g11868 | g11868.t1 | TTS | g11868.t1 | 18840471 | 18840471 |
| chr_1 | g11868 | g11868.t1 | isoform | g11868.t1 | 18840566 | 18844862 |
| chr_1 | g11868 | g11868.t1 | exon | g11868.t1.exon1 | 18840566 | 18840854 |
| chr_1 | g11868 | g11868.t1 | cds | g11868.t1.CDS1 | 18840566 | 18840854 |
| chr_1 | g11868 | g11868.t1 | exon | g11868.t1.exon2 | 18844738 | 18844862 |
| chr_1 | g11868 | g11868.t1 | cds | g11868.t1.CDS2 | 18844738 | 18844862 |
| chr_1 | g11868 | g11868.t1 | TSS | g11868.t1 | 18844935 | 18844935 |
Sequences
>g11868.t1 Gene=g11868 Length=414
ATGGCTCGTACAAAGCAAACTGCTCGAAAATCTACAGGTGGAAAAACACCTCGAAAGCAA
TTAGCTACAAAAGCTGCACGAAAGGGAAGTTTAACTGCAGCAGGAGGATTAAAGAAACCA
CATCGTTACCGTCCAGGAACAGTCGCTCTTCGTGAGATACGTCGCTATCAAAAATCGACT
GAATTATTGATCCGCAAATTGCCTTTCCAACGCTTGGTTCGTGAAATTGCTCAGGATTAC
AAAACTGATTTGCGCTTTCAATCATCTGCTATAATGGCTCTTCAAGAAGCAGCCGAATCT
TATTTGGTCGGACTTTTTGAAGATACAAATTTATGTGCAATACATGCAAAACGTGTTACT
ATCATGCCAAAAGATATGCAACTTGCCCGTCGTATTCGCGGTGAACGTTCCTAA
>g11868.t1 Gene=g11868 Length=137
MARTKQTARKSTGGKTPRKQLATKAARKGSLTAAGGLKKPHRYRPGTVALREIRRYQKST
ELLIRKLPFQRLVREIAQDYKTDLRFQSSAIMALQEAAESYLVGLFEDTNLCAIHAKRVT
IMPKDMQLARRIRGERS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g11868.t1 | Gene3D | G3DSA:1.10.20.10 | Histone | 2 | 137 | 5.2E-76 |
| 15 | g11868.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 18 | - |
| 16 | g11868.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 38 | - |
| 2 | g11868.t1 | PANTHER | PTHR11426 | HISTONE H3 | 1 | 136 | 4.3E-89 |
| 3 | g11868.t1 | PANTHER | PTHR11426:SF194 | HISTONE H3 | 1 | 136 | 4.3E-89 |
| 5 | g11868.t1 | PRINTS | PR00622 | Histone H3 signature | 3 | 17 | 4.2E-82 |
| 6 | g11868.t1 | PRINTS | PR00622 | Histone H3 signature | 17 | 31 | 4.2E-82 |
| 4 | g11868.t1 | PRINTS | PR00622 | Histone H3 signature | 35 | 56 | 4.2E-82 |
| 9 | g11868.t1 | PRINTS | PR00622 | Histone H3 signature | 59 | 76 | 4.2E-82 |
| 8 | g11868.t1 | PRINTS | PR00622 | Histone H3 signature | 81 | 99 | 4.2E-82 |
| 7 | g11868.t1 | PRINTS | PR00622 | Histone H3 signature | 99 | 115 | 4.2E-82 |
| 10 | g11868.t1 | PRINTS | PR00622 | Histone H3 signature | 115 | 136 | 4.2E-82 |
| 1 | g11868.t1 | Pfam | PF00125 | Core histone H2A/H2B/H3/H4 | 1 | 133 | 5.2E-51 |
| 13 | g11868.t1 | ProSitePatterns | PS00959 | Histone H3 signature 2. | 68 | 76 | - |
| 14 | g11868.t1 | SMART | SM00428 | h35 | 35 | 137 | 8.4E-73 |
| 11 | g11868.t1 | SUPERFAMILY | SSF47113 | Histone-fold | 2 | 134 | 7.74E-53 |
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 K11253 (histone H3)
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.
