General information for g5930.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Histone H3-like centromeric protein A.
Parent gene
- The parent gene g5930 is located on chr_2: 12886991..12887593 (- 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 | g5930 | g5930.t1 | TTS | g5930.t1 | 12886766 | 12886766 |
| chr_2 | g5930 | g5930.t1 | isoform | g5930.t1 | 12886991 | 12887593 |
| chr_2 | g5930 | g5930.t1 | exon | g5930.t1.exon1 | 12886991 | 12887516 |
| chr_2 | g5930 | g5930.t1 | cds | g5930.t1.CDS1 | 12886991 | 12887516 |
| chr_2 | g5930 | g5930.t1 | exon | g5930.t1.exon2 | 12887580 | 12887593 |
| chr_2 | g5930 | g5930.t1 | cds | g5930.t1.CDS2 | 12887580 | 12887593 |
| chr_2 | g5930 | g5930.t1 | TSS | g5930.t1 | 12887750 | 12887750 |
Sequences
>g5930.t1 Gene=g5930 Length=540
ATGTTGAGTGAAAGTGAACAAAGTACTATTGAATCAAATGCTGAATCACCTCCACAACGT
TCATCTCAACGAAAAAATCCTCAGAAACAACAAAGCCAAGAACAATCCACTTCAAAAAAC
AGTCAATCAACTCAATCAAAGAAACAGCAAAAAGATGTATCATCAAAAAATCAACGAAAG
CAAGCGGAACCACAGCAAAGAGAGGTACAAGAAAAAGGAAAAAATAATAAAACTGATAAA
CGAAAAAAACAATATCCTTTACATATCAAAGAAATAATGCGATTACAAAAATCGACTGAA
AATCAAATACCTAAATTACCTTTCACGAGATTATTAAAAGAAATATTACAGAAGCATGGT
GATTTTCGAATGCAATCTACTGCAGTTGCTGCTATTCAAGAGGCAACAGAGTTATATTTT
GTACAGCTATTTGACGACGCTTATAAGCTGACACTTCATAGACAACGAGTCACACTCCAT
TCCTCTGACATTTCTCTCGTTTTATATATAAGAGGACAAACAGATCCAGGAGTACGATAA
>g5930.t1 Gene=g5930 Length=179
MLSESEQSTIESNAESPPQRSSQRKNPQKQQSQEQSTSKNSQSTQSKKQQKDVSSKNQRK
QAEPQQREVQEKGKNNKTDKRKKQYPLHIKEIMRLQKSTENQIPKLPFTRLLKEILQKHG
DFRMQSTAVAAIQEATELYFVQLFDDAYKLTLHRQRVTLHSSDISLVLYIRGQTDPGVR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g5930.t1 | Gene3D | G3DSA:1.10.20.10 | Histone | 35 | 174 | 3.7E-32 |
| 10 | g5930.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 86 | - |
| 12 | g5930.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 51 | - |
| 11 | g5930.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 52 | 86 | - |
| 2 | g5930.t1 | PANTHER | PTHR11426 | HISTONE H3 | 21 | 175 | 2.2E-31 |
| 3 | g5930.t1 | PANTHER | PTHR11426:SF191 | HISTONE H3-LIKE CENTROMERIC PROTEIN A | 21 | 175 | 2.2E-31 |
| 4 | g5930.t1 | PRINTS | PR00622 | Histone H3 signature | 49 | 63 | 1.8E-14 |
| 5 | g5930.t1 | PRINTS | PR00622 | Histone H3 signature | 119 | 137 | 1.8E-14 |
| 7 | g5930.t1 | PRINTS | PR00622 | Histone H3 signature | 137 | 153 | 1.8E-14 |
| 6 | g5930.t1 | PRINTS | PR00622 | Histone H3 signature | 153 | 174 | 1.8E-14 |
| 1 | g5930.t1 | Pfam | PF00125 | Core histone H2A/H2B/H3/H4 | 45 | 171 | 2.5E-28 |
| 9 | g5930.t1 | SMART | SM00428 | h35 | 74 | 175 | 2.9E-29 |
| 8 | g5930.t1 | SUPERFAMILY | SSF47113 | Histone-fold | 80 | 172 | 4.03E-27 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5930/g5930.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5930.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.
