General information for g9518.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Chromodomain-helicase-DNA-binding protein Mi-2-like protein.
Parent gene
- The parent gene g9518 is located on chr_1: 3878107..3879929 (+ 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 | g9518 | g9518.t3 | TSS | g9518.t3 | 3871325 | 3871325 |
| chr_1 | g9518 | g9518.t3 | isoform | g9518.t3 | 3871482 | 3872671 |
| chr_1 | g9518 | g9518.t3 | exon | g9518.t3.exon1 | 3871482 | 3871518 |
| chr_1 | g9518 | g9518.t3 | cds | g9518.t3.CDS1 | 3871482 | 3871518 |
| chr_1 | g9518 | g9518.t3 | exon | g9518.t3.exon2 | 3871992 | 3872068 |
| chr_1 | g9518 | g9518.t3 | cds | g9518.t3.CDS2 | 3871992 | 3872068 |
| chr_1 | g9518 | g9518.t3 | exon | g9518.t3.exon3 | 3872123 | 3872671 |
| chr_1 | g9518 | g9518.t3 | cds | g9518.t3.CDS3 | 3872123 | 3872671 |
| chr_1 | g9518 | g9518.t3 | TTS | g9518.t3 | 3872625 | 3872625 |
Sequences
>g9518.t3 Gene=g9518 Length=663
ATGTCAAATAGTGAGGATTATGATGAAAAATTTGGAGCTGAGGATGATAGCGGTAATTTG
GATGAAACATTAGGCGGTTCTGGTGATGAAGAAGCATCAAAGAATGTCAATAATGATGAG
GATGATGATTATGAACCGGAAGATAGAAAAAGAAAGAAGGGAAAGAAACGAAAAGTTCGA
AGTGAAGAAAAATCGAAAGGTAGAAAGAAGAAAAAGCGTAGGAAGAATGAATCTGAAGAA
GAACCAGAAGAGCAAGAACGTGGTGGTGATTCTGATGAATATTCCTTAAGTAAGCGTGGT
AGAAAGAAGCGCGAAAAGGAAGAAAAGAAACAAGCAACTCCACCACCGCCAGCTCAACAA
AGTGAATCAAACATGCCAACAATTGAGGAAGTCTGCAGTACTTTCGACCTAACTGACGTT
CCTATCGAATATTCTGATGCTGATTATCAAAATCTCGTCACATATAAAATGTTTCAACAG
CACGTTCGTCCAATTCTTCAAAAAGAAAACCCACGCGTGCCAATGTCAAAATTAATGATG
CTCGTTGCTGCCAAATGGCGTGAATTTTCAGAAATCAATCCTCATATGCAACAAGAAGAA
GAAGAAGTCGAAAAAGAAGAGGAAGAAGAAGCTTCACCGAAATCTCCTGAATTTACACCA
AAA
>g9518.t3 Gene=g9518 Length=221
MSNSEDYDEKFGAEDDSGNLDETLGGSGDEEASKNVNNDEDDDYEPEDRKRKKGKKRKVR
SEEKSKGRKKKKRRKNESEEEPEEQERGGDSDEYSLSKRGRKKREKEEKKQATPPPPAQQ
SESNMPTIEEVCSTFDLTDVPIEYSDADYQNLVTYKMFQQHVRPILQKENPRVPMSKLMM
LVAAKWREFSEINPHMQQEEEEVEKEEEEEASPKSPEFTPK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g9518.t3 | Gene3D | G3DSA:1.10.30.10 | DNA Binding (I) | 149 | 219 | 3.4E-6 |
| 7 | g9518.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 130 | - |
| 10 | g9518.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 17 | - |
| 9 | g9518.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 51 | 73 | - |
| 8 | g9518.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 89 | 112 | - |
| 6 | g9518.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 114 | 130 | - |
| 5 | g9518.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 193 | 221 | - |
| 2 | g9518.t3 | PANTHER | PTHR45623:SF9 | CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 3 | 36 | 195 | 1.7E-21 |
| 3 | g9518.t3 | PANTHER | PTHR45623 | CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 3-RELATED-RELATED | 36 | 195 | 1.7E-21 |
| 1 | g9518.t3 | Pfam | PF08073 | CHDNT (NUC034) domain | 142 | 194 | 5.0E-30 |
| 4 | g9518.t3 | SUPERFAMILY | SSF47095 | HMG-box | 154 | 209 | 1.83E-5 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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