General information for g9518.t5
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t5 | TSS | g9518.t5 | 3871325 | 3871325 |
| chr_1 | g9518 | g9518.t5 | isoform | g9518.t5 | 3871482 | 3873707 |
| chr_1 | g9518 | g9518.t5 | exon | g9518.t5.exon1 | 3871482 | 3871518 |
| chr_1 | g9518 | g9518.t5 | cds | g9518.t5.CDS1 | 3871482 | 3871518 |
| chr_1 | g9518 | g9518.t5 | exon | g9518.t5.exon2 | 3871992 | 3872068 |
| chr_1 | g9518 | g9518.t5 | cds | g9518.t5.CDS2 | 3871992 | 3872068 |
| chr_1 | g9518 | g9518.t5 | exon | g9518.t5.exon3 | 3872129 | 3873707 |
| chr_1 | g9518 | g9518.t5 | cds | g9518.t5.CDS3 | 3872129 | 3873706 |
| chr_1 | g9518 | g9518.t5 | TTS | g9518.t5 | NA | NA |
Sequences
>g9518.t5 Gene=g9518 Length=1693
ATGTCAAATAGTGAGGATTATGATGAAAAATTTGGAGCTGAGGATGATAGCGGTAATTTG
GATGAAACATTAGGCGGTTCTGGTGATGAAGAAGCATCAAAGAATGTCAATAATGATGAT
GATTATGAACCGGAAGATAGAAAAAGAAAGAAGGGAAAGAAACGAAAAGTTCGAAGTGAA
GAAAAATCGAAAGGTAGAAAGAAGAAAAAGCGTAGGAAGAATGAATCTGAAGAAGAACCA
GAAGAGCAAGAACGTGGTGGTGATTCTGATGAATATTCCTTAAGTAAGCGTGGTAGAAAG
AAGCGCGAAAAGGAAGAAAAGAAACAAGCAACTCCACCACCGCCAGCTCAACAAAGTGAA
TCAAACATGCCAACAATTGAGGAAGTCTGCAGTACTTTCGACCTAACTGACGTTCCTATC
GAATATTCTGATGCTGATTATCAAAATCTCGTCACATATAAAATGTTTCAACAGCACGTT
CGTCCAATTCTTCAAAAAGAAAACCCACGCGTGCCAATGTCAAAATTAATGATGCTCGTT
GCTGCCAAATGGCGTGAATTTTCAGAAATCAATCCTCATATGCAACAAGAAGAAGAAGAA
GTCGAAAAAGAAGAGGAAGAAGAAGCTTCACCGAAATCTCCTGAATTTACACCAAAAGAA
ACGAAATCAAGATCAAGCAAAAAATCTGTAAAAATTGCTGAAGACACTTTTGATGATGAA
TATGAAGAAGAAGAAGTTAAATCAAAATCAAAGAAACGAGGTCGAAGTGGAAATAGTCAA
AAATCAAAAGGTCGAAAACAAAAAGTTCCAACATTAAAAATTAAATTTGGAAAGCGTAAA
AATGCAAGTTCAGAAGATGAACAAGAAGATTCTGCAGAAGGATCAGAACGTGAATCTGAT
ATTGAATTTGAAAAAATGTTGCAGCAAACGGATGAAAATGAATTGGATGAGACACCTGCA
ACTGCTGGTGCAAGCAGAAGTGGCAGTAATAATGGTGCTGGAAGTGAAGAAACAACAACT
GAGCCTGCAGTTCGTAAAAAGGCAAAAACAAAAATTGGCAATAAATCAAAGAAAAAGAAG
CCAAAAAAGACAAATTTTCAAGATGATGACATTGAACATCAAGATTATTGTGAAGCATGT
CAACAAGGTGGTGAAATTATTCTTTGTGACACTTGTCCTAAAGCATATCATCTTGTATGT
TTGGATCCTGAATTGGAAGAAGCACCGGAAGGCAAATGGAGTTGTCCAACTTGTGAAGCA
GAAGGTCCAATTGAGCAAGATGATGATGAACATCAAGAATTTTGTCGAATTTGTAAAGAT
GGCGGTGAACTTTTATGTTGTGACTCATGTCCTTCTGCATATCACACATTCTGCTTAGAT
CCACCACTTAGTGAAATTCCAGATGGTGATTGGCGTTGTCCTCGCTGTGGTTGTCCACCA
TTGCCTGGAAAAGTCGCAAAAATTCTCACATGGCGTTGGGCAGAACCAGTACCAGAAGAT
CCTAACAATCCACAAGCATCAACTTCAAAAGGTCCACCACCACAGGCAAGAACTCGTGAA
TATTTTATTAAATGGAAAGATATGAGCTATTGGCATTGCAGTTGGATTACAGAATTACAA
TTGGATGTTTTTCATCCATTAATGTTTCGTTATTATACACGTAAATATGATATGGAAGAA
CCACCAAGATTTG
>g9518.t5 Gene=g9518 Length=564
MSNSEDYDEKFGAEDDSGNLDETLGGSGDEEASKNVNNDDDYEPEDRKRKKGKKRKVRSE
EKSKGRKKKKRRKNESEEEPEEQERGGDSDEYSLSKRGRKKREKEEKKQATPPPPAQQSE
SNMPTIEEVCSTFDLTDVPIEYSDADYQNLVTYKMFQQHVRPILQKENPRVPMSKLMMLV
AAKWREFSEINPHMQQEEEEVEKEEEEEASPKSPEFTPKETKSRSSKKSVKIAEDTFDDE
YEEEEVKSKSKKRGRSGNSQKSKGRKQKVPTLKIKFGKRKNASSEDEQEDSAEGSERESD
IEFEKMLQQTDENELDETPATAGASRSGSNNGAGSEETTTEPAVRKKAKTKIGNKSKKKK
PKKTNFQDDDIEHQDYCEACQQGGEIILCDTCPKAYHLVCLDPELEEAPEGKWSCPTCEA
EGPIEQDDDEHQEFCRICKDGGELLCCDSCPSAYHTFCLDPPLSEIPDGDWRCPRCGCPP
LPGKVAKILTWRWAEPVPEDPNNPQASTSKGPPPQARTREYFIKWKDMSYWHCSWITELQ
LDVFHPLMFRYYTRKYDMEEPPRF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g9518.t5 | CDD | cd15531 | PHD1_CHD_II | 376 | 418 | 5.54631E-25 |
| 15 | g9518.t5 | CDD | cd15532 | PHD2_CHD_II | 434 | 476 | 6.70014E-26 |
| 14 | g9518.t5 | CDD | cd18667 | CD1_tandem_CHD3-4_like | 481 | 554 | 6.54296E-35 |
| 13 | g9518.t5 | Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain | 337 | 424 | 1.9E-19 |
| 12 | g9518.t5 | Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain | 425 | 482 | 1.9E-20 |
| 11 | g9518.t5 | Gene3D | G3DSA:2.40.50.40 | - | 484 | 556 | 6.0E-8 |
| 25 | g9518.t5 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 130 | - |
| 27 | g9518.t5 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 17 | - |
| 21 | g9518.t5 | MobiDBLite | mobidb-lite | consensus disorder prediction | 33 | 48 | - |
| 20 | g9518.t5 | MobiDBLite | mobidb-lite | consensus disorder prediction | 49 | 71 | - |
| 23 | g9518.t5 | MobiDBLite | mobidb-lite | consensus disorder prediction | 87 | 110 | - |
| 26 | g9518.t5 | MobiDBLite | mobidb-lite | consensus disorder prediction | 112 | 129 | - |
| 24 | g9518.t5 | MobiDBLite | mobidb-lite | consensus disorder prediction | 194 | 365 | - |
| 30 | g9518.t5 | MobiDBLite | mobidb-lite | consensus disorder prediction | 207 | 235 | - |
| 22 | g9518.t5 | MobiDBLite | mobidb-lite | consensus disorder prediction | 253 | 275 | - |
| 28 | g9518.t5 | MobiDBLite | mobidb-lite | consensus disorder prediction | 298 | 312 | - |
| 29 | g9518.t5 | MobiDBLite | mobidb-lite | consensus disorder prediction | 313 | 338 | - |
| 4 | g9518.t5 | PANTHER | PTHR45623:SF6 | CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 5 | 41 | 193 | 2.4E-80 |
| 6 | g9518.t5 | PANTHER | PTHR45623 | CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 3-RELATED-RELATED | 41 | 193 | 2.4E-80 |
| 5 | g9518.t5 | PANTHER | PTHR45623:SF6 | CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 5 | 343 | 557 | 2.4E-80 |
| 7 | g9518.t5 | PANTHER | PTHR45623 | CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 3-RELATED-RELATED | 343 | 557 | 2.4E-80 |
| 3 | g9518.t5 | Pfam | PF08073 | CHDNT (NUC034) domain | 140 | 192 | 2.1E-29 |
| 2 | g9518.t5 | Pfam | PF00628 | PHD-finger | 376 | 420 | 3.0E-11 |
| 1 | g9518.t5 | Pfam | PF00628 | PHD-finger | 434 | 477 | 9.6E-11 |
| 33 | g9518.t5 | ProSiteProfiles | PS50016 | Zinc finger PHD-type profile. | 374 | 421 | 10.522 |
| 32 | g9518.t5 | ProSiteProfiles | PS50016 | Zinc finger PHD-type profile. | 432 | 479 | 10.424 |
| 31 | g9518.t5 | ProSiteProfiles | PS50013 | Chromo and chromo shadow domain profile. | 496 | 563 | 9.444 |
| 18 | g9518.t5 | SMART | SM00249 | PHD_3 | 376 | 419 | 1.0E-13 |
| 17 | g9518.t5 | SMART | SM00249 | PHD_3 | 434 | 477 | 5.8E-14 |
| 19 | g9518.t5 | SMART | SM00298 | chromo_7 | 481 | 557 | 9.1E-10 |
| 9 | g9518.t5 | SUPERFAMILY | SSF47095 | HMG-box | 152 | 206 | 8.38E-5 |
| 10 | g9518.t5 | SUPERFAMILY | SSF57903 | FYVE/PHD zinc finger | 345 | 419 | 3.32E-17 |
| 8 | g9518.t5 | SUPERFAMILY | SSF54160 | Chromo domain-like | 447 | 562 | 1.59E-17 |
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:0003678 | DNA helicase activity | MF |
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