General information for g16110.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Histone-lysine N-methyltransferase SMYD3.
Parent gene
- The parent gene g16110 is located on chr_4: 8188385..8189918 (+ 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_4 | g16110 | g16110.t1 | TSS | g16110.t1 | 8188320 | 8188320 |
| chr_4 | g16110 | g16110.t1 | isoform | g16110.t1 | 8188385 | 8189918 |
| chr_4 | g16110 | g16110.t1 | exon | g16110.t1.exon1 | 8188385 | 8189333 |
| chr_4 | g16110 | g16110.t1 | cds | g16110.t1.CDS1 | 8188385 | 8189333 |
| chr_4 | g16110 | g16110.t1 | exon | g16110.t1.exon2 | 8189399 | 8189561 |
| chr_4 | g16110 | g16110.t1 | cds | g16110.t1.CDS2 | 8189399 | 8189561 |
| chr_4 | g16110 | g16110.t1 | exon | g16110.t1.exon3 | 8189633 | 8189918 |
| chr_4 | g16110 | g16110.t1 | cds | g16110.t1.CDS3 | 8189633 | 8189918 |
| chr_4 | g16110 | g16110.t1 | TTS | g16110.t1 | NA | NA |
Sequences
>g16110.t1 Gene=g16110 Length=1398
ATGAGTAAAAAACCAGAGCCATTGTCAAAAGGAGCATTAATTCTTCAGGAGAAACCATTT
GCTTATATTGTGCAATCCAAGTTTATTAAAGAACGTTGCGATTTTTGTCTTTCATCTGGC
AAACTTTTAAAATGTAGTGGTTGTGAATTTTCTCATTATTGCGGAGTGTTATGTCAACGT
GATGCATGGGCTGAGCACAAATATGAATGCTTGTGCATGAAAAAAATTCTACCACGAACA
ATTCCAGATGCTGCACGTATTATGGCAAAAATTATATGGAAATTGCAATATGGTGGATAT
TTGCAAAAATTTTACTATTCACGTAATGGATATCGAAAGTTCAATGACCTTATGCCACAT
TTAGAAGATATTAAATGGGATGAACATCGAATGGATCATGTACAAACTTTATATGCTGTA
CTTAAAGATTATCTGGCACCAGAACATTTGCCAAATCAATCAGAATTCCTCGGTATTTAT
GGCCGTCTATGCATCAATAGTTTCAATATTCTCGATGATGATTTGAATTCAATTGGCACT
GGCATCTACTTGGCAAGTAGTATACTTGATCACAGTTGTAAACCAAATGCAGTTGCAACA
TTTGAAGGACCACAATTGAGTATCAGATTAATTGAAGATATACCAGAACTTAAATGGGAA
GATATAAGAATTTCATACATTGAACTTTTAGATTTGCCTGAGACACGTCGTGAACAGCTC
AGAAAATGTTACTATTTTGATTGCGAATGTGAAAGATGCAAAGATGAAAAAGAAAGAGCA
ACAATGGTTGCAATGGCATGTCCAAAAGAGAATTGTGATGGCCAAATTGATGTCCTGGAT
GAAAAATGCAAAGAATGTTCGACAGAAATCAAAGAAGAACATCGTCAGAATTTTGATGAT
ATTCTTGATATGACAAAAACTTTATTAGCTGAAATGCAGGAAACAAGATATATTGATATG
TGTAGAAATCTCGTAAAAAGACAAACGAATGTGCTTCATGAAAAAAATATCTGGCGCTTA
AAGACATTAGATCTTGCATTTGAGGCTGCAATTGATTTTGAAGCATGGCCAGAAGCTGTA
GAATATGGAAAAAGATTCGTAAAAGGACTTAGCCATTACACATCGTCACTCAATCCACTT
GTCGGCATCGATCACCTGAAATTGGGTAAAATTTATCCTCATTTAAATGAATTTCAAACT
GCAATTCATCATATAAGAGAAGCCGGTGATGTGCTTAAAATTACACATGGTGATCAATCA
CGTTTAATGCGTGATTTTGTGAGACCACTTTTACGTGAAACACAAATACTGCTTGAAGAA
AGTCAGAGAGTTAAACTTCCACCACCAACTGAAGATGATGAAGAAGCAGAAGAAAGTGGT
GAACAAGCAACTGCATAA
>g16110.t1 Gene=g16110 Length=465
MSKKPEPLSKGALILQEKPFAYIVQSKFIKERCDFCLSSGKLLKCSGCEFSHYCGVLCQR
DAWAEHKYECLCMKKILPRTIPDAARIMAKIIWKLQYGGYLQKFYYSRNGYRKFNDLMPH
LEDIKWDEHRMDHVQTLYAVLKDYLAPEHLPNQSEFLGIYGRLCINSFNILDDDLNSIGT
GIYLASSILDHSCKPNAVATFEGPQLSIRLIEDIPELKWEDIRISYIELLDLPETRREQL
RKCYYFDCECERCKDEKERATMVAMACPKENCDGQIDVLDEKCKECSTEIKEEHRQNFDD
ILDMTKTLLAEMQETRYIDMCRNLVKRQTNVLHEKNIWRLKTLDLAFEAAIDFEAWPEAV
EYGKRFVKGLSHYTSSLNPLVGIDHLKLGKIYPHLNEFQTAIHHIREAGDVLKITHGDQS
RLMRDFVRPLLRETQILLEESQRVKLPPPTEDDEEAEESGEQATA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g16110.t1 | Gene3D | G3DSA:2.170.270.10 | SET domain | 7 | 254 | 9.7E-69 |
| 10 | g16110.t1 | Gene3D | G3DSA:3.30.60.180 | - | 32 | 79 | 9.7E-69 |
| 9 | g16110.t1 | Gene3D | G3DSA:3.30.70.3410 | - | 80 | 167 | 9.7E-69 |
| 13 | g16110.t1 | Gene3D | G3DSA:1.25.40.970 | - | 288 | 365 | 1.9E-11 |
| 12 | g16110.t1 | Gene3D | G3DSA:1.25.40.10 | - | 369 | 445 | 8.3E-13 |
| 7 | g16110.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 441 | 465 | - |
| 8 | g16110.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 451 | 465 | - |
| 2 | g16110.t1 | PANTHER | PTHR12197 | HISTONE-LYSINE N-METHYLTRANSFERASE SMYD | 8 | 432 | 2.4E-62 |
| 3 | g16110.t1 | PANTHER | PTHR12197:SF285 | HISTONE-LYSINE N-METHYLTRANSFERASE ASHR1 | 8 | 432 | 2.4E-62 |
| 1 | g16110.t1 | Pfam | PF01753 | MYND finger | 33 | 70 | 1.2E-7 |
| 6 | g16110.t1 | ProSitePatterns | PS01360 | Zinc finger MYND-type signature. | 33 | 70 | - |
| 14 | g16110.t1 | ProSiteProfiles | PS50865 | Zinc finger MYND-type profile. | 33 | 70 | 11.05 |
| 5 | g16110.t1 | SUPERFAMILY | SSF144232 | HIT/MYND zinc finger-like | 26 | 76 | 7.15E-10 |
| 4 | g16110.t1 | SUPERFAMILY | SSF82199 | SET domain | 166 | 255 | 7.03E-12 |
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:0005515 | protein binding | MF |
KEGG
Orthology
- This transcript has been annotated with K11426 ([histone H3]-lysine4/36 N-trimethyltransferase SMYD)
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.
