General information for g3319.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Possible lysine-specific histone demethylase 1.
Parent gene
- The parent gene g3319 is located on chr_3: 24630124..24631757 (- 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_3 | g3319 | g3319.t1 | isoform | g3319.t1 | 24630124 | 24631757 |
| chr_3 | g3319 | g3319.t1 | exon | g3319.t1.exon1 | 24630124 | 24630835 |
| chr_3 | g3319 | g3319.t1 | cds | g3319.t1.CDS1 | 24630124 | 24630835 |
| chr_3 | g3319 | g3319.t1 | exon | g3319.t1.exon2 | 24630903 | 24631528 |
| chr_3 | g3319 | g3319.t1 | cds | g3319.t1.CDS2 | 24630903 | 24631528 |
| chr_3 | g3319 | g3319.t1 | exon | g3319.t1.exon3 | 24631629 | 24631757 |
| chr_3 | g3319 | g3319.t1 | cds | g3319.t1.CDS3 | 24631629 | 24631757 |
| chr_3 | g3319 | g3319.t1 | TSS | g3319.t1 | 24631828 | 24631828 |
| chr_3 | g3319 | g3319.t1 | TTS | g3319.t1 | NA | NA |
Sequences
>g3319.t1 Gene=g3319 Length=1467
ATGGAAACGGAAACTATTTTACTAATTTCTGACGAATCTGAACCAGAGGATTCAACAACT
AATCGTAGACGTGCAGAAGAGCAAGATCCACTAGAGGGAAAACGAAATTTACGCAAGAAG
AAACCTAAAATTGATAATGACCGTAAAGATCAAATGCCAACAACAAGTGATAAGAAAGAT
GACGAAAATCAAGAACCAGCTAAAATTGATCCTATCGAATATGAGACTGATACCAGATAC
GAAATTCTCACTACCCTTGAAGGCGCTTGCTTCCAATCACGCTTTCCTTATGATAAAATG
ACTACTTATGAAATTGTTGCATTTCCAGAGTTTACAAAAAAGACTACAATCGAACAACGT
CGCATATATTTGGGCATTCGTAATCGCATATTGAAAATGTGGCTAGAGAATGTTAAACAG
CAACTTACATATGATTTTGTTGTTAAAAACATTGAGAAACCCTTTGACATTGATCCAGTT
CTTATTAAACGTATTTTTACATTCCTCGAACGATATGGATACATTAACTATGGTATTTTT
ACAAAACTTGAAGAGATAAAAGAAAAGCGTCGTGAAAAGATCATCGTTATTGGAGCAGGA
ATAAGCGGTTTGATTGCAGCACAAAAATTGCAGAGTTTTGGTTTTGAAGTCATAGTTTTA
GAAGCTAGAGATAGAGTTGGTGGTCGTGTTGCAACATTTAGAAAAAGCAATTATATTGCT
GATCTCGGAGCGATGGTTGTAACTGGCATATATGGAAATCCAATTACAATTTTGGCTAAA
CAACTCGATCTTGAGCTCAAAAAAATTAAGGCTCAATGTCCACTTTTCGGTTCGAATGGA
AAACTCATTTCAAAGAGCAAGGATGAGATTATGGAACTCGAATTCAACAAGATTCTCGAG
TGTACAAGCTACTTATCGCATGTGCTTGATTTCAATTATGCTGACAACACACCTATATCT
CTCGGCCAAGCTATCGAGTGGATTATCAAGTTGCAAGAGAAGAAAATCAAGATGAAGAAG
ATTAATTATTTGAAAAACATTAAAGAAATACAACAGGAAGTCATTTCAAATGAACAAGCA
ATCGCGGATATCAATAGTGACATCTTAGTACTTAAAGACAATTTGATGCAAATTTTGGAT
CATCAGAAAGTTGCTGATGATGAAGAGAATCGCTTGAGACTTGAGTTTAAAAAGCGAGAA
ATCATTCGCGATCTCACGAAGAAGCGTAAGGAAAAGAATGACAAGAAGAAAAGAAATCAA
GAGCTTGATGCGAAATTGAAAGAGCTTGACGAGCCACCCAGTGATGTTTATTTGAGTTCA
GAAGATCGCGCTATACTTGATTGGCATCTAGCAAATCTAGAATTTGCAAACGCAACTCCG
CTTCAAAATTTATCTCTTAAGCATTGGGATCAAGATGACGACTTTGAATTTATTGGACAT
CATACAACGGGTGAGTACACACTTTAA
>g3319.t1 Gene=g3319 Length=488
METETILLISDESEPEDSTTNRRRAEEQDPLEGKRNLRKKKPKIDNDRKDQMPTTSDKKD
DENQEPAKIDPIEYETDTRYEILTTLEGACFQSRFPYDKMTTYEIVAFPEFTKKTTIEQR
RIYLGIRNRILKMWLENVKQQLTYDFVVKNIEKPFDIDPVLIKRIFTFLERYGYINYGIF
TKLEEIKEKRREKIIVIGAGISGLIAAQKLQSFGFEVIVLEARDRVGGRVATFRKSNYIA
DLGAMVVTGIYGNPITILAKQLDLELKKIKAQCPLFGSNGKLISKSKDEIMELEFNKILE
CTSYLSHVLDFNYADNTPISLGQAIEWIIKLQEKKIKMKKINYLKNIKEIQQEVISNEQA
IADINSDILVLKDNLMQILDHQKVADDEENRLRLEFKKREIIRDLTKKRKEKNDKKKRNQ
ELDAKLKELDEPPSDVYLSSEDRAILDWHLANLEFANATPLQNLSLKHWDQDDDFEFIGH
HTTGEYTL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g3319.t1 | Coils | Coil | Coil | 402 | 425 | - |
| 11 | g3319.t1 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 84 | 190 | 3.7E-35 |
| 10 | g3319.t1 | Gene3D | G3DSA:3.50.50.60 | - | 191 | 272 | 8.0E-17 |
| 9 | g3319.t1 | Gene3D | G3DSA:1.10.287.80 | - | 319 | 438 | 2.0E-20 |
| 7 | g3319.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 71 | - |
| 8 | g3319.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 15 | 71 | - |
| 3 | g3319.t1 | PANTHER | PTHR10742 | FLAVIN MONOAMINE OXIDASE | 86 | 483 | 2.8E-80 |
| 4 | g3319.t1 | PANTHER | PTHR10742:SF397 | LYSINE-SPECIFIC HISTONE DEMETHYLASE 1A | 86 | 483 | 2.8E-80 |
| 1 | g3319.t1 | Pfam | PF04433 | SWIRM domain | 94 | 177 | 3.4E-16 |
| 2 | g3319.t1 | Pfam | PF01593 | Flavin containing amine oxidoreductase | 201 | 484 | 2.8E-34 |
| 13 | g3319.t1 | ProSiteProfiles | PS50934 | SWIRM domain profile. | 86 | 186 | 20.269 |
| 6 | g3319.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 85 | 183 | 2.09E-24 |
| 5 | g3319.t1 | SUPERFAMILY | SSF51905 | FAD/NAD(P)-binding domain | 190 | 480 | 3.04E-37 |
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 |
| GO:0055114 | NA | NA |
| GO:0016491 | oxidoreductase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K11450 ([histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase)
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.
