General information for g8243.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Lysine-specific demethylase 3A.
Parent gene
- The parent gene g8243 is located on chr_2: 29269771..29271353 (+ 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 | g8243 | g8243.t1 | TSS | g8243.t1 | 29266863 | 29266863 |
| chr_2 | g8243 | g8243.t1 | isoform | g8243.t1 | 29266957 | 29269771 |
| chr_2 | g8243 | g8243.t1 | exon | g8243.t1.exon1 | 29266957 | 29267047 |
| chr_2 | g8243 | g8243.t1 | cds | g8243.t1.CDS1 | 29266957 | 29267047 |
| chr_2 | g8243 | g8243.t1 | exon | g8243.t1.exon2 | 29267116 | 29268964 |
| chr_2 | g8243 | g8243.t1 | cds | g8243.t1.CDS2 | 29267116 | 29268964 |
| chr_2 | g8243 | g8243.t1 | exon | g8243.t1.exon3 | 29269021 | 29269582 |
| chr_2 | g8243 | g8243.t1 | cds | g8243.t1.CDS3 | 29269021 | 29269582 |
| chr_2 | g8243 | g8243.t1 | exon | g8243.t1.exon4 | 29269640 | 29269771 |
| chr_2 | g8243 | g8243.t1 | cds | g8243.t1.CDS4 | 29269640 | 29269771 |
| chr_2 | g8243 | g8243.t1 | TTS | g8243.t1 | 29269808 | 29269808 |
Sequences
>g8243.t1 Gene=g8243 Length=2634
ATGACAGAGACAGATGATCATCATTGTGATCCATTTGCTAATATGTATCTTCAAGAAAAT
CCAACGAATGTTGATATTCCTTCTTCAGCGGAAATAAATTATCCGTTAGAAGAGACCATT
GAAAATAGTTCAATGATGTTTGAGAATGATGAACCAGCACAAGTATCTTCTTACATGCGA
GAAGCAGTGATTGATGATGAAGAAGAAGAAAACAGTAATTTTGTAAAATCTGCCGAAAGT
CAGAACAACTCATCTCAAAATTCAGAAAATGAAGGTCCAAAAAGTGCAAAAAAGAAAGGT
CGACCAAAAGGTTCTTTGGGTGTAAAAAAAGATTTTACTAAAAGTACTACTTCTTTTAAG
AAAGTTCATTTAACTTTTGATGGGCAACAAAATGCACAATCGAACGAAAGATTGCCAAGA
ATGAGAGCAAATGTGCATAATATGAAGCTGACACAAGATCAAATTGATCAGCTTAAGGCA
GAAGGCAAAAATTTCTATCAGCCTGGAGTATGCTTCATAATAGCACCTGAGCTGGAACAT
TGCATAGAATGTATAAAGCAAAAGAGAAAGTCAAGAACAAAAAGAGAAGTCGATTGCAGA
TTTTATCATTTTCGAAAACTACGGTATGAGGATGGAAAGCTCATTGTAGCTGGATTTTTA
GACCCTCATGAAGATCCAAAAGAGATTGATAAAATTATTTGGTTACCTCAATCTGAAAAA
ACTTTTCGATTTAAAGGTATGAGTGTGCAGCATGCAAAATTAATTATTGCACATGTTGGT
GATGAGTTGTGTTTAATAATTGATAAAGAACGAAAATATTATGAAAAATATAATTCTGCT
TCGAAACCTATAATTTGGAAACGACTAATTGATCAAGTAATTGAAATTTGTGATTTATGC
TCGACTACTCTCTTTAATTATCATCTTATTTGTACCAAATGTGGTCTTTCTCTGTGTATT
GATTGCGCCAATGAGAGAAATCCAAAAATTTCCAGTGCACAATGTTCAATAAAAGAAGAA
GTTCATACATATGAGGACTTGTACTTAACACAAATTATTGTTGGAGATTCCTTAGATATT
CTTCAACGAATGCTTCATGATATTTGTCGTTTGTGGAAAATTGATCATCATTGCAAATTT
AAGACAGAGAAATATATTGAAATTGATAAACAGCTTGAAAATGTCATTTATAATCTTATG
AAAGAAGATGGTGAGAAAACTTTTATAACTCGAGAACTTGCACATACTTTCAAAATTGTT
GATGTTGATTTTCAAAAAATACCATATAATGAGGAGGGTAATAAAGAGCCTAATCATGAA
TTTCCTGGTGTATACAAACATCAACCAGAAGTCAAAGATATTTTACCTGTAAGATATAAA
TCTAAATTCGGAAGTGAAAGTGTGATTAGTATATCTAGAATTATGAACCAAGCAACTTCC
GATTTATTTTACAAAAATATTCCTCATAAATGGCTTTGCGAAGGAAAACTCTTAAGACTT
CTTGATCCAATGAATCCTGGAAATGAACGTTTTTTCGGTGATCAATGGCAACGAGGACAA
CCTGTTTTAATAAGTAATGTTCTCGATCATCTCGACAGAAAAATTTGGTTACCTCAATCA
TTTTCGAATGAGTTTGGTAGCGAAAAATCTGATTTTATCAATTGCATGACTGGAAATCTT
GTTCGTAATAAAGAGATCGCAGTATTTTGGGATGGATTTGAAGTTGTTGAGAAAAGATTA
AGAGATAACGATGGAGTTCCAATGCTGTTAAAACTGAAAGATTGGCCACCAGATTCCGAT
TTTAAGAAAATTATGCCAACGCGGTTTGATGATATTATGAAAAACTTGCCGATGAATGCA
TACACCAATCGAACAGGCGATTTAAATATTATTAAATACCTTCCGCAATGTTTCATTCAT
CCCGATTTAGGGCCCAAAGGATATTTCGCATATGGTTCACCATATTATCTCAAAGAGGGA
ACCACAAATTTGCATTTAGATGTATCAGATGCTTGTAATGTTATGTGTTATATTGGTTTT
CCACGTGATAAAGAAAAGTCAGTTGATGAATATATTGAACAGGGATTTTTAGCCATAATT
GATGCCAATTGTGATCAATCAAATATTGATCGAGTAATACGCGATGGAGAAATTCCTGGT
GCAATTTGGCATATTTATGAAGCAGCTGACACAGATAAAATTCGAGATTTTTTGCTGAAA
GTTGCTGTTGAGAAAGGTTTTAAAGTCGCTCGTGACCATGATGTTATTCACGATCAAAAT
TGGTATTTAGATAATGAAATGAGAAAAAGATTGTATGCAGAATATGGTGTAAAAGGTTAT
GCGATTGTTCAATGCTTGGGAGATTGCATTATATTGCCAGCTGGAACACCACATCAAGTT
AGAAATATTTATTCATGCATCAAAATTGCAGAAGATTTTGTTTCTCCACAGCAAATGGCT
CACTGCTTACATTTGAGTGAAGAATTCCGTAAATTAACAAAAACTCATACAAACAATGAA
GAAAAACTTAATATTAAAAACATTGCTTATCATAGCATCAAAGAGGCAATTGCTGGATTA
ATACACGCCGTGAATACAGTTTATAATGTCGGGACAAAAATGATGAAAAATTAA
>g8243.t1 Gene=g8243 Length=877
MTETDDHHCDPFANMYLQENPTNVDIPSSAEINYPLEETIENSSMMFENDEPAQVSSYMR
EAVIDDEEEENSNFVKSAESQNNSSQNSENEGPKSAKKKGRPKGSLGVKKDFTKSTTSFK
KVHLTFDGQQNAQSNERLPRMRANVHNMKLTQDQIDQLKAEGKNFYQPGVCFIIAPELEH
CIECIKQKRKSRTKREVDCRFYHFRKLRYEDGKLIVAGFLDPHEDPKEIDKIIWLPQSEK
TFRFKGMSVQHAKLIIAHVGDELCLIIDKERKYYEKYNSASKPIIWKRLIDQVIEICDLC
STTLFNYHLICTKCGLSLCIDCANERNPKISSAQCSIKEEVHTYEDLYLTQIIVGDSLDI
LQRMLHDICRLWKIDHHCKFKTEKYIEIDKQLENVIYNLMKEDGEKTFITRELAHTFKIV
DVDFQKIPYNEEGNKEPNHEFPGVYKHQPEVKDILPVRYKSKFGSESVISISRIMNQATS
DLFYKNIPHKWLCEGKLLRLLDPMNPGNERFFGDQWQRGQPVLISNVLDHLDRKIWLPQS
FSNEFGSEKSDFINCMTGNLVRNKEIAVFWDGFEVVEKRLRDNDGVPMLLKLKDWPPDSD
FKKIMPTRFDDIMKNLPMNAYTNRTGDLNIIKYLPQCFIHPDLGPKGYFAYGSPYYLKEG
TTNLHLDVSDACNVMCYIGFPRDKEKSVDEYIEQGFLAIIDANCDQSNIDRVIRDGEIPG
AIWHIYEAADTDKIRDFLLKVAVEKGFKVARDHDVIHDQNWYLDNEMRKRLYAEYGVKGY
AIVQCLGDCIILPAGTPHQVRNIYSCIKIAEDFVSPQQMAHCLHLSEEFRKLTKTHTNNE
EKLNIKNIAYHSIKEAIAGLIHAVNTVYNVGTKMMKN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g8243.t1 | Gene3D | G3DSA:2.60.120.650 | Cupin | 487 | 839 | 7.5E-118 |
| 9 | g8243.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 67 | 112 | - |
| 8 | g8243.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 75 | 91 | - |
| 2 | g8243.t1 | PANTHER | PTHR12549 | JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN | 73 | 394 | 8.7E-191 |
| 4 | g8243.t1 | PANTHER | PTHR12549:SF8 | LYSINE-SPECIFIC DEMETHYLASE 3B | 73 | 394 | 8.7E-191 |
| 3 | g8243.t1 | PANTHER | PTHR12549 | JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN | 485 | 860 | 8.7E-191 |
| 5 | g8243.t1 | PANTHER | PTHR12549:SF8 | LYSINE-SPECIFIC DEMETHYLASE 3B | 485 | 860 | 8.7E-191 |
| 1 | g8243.t1 | Pfam | PF02373 | JmjC domain, hydroxylase | 720 | 813 | 7.3E-11 |
| 11 | g8243.t1 | ProSiteProfiles | PS51184 | JmjC domain profile. | 623 | 830 | 23.524 |
| 7 | g8243.t1 | SMART | SM00558 | cupin_9 | 605 | 830 | 8.4E-40 |
| 6 | g8243.t1 | SUPERFAMILY | SSF51197 | Clavaminate synthase-like | 479 | 855 | 1.51E-34 |
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 transcript has been annotated with K15601 ([histone H3]-dimethyl-L-lysine9 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.
