General information for g12953.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Lysine-specific demethylase 6A.
Parent gene
- The parent gene g12953 is located on chr_1: 27134389..27138854 (+ 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 | g12953 | g12953.t4 | isoform | g12953.t4 | 27134242 | 27138854 |
| chr_1 | g12953 | g12953.t4 | exon | g12953.t4.exon1 | 27134242 | 27134410 |
| chr_1 | g12953 | g12953.t4 | exon | g12953.t4.exon2 | 27134639 | 27134785 |
| chr_1 | g12953 | g12953.t4 | cds | g12953.t4.CDS1 | 27134777 | 27134785 |
| chr_1 | g12953 | g12953.t4 | exon | g12953.t4.exon3 | 27134874 | 27135246 |
| chr_1 | g12953 | g12953.t4 | cds | g12953.t4.CDS2 | 27134874 | 27135246 |
| chr_1 | g12953 | g12953.t4 | exon | g12953.t4.exon4 | 27135523 | 27135853 |
| chr_1 | g12953 | g12953.t4 | cds | g12953.t4.CDS3 | 27135523 | 27135853 |
| chr_1 | g12953 | g12953.t4 | exon | g12953.t4.exon5 | 27135919 | 27136154 |
| chr_1 | g12953 | g12953.t4 | cds | g12953.t4.CDS4 | 27135919 | 27136154 |
| chr_1 | g12953 | g12953.t4 | exon | g12953.t4.exon6 | 27136324 | 27136529 |
| chr_1 | g12953 | g12953.t4 | cds | g12953.t4.CDS5 | 27136324 | 27136529 |
| chr_1 | g12953 | g12953.t4 | exon | g12953.t4.exon7 | 27136786 | 27136913 |
| chr_1 | g12953 | g12953.t4 | cds | g12953.t4.CDS6 | 27136786 | 27136913 |
| chr_1 | g12953 | g12953.t4 | exon | g12953.t4.exon8 | 27137506 | 27137925 |
| chr_1 | g12953 | g12953.t4 | cds | g12953.t4.CDS7 | 27137506 | 27137925 |
| chr_1 | g12953 | g12953.t4 | exon | g12953.t4.exon9 | 27138123 | 27138332 |
| chr_1 | g12953 | g12953.t4 | cds | g12953.t4.CDS8 | 27138123 | 27138332 |
| chr_1 | g12953 | g12953.t4 | exon | g12953.t4.exon10 | 27138400 | 27138526 |
| chr_1 | g12953 | g12953.t4 | cds | g12953.t4.CDS9 | 27138400 | 27138526 |
| chr_1 | g12953 | g12953.t4 | exon | g12953.t4.exon11 | 27138594 | 27138854 |
| chr_1 | g12953 | g12953.t4 | cds | g12953.t4.CDS10 | 27138594 | 27138854 |
| chr_1 | g12953 | g12953.t4 | TTS | g12953.t4 | 27138947 | 27138947 |
| chr_1 | g12953 | g12953.t4 | TSS | g12953.t4 | NA | NA |
Sequences
>g12953.t4 Gene=g12953 Length=2608
AGTAAGTCTTTTAGTCTATTGCCATAAAATTTTTTGAACATAAAGTCGCAGTCACATGAG
CGTTTTTTATTTCATGTGAGTGCGACAAAAAAAAAAAAAAGAATGTAGAGGTGAAGTGAT
AAGTGTCATGTAAATTCTAGTTTTAAGAAATATTAGATTTAGGTTTAAGACAAATTCATC
AGCACCACCGCCTTATCCACAACAAGGCAATGCAATTCCAGCAAAGAGATTTAAACATGG
TGAGGACCAGCAGCAGCAACCACCAATTGCACGTCCTCCATTCTATCTTACCCCGCAACA
ACTTCAAATGCTTCAGGCGTTGCAGAATACACCAAATCTTACGCCACAGCAACAAAATGC
TTTGCAACAGCTGACACATCAATTTAAATTAATGCAACAACATCAACAGCAATTGAGATT
ACAGCAAGCACAGCTTCGTGGAGGTGGATTGCCAATTCGAGGTCAACCACCGCAAGCTCA
ACAATTTCCACAACAAAATCCAACAAATTTTCCAACACAGCCAATTGGTAATAGAACACC
ACAATCAGGAACTACTGCACAAACTGGATTTATGAATGATGGAAGTTTTTCACCTGCAAC
TGGTCATTCACAAGCTGGCATGCCATTTAAATCAGCTGGTGGTTTTCAACAACAGCAAAT
CACATCGACAACGAACAATCAAGATTTAAATGTAAGCGATCAAGAACTTCAAGCTTTGTT
ATCTCAACGTGATCTCACAACAACTTTTGCTGAAAATATTTTAAAACAAATTGAAAATGA
AGAGCCAATTGATTCAAAAACCAAATTGCATGAAACACTCAATGTAGATGCCATTAATCA
ACGAAATAATAAATCACCAACGATAAAATGCGAAGCGACATCAACATCGACGCAGGCTCT
TTTAAATAAACATGACATAAAATCAGAGCCGGTTGTTAAAATTGAAAAATTGGTTGAGTT
TGATAATAAAGTTGAATTCCATAATAAAATGACAGCAAAGGAAGTTTTTGAGACAGTAAA
AAGAATGGATAACAGTGAATGTCCATCAACGTGTTCAGTTTTGGCACTTGATTTACCACC
ACCTAGTCCACCTGAAAATCCAACACCACACCGTCTCACACGTGATCAACTTCTTCCACC
AACTCCATCAGTATTTCTAGAAAATAAAAAACACGCGTTTAGTCCGCAGTTACAAGAATT
TTGCTTAAAGCATCCAATTGCTGTTGTTAGACAAATGGCATCAGCTTTAAAATTAGATTT
GGGTTTATTTTCAACAAAAACCCTTGTCGATACCGCACCAGAACAAACATGTGAAGTTAG
AACACAGATGAATCAATCAGCTGATGAAAATTGGGATCCACAACATAAGGAACAAGTGTG
GGCTTGCGTTTCACATCGATCTCATACAACAATCGCTAAATACGCTGCGTATCAAGCATC
AACCTTTCATGAAAGCATCAAGGATGAACGTGATAAAGGCTCAGGAATAAGCACAGTTCC
AAATTCAGATTCAGATTCCAAAGATTCTTTTTCGAATGGTGCAAATGGAAAGAAAACAAA
AAGGCTTAAAAATGGCATAAAAATGTTAAAATTCGGAACGAATGTTGACTTGTCAGATGA
ACGTAAATGGCGAGCACAACTTAATGAATTACAAAAGCTTCCACCATTTGCACGTGTTGT
GTCAGCTGCAAATATGCTTTCACATGTCGGTCATATGATCCTTGGCATGAATACTGTACA
ACTTTATATGAAAGTACCAAACGCACGTACTCCCGGACATCAGGAGAATAATAACTTTTG
CTCAATTAATATTAATATTGGACCTGGTGATTGCGAATGGTTTGCAACACCTGATTCGTA
CTGGGGCGGAATTCAGCAACTTTGTGAAAAGAATAACACCAATTATTTGCATGGCAGTTG
GTGGCCATCGATGGAAGATCTATACAATGCGAATATTCCCGTCTATCGATTCACACAACG
ACCGGGTGATCTTGTGTGGGTTAATGCTGGATGTGTTCATTGGGTTCAAGCAATTGGCTG
GTGTAATAATATAGCATGGAACGTTGGTCCGCTAACAGCACGACAGTTTGAGCTCGCTAT
AGTTCGCTATGAATGGAACAAATTAGAGGCATACAAATCAATTGTGCCGATGATTCATCT
CAGCTGGAATTTAGCAAGAAATATTAAAGTTTCGGATCCAAAACTTTATGATCTAATCAA
AAATTGTCTCTTGCAAACATTGCGTCATACTATGCAAGTACTCGAATGTGTCAAGTCGAA
GGGCATTGAAGTAAAATTTCATGGTCGTGCTAAGAATGAAGCATCACATTATTGTGGCGT
GTGTGAGATTGAAGTCTTCAACATTTTGTTCATTCGCGAGCAAGAAAAGCGTCATGTGGT
GCATTGTTTGGGCTGTGCCCGTAAACAATCCCCATCACTTCAAGGATTTGTGTGTTTGGA
GGAATATAAATTGACAGAATTGATGCAAGTTTATGATGCATTCATGCTACACAAGCCACC
ACCACAACCAATGTTTATGCCACCACCAACACCTCAACCGGCTATTTTACAGCAAATGCA
GCAACCAATTCCATCCGTCGTATCGTAA
>g12953.t4 Gene=g12953 Length=766
MLQALQNTPNLTPQQQNALQQLTHQFKLMQQHQQQLRLQQAQLRGGGLPIRGQPPQAQQF
PQQNPTNFPTQPIGNRTPQSGTTAQTGFMNDGSFSPATGHSQAGMPFKSAGGFQQQQITS
TTNNQDLNVSDQELQALLSQRDLTTTFAENILKQIENEEPIDSKTKLHETLNVDAINQRN
NKSPTIKCEATSTSTQALLNKHDIKSEPVVKIEKLVEFDNKVEFHNKMTAKEVFETVKRM
DNSECPSTCSVLALDLPPPSPPENPTPHRLTRDQLLPPTPSVFLENKKHAFSPQLQEFCL
KHPIAVVRQMASALKLDLGLFSTKTLVDTAPEQTCEVRTQMNQSADENWDPQHKEQVWAC
VSHRSHTTIAKYAAYQASTFHESIKDERDKGSGISTVPNSDSDSKDSFSNGANGKKTKRL
KNGIKMLKFGTNVDLSDERKWRAQLNELQKLPPFARVVSAANMLSHVGHMILGMNTVQLY
MKVPNARTPGHQENNNFCSININIGPGDCEWFATPDSYWGGIQQLCEKNNTNYLHGSWWP
SMEDLYNANIPVYRFTQRPGDLVWVNAGCVHWVQAIGWCNNIAWNVGPLTARQFELAIVR
YEWNKLEAYKSIVPMIHLSWNLARNIKVSDPKLYDLIKNCLLQTLRHTMQVLECVKSKGI
EVKFHGRAKNEASHYCGVCEIEVFNILFIREQEKRHVVHCLGCARKQSPSLQGFVCLEEY
KLTELMQVYDAFMLHKPPPQPMFMPPPTPQPAILQQMQQPIPSVVS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g12953.t4 | Gene3D | G3DSA:2.60.120.650 | Cupin | 241 | 590 | 1.0E-170 |
| 10 | g12953.t4 | Gene3D | G3DSA:1.20.58.1370 | - | 591 | 734 | 2.2E-62 |
| 9 | g12953.t4 | Gene3D | G3DSA:2.10.110.20 | - | 659 | 720 | 2.2E-62 |
| 7 | g12953.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 385 | 415 | - |
| 6 | g12953.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 393 | 415 | - |
| 2 | g12953.t4 | PANTHER | PTHR14017:SF5 | LYSINE-SPECIFIC DEMETHYLASE 6B | 266 | 736 | 1.6E-230 |
| 3 | g12953.t4 | PANTHER | PTHR14017 | LYSINE-SPECIFIC DEMETHYLASE | 266 | 736 | 1.6E-230 |
| 1 | g12953.t4 | Pfam | PF02373 | JmjC domain, hydroxylase | 478 | 586 | 1.8E-29 |
| 11 | g12953.t4 | ProSiteProfiles | PS51184 | JmjC domain profile. | 440 | 603 | 28.051 |
| 5 | g12953.t4 | SMART | SM00558 | cupin_9 | 440 | 603 | 5.2E-41 |
| 4 | g12953.t4 | SUPERFAMILY | SSF51197 | Clavaminate synthase-like | 291 | 641 | 5.36E-41 |
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:0046872 | metal ion binding | MF |
| GO:0005634 | nucleus | CC |
| GO:0071557 | histone H3-K27 demethylation | BP |
| GO:0071558 | histone H3-tri/di-methyl-lysine-27 demethylase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K11447 (lysine-specific demethylase 6A)
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.
