General information for g12953.t1
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.t1 | TSS | g12953.t1 | 27115752 | 27115752 |
| chr_1 | g12953 | g12953.t1 | isoform | g12953.t1 | 27115897 | 27138854 |
| chr_1 | g12953 | g12953.t1 | exon | g12953.t1.exon1 | 27115897 | 27115967 |
| chr_1 | g12953 | g12953.t1 | cds | g12953.t1.CDS1 | 27115897 | 27115967 |
| chr_1 | g12953 | g12953.t1 | exon | g12953.t1.exon2 | 27116033 | 27116099 |
| chr_1 | g12953 | g12953.t1 | cds | g12953.t1.CDS2 | 27116033 | 27116099 |
| chr_1 | g12953 | g12953.t1 | exon | g12953.t1.exon3 | 27116195 | 27116549 |
| chr_1 | g12953 | g12953.t1 | cds | g12953.t1.CDS3 | 27116195 | 27116549 |
| chr_1 | g12953 | g12953.t1 | exon | g12953.t1.exon4 | 27116615 | 27116723 |
| chr_1 | g12953 | g12953.t1 | cds | g12953.t1.CDS4 | 27116615 | 27116723 |
| chr_1 | g12953 | g12953.t1 | exon | g12953.t1.exon5 | 27133219 | 27133397 |
| chr_1 | g12953 | g12953.t1 | cds | g12953.t1.CDS5 | 27133219 | 27133397 |
| chr_1 | g12953 | g12953.t1 | exon | g12953.t1.exon6 | 27133455 | 27134242 |
| chr_1 | g12953 | g12953.t1 | cds | g12953.t1.CDS6 | 27133455 | 27134242 |
| chr_1 | g12953 | g12953.t1 | exon | g12953.t1.exon7 | 27134639 | 27134785 |
| chr_1 | g12953 | g12953.t1 | cds | g12953.t1.CDS7 | 27134639 | 27134785 |
| chr_1 | g12953 | g12953.t1 | exon | g12953.t1.exon8 | 27134874 | 27135246 |
| chr_1 | g12953 | g12953.t1 | cds | g12953.t1.CDS8 | 27134874 | 27135246 |
| chr_1 | g12953 | g12953.t1 | exon | g12953.t1.exon9 | 27135523 | 27135853 |
| chr_1 | g12953 | g12953.t1 | cds | g12953.t1.CDS9 | 27135523 | 27135853 |
| chr_1 | g12953 | g12953.t1 | exon | g12953.t1.exon10 | 27135919 | 27136154 |
| chr_1 | g12953 | g12953.t1 | cds | g12953.t1.CDS10 | 27135919 | 27136154 |
| chr_1 | g12953 | g12953.t1 | exon | g12953.t1.exon11 | 27136324 | 27136529 |
| chr_1 | g12953 | g12953.t1 | cds | g12953.t1.CDS11 | 27136324 | 27136529 |
| chr_1 | g12953 | g12953.t1 | exon | g12953.t1.exon12 | 27136786 | 27136913 |
| chr_1 | g12953 | g12953.t1 | cds | g12953.t1.CDS12 | 27136786 | 27136913 |
| chr_1 | g12953 | g12953.t1 | exon | g12953.t1.exon13 | 27137506 | 27137925 |
| chr_1 | g12953 | g12953.t1 | cds | g12953.t1.CDS13 | 27137506 | 27137925 |
| chr_1 | g12953 | g12953.t1 | exon | g12953.t1.exon14 | 27138123 | 27138332 |
| chr_1 | g12953 | g12953.t1 | cds | g12953.t1.CDS14 | 27138123 | 27138332 |
| chr_1 | g12953 | g12953.t1 | exon | g12953.t1.exon15 | 27138400 | 27138526 |
| chr_1 | g12953 | g12953.t1 | cds | g12953.t1.CDS15 | 27138400 | 27138526 |
| chr_1 | g12953 | g12953.t1 | exon | g12953.t1.exon16 | 27138594 | 27138854 |
| chr_1 | g12953 | g12953.t1 | cds | g12953.t1.CDS16 | 27138594 | 27138854 |
| chr_1 | g12953 | g12953.t1 | TTS | g12953.t1 | 27138947 | 27138947 |
Sequences
>g12953.t1 Gene=g12953 Length=4008
ATGATATTAGAAAACGAGGAAAATGAAAATTTATCATCATACGAGTTGATCAATTTACAG
AGTTTAGATAGCCGCCAATTTGGGTTCTTTAAGTTAAATGCACCAGAGAATGCAAAAAAG
AAAGTTTGGGTGCTTAAAGCAATAAAATATTTGGAGCAAATTCTCATAGAGGCACAAGCT
CGAAAACTTCTTAGTGAACACATAAAACCGGTGCCTAAAAATGAACAACTTCAGCCAGAG
AAAACATCAACTCCTGCACCAATGGAAGTCGATCAAAATGTTAGTGAGTCAGAAAAGAAA
GAAGAAAGTGAGGACGTTGAAATGAAGGATGATGAAAAGAAAGAGGCAATAGTTGATGAA
ACAAAACCGTCTGCTGCAAGTGAAGAAAATAGTAATAATAATAATGAACCGGATGAAGTC
ACAATTGATATTGACCCAAAAACTTATTGCAAATTAGGACATTTTCACTTGTTGCTTGGT
GATTTTGCAAAAGCATTGTCAGCATATCAAAAGTACAAAAGTCTTCGTTATGATTATTGG
AAGGATACTGCTTTCCTATATGGCCTTGGAATTGTTTATCAACATTATAATGCCTTTCGA
TGGTCTGTTCGAGCATTTCAAGAATTGCTATACGTGTGTCCTGACTTTCAACGCGCCAAC
GAAGCTCATTTGCGACTTGGTTTCCTCTTTAAGGTAGTTGGTGATTACGAGAGAAGTCTT
AAACATTATCAACTTGCTTTAATTGATCAAAGATCAAGTTGTACATTTACACCATTAGAA
ATAAAATTTCATATCGCACATCTGTATGAAGTGCAAAACAACTATAAAAAGGCAAAAGAA
GGTTATGAGCAGTTGCTGGGTGATAAACAGTTGACACAGCAACTTAAAGCTGACGTTTGT
AGGCAATTGGGATGGATGCTGCATTGCGTTGATAATTTAGGTGAAAAGAGACAACGTGAA
ACTGTTGCAATCCATTGTTTACAGAAATCAATTGAATCAGATCCAAAATCAGGACAATCA
TTATATTTACTTGGAAGGTGTTTTGCTGCCTTTAATAAAGTTCATGATGCATTTATAGCC
TATCGCAATTCAGTAGAAAAGAGCGAAGGCAACGCAGATACATGGTGCTCCATTGGAGTA
CTCTATCAGCAGCAGAATCAGCCTATGGATGCATTGCAGGCTTACATATGTGCCGTGCAA
TTAGATAAAAGTCATTCTGCCGCTTGGACAAATTTGGGAATTTTATATGAATCTTGCGGT
CAACCGCGTGATGCATTTGCATGTTATTTGAATGCAACAAAAGGTGAAAATAGTTCGAAG
GAAGTTCAAAATCTGTCAATTAGTAGTAGCAACAGTACAACAAGCAATTTAAAAGAATTA
CCGTCAACCACAATTGGTTCAAAACCACAAACACTACAGCAGAGAATAAAGTTTCTGCAA
ACTAACTTGGCGCAAGCTCCTATGCCATCAATCACATCTAAACGACGCCAGTTACCTTCA
ATTGAGGAGGCCTGGAATCTACCTATTTCGAATGAAATGAGTTCACGACAGCAGAGGCAA
TTGCAAAAAACAAATTCATCAGCACCACCGCCTTATCCACAACAAGGCAATGCAATTCCA
GCAAAGAGATTTAAACATGGTGAGGACCAGCAGCAGCAACCACCAATTGCACGTCCTCCA
TTCTATCTTACCCCGCAACAACTTCAAATGCTTCAGGCGTTGCAGAATACACCAAATCTT
ACGCCACAGCAACAAAATGCTTTGCAACAGCTGACACATCAATTTAAATTAATGCAACAA
CATCAACAGCAATTGAGATTACAGCAAGCACAGCTTCGTGGAGGTGGATTGCCAATTCGA
GGTCAACCACCGCAAGCTCAACAATTTCCACAACAAAATCCAACAAATTTTCCAACACAG
CCAATTGGTAATAGAACACCACAATCAGGAACTACTGCACAAACTGGATTTATGAATGAT
GGAAGTTTTTCACCTGCAACTGGTCATTCACAAGCTGGCATGCCATTTAAATCAGCTGGT
GGTTTTCAACAACAGCAAATCACATCGACAACGAACAATCAAGATTTAAATGTAAGCGAT
CAAGAACTTCAAGCTTTGTTATCTCAACGTGATCTCACAACAACTTTTGCTGAAAATATT
TTAAAACAAATTGAAAATGAAGAGCCAATTGATTCAAAAACCAAATTGCATGAAACACTC
AATGTAGATGCCATTAATCAACGAAATAATAAATCACCAACGATAAAATGCGAAGCGACA
TCAACATCGACGCAGGCTCTTTTAAATAAACATGACATAAAATCAGAGCCGGTTGTTAAA
ATTGAAAAATTGGTTGAGTTTGATAATAAAGTTGAATTCCATAATAAAATGACAGCAAAG
GAAGTTTTTGAGACAGTAAAAAGAATGGATAACAGTGAATGTCCATCAACGTGTTCAGTT
TTGGCACTTGATTTACCACCACCTAGTCCACCTGAAAATCCAACACCACACCGTCTCACA
CGTGATCAACTTCTTCCACCAACTCCATCAGTATTTCTAGAAAATAAAAAACACGCGTTT
AGTCCGCAGTTACAAGAATTTTGCTTAAAGCATCCAATTGCTGTTGTTAGACAAATGGCA
TCAGCTTTAAAATTAGATTTGGGTTTATTTTCAACAAAAACCCTTGTCGATACCGCACCA
GAACAAACATGTGAAGTTAGAACACAGATGAATCAATCAGCTGATGAAAATTGGGATCCA
CAACATAAGGAACAAGTGTGGGCTTGCGTTTCACATCGATCTCATACAACAATCGCTAAA
TACGCTGCGTATCAAGCATCAACCTTTCATGAAAGCATCAAGGATGAACGTGATAAAGGC
TCAGGAATAAGCACAGTTCCAAATTCAGATTCAGATTCCAAAGATTCTTTTTCGAATGGT
GCAAATGGAAAGAAAACAAAAAGGCTTAAAAATGGCATAAAAATGTTAAAATTCGGAACG
AATGTTGACTTGTCAGATGAACGTAAATGGCGAGCACAACTTAATGAATTACAAAAGCTT
CCACCATTTGCACGTGTTGTGTCAGCTGCAAATATGCTTTCACATGTCGGTCATATGATC
CTTGGCATGAATACTGTACAACTTTATATGAAAGTACCAAACGCACGTACTCCCGGACAT
CAGGAGAATAATAACTTTTGCTCAATTAATATTAATATTGGACCTGGTGATTGCGAATGG
TTTGCAACACCTGATTCGTACTGGGGCGGAATTCAGCAACTTTGTGAAAAGAATAACACC
AATTATTTGCATGGCAGTTGGTGGCCATCGATGGAAGATCTATACAATGCGAATATTCCC
GTCTATCGATTCACACAACGACCGGGTGATCTTGTGTGGGTTAATGCTGGATGTGTTCAT
TGGGTTCAAGCAATTGGCTGGTGTAATAATATAGCATGGAACGTTGGTCCGCTAACAGCA
CGACAGTTTGAGCTCGCTATAGTTCGCTATGAATGGAACAAATTAGAGGCATACAAATCA
ATTGTGCCGATGATTCATCTCAGCTGGAATTTAGCAAGAAATATTAAAGTTTCGGATCCA
AAACTTTATGATCTAATCAAAAATTGTCTCTTGCAAACATTGCGTCATACTATGCAAGTA
CTCGAATGTGTCAAGTCGAAGGGCATTGAAGTAAAATTTCATGGTCGTGCTAAGAATGAA
GCATCACATTATTGTGGCGTGTGTGAGATTGAAGTCTTCAACATTTTGTTCATTCGCGAG
CAAGAAAAGCGTCATGTGGTGCATTGTTTGGGCTGTGCCCGTAAACAATCCCCATCACTT
CAAGGATTTGTGTGTTTGGAGGAATATAAATTGACAGAATTGATGCAAGTTTATGATGCA
TTCATGCTACACAAGCCACCACCACAACCAATGTTTATGCCACCACCAACACCTCAACCG
GCTATTTTACAGCAAATGCAGCAACCAATTCCATCCGTCGTATCGTAA
>g12953.t1 Gene=g12953 Length=1335
MILENEENENLSSYELINLQSLDSRQFGFFKLNAPENAKKKVWVLKAIKYLEQILIEAQA
RKLLSEHIKPVPKNEQLQPEKTSTPAPMEVDQNVSESEKKEESEDVEMKDDEKKEAIVDE
TKPSAASEENSNNNNEPDEVTIDIDPKTYCKLGHFHLLLGDFAKALSAYQKYKSLRYDYW
KDTAFLYGLGIVYQHYNAFRWSVRAFQELLYVCPDFQRANEAHLRLGFLFKVVGDYERSL
KHYQLALIDQRSSCTFTPLEIKFHIAHLYEVQNNYKKAKEGYEQLLGDKQLTQQLKADVC
RQLGWMLHCVDNLGEKRQRETVAIHCLQKSIESDPKSGQSLYLLGRCFAAFNKVHDAFIA
YRNSVEKSEGNADTWCSIGVLYQQQNQPMDALQAYICAVQLDKSHSAAWTNLGILYESCG
QPRDAFACYLNATKGENSSKEVQNLSISSSNSTTSNLKELPSTTIGSKPQTLQQRIKFLQ
TNLAQAPMPSITSKRRQLPSIEEAWNLPISNEMSSRQQRQLQKTNSSAPPPYPQQGNAIP
AKRFKHGEDQQQQPPIARPPFYLTPQQLQMLQALQNTPNLTPQQQNALQQLTHQFKLMQQ
HQQQLRLQQAQLRGGGLPIRGQPPQAQQFPQQNPTNFPTQPIGNRTPQSGTTAQTGFMND
GSFSPATGHSQAGMPFKSAGGFQQQQITSTTNNQDLNVSDQELQALLSQRDLTTTFAENI
LKQIENEEPIDSKTKLHETLNVDAINQRNNKSPTIKCEATSTSTQALLNKHDIKSEPVVK
IEKLVEFDNKVEFHNKMTAKEVFETVKRMDNSECPSTCSVLALDLPPPSPPENPTPHRLT
RDQLLPPTPSVFLENKKHAFSPQLQEFCLKHPIAVVRQMASALKLDLGLFSTKTLVDTAP
EQTCEVRTQMNQSADENWDPQHKEQVWACVSHRSHTTIAKYAAYQASTFHESIKDERDKG
SGISTVPNSDSDSKDSFSNGANGKKTKRLKNGIKMLKFGTNVDLSDERKWRAQLNELQKL
PPFARVVSAANMLSHVGHMILGMNTVQLYMKVPNARTPGHQENNNFCSININIGPGDCEW
FATPDSYWGGIQQLCEKNNTNYLHGSWWPSMEDLYNANIPVYRFTQRPGDLVWVNAGCVH
WVQAIGWCNNIAWNVGPLTARQFELAIVRYEWNKLEAYKSIVPMIHLSWNLARNIKVSDP
KLYDLIKNCLLQTLRHTMQVLECVKSKGIEVKFHGRAKNEASHYCGVCEIEVFNILFIRE
QEKRHVVHCLGCARKQSPSLQGFVCLEEYKLTELMQVYDAFMLHKPPPQPMFMPPPTPQP
AILQQMQQPIPSVVS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 28 | g12953.t1 | Gene3D | G3DSA:1.25.40.10 | - | 133 | 301 | 3.0E-15 |
| 27 | g12953.t1 | Gene3D | G3DSA:1.25.40.10 | - | 302 | 459 | 9.6E-24 |
| 26 | g12953.t1 | Gene3D | G3DSA:2.60.120.650 | Cupin | 810 | 1159 | 3.1E-170 |
| 30 | g12953.t1 | Gene3D | G3DSA:1.20.58.1370 | - | 1160 | 1303 | 5.0E-62 |
| 29 | g12953.t1 | Gene3D | G3DSA:2.10.110.20 | - | 1228 | 1289 | 5.0E-62 |
| 20 | g12953.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 71 | 140 | - |
| 21 | g12953.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 76 | 91 | - |
| 24 | g12953.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 93 | 122 | - |
| 23 | g12953.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 124 | 139 | - |
| 19 | g12953.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 440 | 466 | - |
| 17 | g12953.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 509 | 532 | - |
| 25 | g12953.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 509 | 533 | - |
| 22 | g12953.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 954 | 984 | - |
| 18 | g12953.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 962 | 984 | - |
| 3 | g12953.t1 | PANTHER | PTHR14017 | LYSINE-SPECIFIC DEMETHYLASE | 144 | 739 | 0.0 |
| 5 | g12953.t1 | PANTHER | PTHR14017:SF9 | LYSINE-SPECIFIC DEMETHYLASE 6A | 144 | 739 | 0.0 |
| 4 | g12953.t1 | PANTHER | PTHR14017 | LYSINE-SPECIFIC DEMETHYLASE | 816 | 1304 | 0.0 |
| 6 | g12953.t1 | PANTHER | PTHR14017:SF9 | LYSINE-SPECIFIC DEMETHYLASE 6A | 816 | 1304 | 0.0 |
| 2 | g12953.t1 | Pfam | PF13181 | Tetratricopeptide repeat | 147 | 176 | 0.011 |
| 1 | g12953.t1 | Pfam | PF02373 | JmjC domain, hydroxylase | 1047 | 1155 | 3.9E-29 |
| 36 | g12953.t1 | ProSiteProfiles | PS50005 | TPR repeat profile. | 146 | 179 | 8.231 |
| 39 | g12953.t1 | ProSiteProfiles | PS50293 | TPR repeat region circular profile. | 146 | 439 | 27.383 |
| 34 | g12953.t1 | ProSiteProfiles | PS50005 | TPR repeat profile. | 183 | 216 | 7.139 |
| 33 | g12953.t1 | ProSiteProfiles | PS50005 | TPR repeat profile. | 220 | 253 | 7.641 |
| 32 | g12953.t1 | ProSiteProfiles | PS50005 | TPR repeat profile. | 259 | 292 | 6.018 |
| 31 | g12953.t1 | ProSiteProfiles | PS50005 | TPR repeat profile. | 338 | 371 | 5.93 |
| 37 | g12953.t1 | ProSiteProfiles | PS50005 | TPR repeat profile. | 372 | 405 | 8.732 |
| 35 | g12953.t1 | ProSiteProfiles | PS50005 | TPR repeat profile. | 406 | 439 | 6.608 |
| 38 | g12953.t1 | ProSiteProfiles | PS51184 | JmjC domain profile. | 1009 | 1172 | 28.051 |
| 15 | g12953.t1 | SMART | SM00028 | tpr_5 | 146 | 179 | 0.32 |
| 13 | g12953.t1 | SMART | SM00028 | tpr_5 | 183 | 216 | 34.0 |
| 12 | g12953.t1 | SMART | SM00028 | tpr_5 | 220 | 253 | 38.0 |
| 11 | g12953.t1 | SMART | SM00028 | tpr_5 | 338 | 371 | 24.0 |
| 16 | g12953.t1 | SMART | SM00028 | tpr_5 | 372 | 405 | 0.0016 |
| 14 | g12953.t1 | SMART | SM00028 | tpr_5 | 406 | 439 | 11.0 |
| 10 | g12953.t1 | SMART | SM00558 | cupin_9 | 1009 | 1172 | 5.2E-41 |
| 7 | g12953.t1 | SUPERFAMILY | SSF48452 | TPR-like | 147 | 314 | 6.96E-15 |
| 8 | g12953.t1 | SUPERFAMILY | SSF48452 | TPR-like | 319 | 437 | 3.68E-19 |
| 9 | g12953.t1 | SUPERFAMILY | SSF51197 | Clavaminate synthase-like | 860 | 1210 | 1.07E-40 |
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 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.
