General information for g2339.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 g2339 is located on chr_3: 16907624..16909276 (+ 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 | g2339 | g2339.t1 | isoform | g2339.t1 | 16905306 | 16907624 |
| chr_3 | g2339 | g2339.t1 | exon | g2339.t1.exon1 | 16905306 | 16905335 |
| chr_3 | g2339 | g2339.t1 | cds | g2339.t1.CDS1 | 16905306 | 16905335 |
| chr_3 | g2339 | g2339.t1 | exon | g2339.t1.exon2 | 16905402 | 16906013 |
| chr_3 | g2339 | g2339.t1 | cds | g2339.t1.CDS2 | 16905402 | 16906013 |
| chr_3 | g2339 | g2339.t1 | exon | g2339.t1.exon3 | 16906071 | 16907624 |
| chr_3 | g2339 | g2339.t1 | cds | g2339.t1.CDS3 | 16906071 | 16907624 |
| chr_3 | g2339 | g2339.t1 | TSS | g2339.t1 | NA | NA |
| chr_3 | g2339 | g2339.t1 | TTS | g2339.t1 | NA | NA |
Sequences
>g2339.t1 Gene=g2339 Length=2196
ATGAATAATAATTCAGATCAAAGCACAACGAATCAAAGCGTTTTCATAAATTTCATTTCT
GCCGGAATAAAGCGCAAAAATAATGATACGGAAAAAGAAACTGATCTGAACGAAAACAAA
AATCCAAAATTACAAAATGAATCAGATTCACATTCGGTAAGCAGTTTTGATTATGATGAT
TTGATAACTTATAGTCCGGAAAGTTTCGATGCACAAGATGATGAAGATATGCTTCGTGAT
CGGGAAGAATTTTTACAATTTGAGAATTGCTTTAACACATCTTTGCACATACCTCAATGT
ACAGAATGCCGATTAAATAAGGATTGTCATAAATATAACTGCAGATTTTACAAATTTCGA
AAAATAGAACGAGATAATGGCTTTTGTCGTGTCGTTGGATTTTCTGACGAAATCTCTGAA
TCAATACAAATTGCTGATATCGATTTATGGCGCCAATCTGATCCAAGTATTTTAAGAGAT
TGCGATTTAGTATCAAGAAAAAATATTTTACGCTGTGTTGCCTCACAATTTTGTGATTTG
GTTAAAGAAGAAGAGAATGTGCATAAATCATACATCATAAACAAAAAGGATCCTGTTTTA
GCGTGGAAAAGAGCTTTATATAAAATCAGAGAAATGTGCGATACATGTTCAACAAGTATT
TTTAATTTTCACTTTGTCTGCACAGAATGTGGTACAGTAGTTTGTATTGATTGTTTTAAA
GAACGAAATGAAGGTCAAATTATACAAAAATTATCAAAATCAGAAAAAGAGGAGCGCGAT
GACTTTTTTTGGTTGAAATGTACTGACGAAATGCAACACAAAATGATTTTAAGCAAAATG
ATTCCAGGCAATATTCTTTCAAAAATTAATGAACAACTTCATAAATACTGCGATTCTCAG
AAGATAGAACTTTTGTGTTCATGTCGAGATGACGATATTCCACCACTTTCACCATTTGAT
AAATTAGATTATCAGCGAAATATTCAGATAAAGAGAAGAAAAAAAATTCGAAGACAAATC
GTTCGCAGAAGAAGTATTCTAGATTTTGAACAAAATTTAAAGTTAATACATCATACTTAT
ATATCACAACAAAGTGTGCTGAAATTTGAAAGTCCATCAGAATCATCTGAGAGTTATTCA
ATATTTCAATGCGAATGGGAAAGATCTAAGCCAATTGTGGTAGCAAATGTTAAACTTAAT
AAAACTATTTGGAGACCTCAATATTTTCTTGAGAAGTTTGGTTCAGTCAGACACTCACTT
GTAAATTGTCAAGCAGATCAAGTGATAAAACGAGTTCCTATGAGAGATTTTTGGCTTGGA
TTTGAATCATACAAAAATCGATTGCCTCATAACAGCCAAAATAAAATGATTTTGAAGCTT
AAAGATTGGCCAGATACTCAAGATTTCGCAGATGTACTACAAGAACATTATAACGATTTA
ATGAACTCCATTCCATTTAAATTATACACACGTCGCAATGGAATATTCAATTTAGCCAAA
TATCAGCATTTGCATTTTTTGAAACCCGACCTCGGTCCAAAAATTTATTCCGCGTATGGA
AATTTTGAAAAAACGACAGTAATGAGAGCCTCAACTAATTTACATCTTGATATATCTGAT
GCTGTCAATATTCTTGCACATGTAAGTCGACCCGAAGATTATAAATTAGCAAATAAGCAA
TACGATAAAGAAGAAATAAGTAAAGTCCTCGAACAATTAGGATGTGATGAAGCTGATTTA
CAAACATTTATGACAAGTAATAAATTACCAGGAGCACTTTGGTTAATGTTTCATTCAACT
GATGTCAATAAACTTCGAAATGCTTTACGCGAATATGCCAAAGAGAACAATATACCACTG
AAATCAAAGGAAGATCCGATCCATAATCAAGACTGGTATGTAGATGTAAAGTTAAAAAGA
GCACTTGAAAAAAAGGGTATTCGTTCGTATAGTATCATTCAATATGAAGGTGATTGCGTT
TTTATTCCTGCAAAAACACCACATCAAGTTACCAACATATTTGATTGCATTAAAATAGCA
TTAGACTTTGTGTCGCCTGAGAACGTTGTCGAATGCATCAATCTCACAAATGAATTTAGA
TTATTAAGCTCAAAACACGTTAATCGTGAAGATAAGTTGCAAATTAAATCCATTTTGTAT
CATACAATTAAAAATTTAGTACAGCCTACAAATTAA
>g2339.t1 Gene=g2339 Length=731
MNNNSDQSTTNQSVFINFISAGIKRKNNDTEKETDLNENKNPKLQNESDSHSVSSFDYDD
LITYSPESFDAQDDEDMLRDREEFLQFENCFNTSLHIPQCTECRLNKDCHKYNCRFYKFR
KIERDNGFCRVVGFSDEISESIQIADIDLWRQSDPSILRDCDLVSRKNILRCVASQFCDL
VKEEENVHKSYIINKKDPVLAWKRALYKIREMCDTCSTSIFNFHFVCTECGTVVCIDCFK
ERNEGQIIQKLSKSEKEERDDFFWLKCTDEMQHKMILSKMIPGNILSKINEQLHKYCDSQ
KIELLCSCRDDDIPPLSPFDKLDYQRNIQIKRRKKIRRQIVRRRSILDFEQNLKLIHHTY
ISQQSVLKFESPSESSESYSIFQCEWERSKPIVVANVKLNKTIWRPQYFLEKFGSVRHSL
VNCQADQVIKRVPMRDFWLGFESYKNRLPHNSQNKMILKLKDWPDTQDFADVLQEHYNDL
MNSIPFKLYTRRNGIFNLAKYQHLHFLKPDLGPKIYSAYGNFEKTTVMRASTNLHLDISD
AVNILAHVSRPEDYKLANKQYDKEEISKVLEQLGCDEADLQTFMTSNKLPGALWLMFHST
DVNKLRNALREYAKENNIPLKSKEDPIHNQDWYVDVKLKRALEKKGIRSYSIIQYEGDCV
FIPAKTPHQVTNIFDCIKIALDFVSPENVVECINLTNEFRLLSSKHVNREDKLQIKSILY
HTIKNLVQPTN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g2339.t1 | Gene3D | G3DSA:2.60.120.650 | Cupin | 356 | 708 | 1.3E-109 |
| 8 | g2339.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 27 | 53 | - |
| 9 | g2339.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 27 | 45 | - |
| 2 | g2339.t1 | PANTHER | PTHR12549 | JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN | 81 | 295 | 6.7E-135 |
| 4 | g2339.t1 | PANTHER | PTHR12549:SF8 | LYSINE-SPECIFIC DEMETHYLASE 3B | 81 | 295 | 6.7E-135 |
| 3 | g2339.t1 | PANTHER | PTHR12549 | JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN | 356 | 727 | 6.7E-135 |
| 5 | g2339.t1 | PANTHER | PTHR12549:SF8 | LYSINE-SPECIFIC DEMETHYLASE 3B | 356 | 727 | 6.7E-135 |
| 1 | g2339.t1 | Pfam | PF02373 | JmjC domain, hydroxylase | 593 | 683 | 3.0E-13 |
| 11 | g2339.t1 | ProSiteProfiles | PS51184 | JmjC domain profile. | 461 | 700 | 20.638 |
| 7 | g2339.t1 | SMART | SM00558 | cupin_9 | 473 | 700 | 1.3E-36 |
| 6 | g2339.t1 | SUPERFAMILY | SSF51197 | Clavaminate synthase-like | 378 | 722 | 2.75E-27 |
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.
