General information for g8243.t2
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.t2 | isoform | g8243.t2 | 29269021 | 29269771 |
| chr_2 | g8243 | g8243.t2 | exon | g8243.t2.exon1 | 29269021 | 29269582 |
| chr_2 | g8243 | g8243.t2 | cds | g8243.t2.CDS1 | 29269103 | 29269582 |
| chr_2 | g8243 | g8243.t2 | exon | g8243.t2.exon2 | 29269640 | 29269771 |
| chr_2 | g8243 | g8243.t2 | cds | g8243.t2.CDS2 | 29269640 | 29269771 |
| chr_2 | g8243 | g8243.t2 | TTS | g8243.t2 | 29269808 | 29269808 |
| chr_2 | g8243 | g8243.t2 | TSS | g8243.t2 | NA | NA |
Sequences
>g8243.t2 Gene=g8243 Length=694
ATATTTCGCATATGGTTCACCATATTATCTCAAAGAGGGAACCACAAATTTGCATTTAGA
TGTATCAGATGCTTGTAATGTTATGTGTTATATTGGTTTTCCACGTGATAAAGAAAAGTC
AGTTGATGAATATATTGAACAGGGATTTTTAGCCATAATTGATGCCAATTGTGATCAATC
AAATATTGATCGAGTAATACGCGATGGAGAAATTCCTGGTGCAATTTGGCATATTTATGA
AGCAGCTGACACAGATAAAATTCGAGATTTTTTGCTGAAAGTTGCTGTTGAGAAAGGTTT
TAAAGTCGCTCGTGACCATGATGTTATTCACGATCAAAATTGGTATTTAGATAATGAAAT
GAGAAAAAGATTGTATGCAGAATATGGTGTAAAAGGTTATGCGATTGTTCAATGCTTGGG
AGATTGCATTATATTGCCAGCTGGAACACCACATCAAGTTAGAAATATTTATTCATGCAT
CAAAATTGCAGAAGATTTTGTTTCTCCACAGCAAATGGCTCACTGCTTACATTTGAGTGA
AGAATTCCGTAAATTAACAAAAACTCATACAAACAATGAAGAAAAACTTAATATTAAAAA
CATTGCTTATCATAGCATCAAAGAGGCAATTGCTGGATTAATACACGCCGTGAATACAGT
TTATAATGTCGGGACAAAAATGATGAAAAATTAA
>g8243.t2 Gene=g8243 Length=203
MCYIGFPRDKEKSVDEYIEQGFLAIIDANCDQSNIDRVIRDGEIPGAIWHIYEAADTDKI
RDFLLKVAVEKGFKVARDHDVIHDQNWYLDNEMRKRLYAEYGVKGYAIVQCLGDCIILPA
GTPHQVRNIYSCIKIAEDFVSPQQMAHCLHLSEEFRKLTKTHTNNEEKLNIKNIAYHSIK
EAIAGLIHAVNTVYNVGTKMMKN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g8243.t2 | Gene3D | G3DSA:2.60.120.650 | Cupin | 1 | 165 | 0.000 |
| 2 | g8243.t2 | PANTHER | PTHR12549 | JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN | 1 | 186 | 0.000 |
| 3 | g8243.t2 | PANTHER | PTHR12549:SF8 | LYSINE-SPECIFIC DEMETHYLASE 3B | 1 | 186 | 0.000 |
| 1 | g8243.t2 | Pfam | PF02373 | JmjC domain, hydroxylase | 46 | 139 | 0.000 |
| 7 | g8243.t2 | ProSiteProfiles | PS51184 | JmjC domain profile. | 1 | 156 | 18.553 |
| 5 | g8243.t2 | SMART | SM00558 | cupin_9 | 2 | 156 | 0.000 |
| 4 | g8243.t2 | SUPERFAMILY | SSF51197 | Clavaminate synthase-like | 46 | 181 | 0.000 |
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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
