General information for g2339.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Lysine-specific demethylase 3B.
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.t2 | isoform | g2339.t2 | 16906835 | 16907712 |
| chr_3 | g2339 | g2339.t2 | exon | g2339.t2.exon1 | 16906835 | 16907712 |
| chr_3 | g2339 | g2339.t2 | cds | g2339.t2.CDS1 | 16906869 | 16907624 |
| chr_3 | g2339 | g2339.t2 | TSS | g2339.t2 | NA | NA |
| chr_3 | g2339 | g2339.t2 | TTS | g2339.t2 | NA | NA |
Sequences
>g2339.t2 Gene=g2339 Length=878
CGCAGATGTACTACAAGAACATTATAACGATTTAATGAACTCCATTCCATTTAAATTATA
CACACGTCGCAATGGAATATTCAATTTAGCCAAATATCAGCATTTGCATTTTTTGAAACC
CGACCTCGGTCCAAAAATTTATTCCGCGTATGGAAATTTTGAAAAAACGACAGTAATGAG
AGCCTCAACTAATTTACATCTTGATATATCTGATGCTGTCAATATTCTTGCACATGTAAG
TCGACCCGAAGATTATAAATTAGCAAATAAGCAATACGATAAAGAAGAAATAAGTAAAGT
CCTCGAACAATTAGGATGTGATGAAGCTGATTTACAAACATTTATGACAAGTAATAAATT
ACCAGGAGCACTTTGGTTAATGTTTCATTCAACTGATGTCAATAAACTTCGAAATGCTTT
ACGCGAATATGCCAAAGAGAACAATATACCACTGAAATCAAAGGAAGATCCGATCCATAA
TCAAGACTGGTATGTAGATGTAAAGTTAAAAAGAGCACTTGAAAAAAAGGGTATTCGTTC
GTATAGTATCATTCAATATGAAGGTGATTGCGTTTTTATTCCTGCAAAAACACCACATCA
AGTTACCAACATATTTGATTGCATTAAAATAGCATTAGACTTTGTGTCGCCTGAGAACGT
TGTCGAATGCATCAATCTCACAAATGAATTTAGATTATTAAGCTCAAAACACGTTAATCG
TGAAGATAAGTTGCAAATTAAATCCATTTTGTATCATACAATTAAAAATTTAGTACAGCC
TACAAATTAAACGATAAAATAATTTTTCTTCCAATTTATTCAATAAATAAAGAACAACTG
CTGAATTTTAAAAATTTAAACATGTAATGTTTTCAAAT
>g2339.t2 Gene=g2339 Length=251
MNSIPFKLYTRRNGIFNLAKYQHLHFLKPDLGPKIYSAYGNFEKTTVMRASTNLHLDISD
AVNILAHVSRPEDYKLANKQYDKEEISKVLEQLGCDEADLQTFMTSNKLPGALWLMFHST
DVNKLRNALREYAKENNIPLKSKEDPIHNQDWYVDVKLKRALEKKGIRSYSIIQYEGDCV
FIPAKTPHQVTNIFDCIKIALDFVSPENVVECINLTNEFRLLSSKHVNREDKLQIKSILY
HTIKNLVQPTN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g2339.t2 | Gene3D | G3DSA:2.60.120.650 | Cupin | 1 | 228 | 0.000 |
| 2 | g2339.t2 | PANTHER | PTHR12549:SF11 | JMJC DOMAIN-CONTAINING HISTONE DEMETHYLASE 2, ISOFORM A | 1 | 247 | 0.000 |
| 3 | g2339.t2 | PANTHER | PTHR12549 | JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN | 1 | 247 | 0.000 |
| 1 | g2339.t2 | Pfam | PF02373 | JmjC domain, hydroxylase | 112 | 203 | 0.000 |
| 7 | g2339.t2 | ProSiteProfiles | PS51184 | JmjC domain profile. | 7 | 220 | 20.503 |
| 5 | g2339.t2 | SMART | SM00558 | cupin_9 | 1 | 220 | 0.000 |
| 4 | g2339.t2 | SUPERFAMILY | SSF51197 | Clavaminate synthase-like | 43 | 242 | 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.
