General information for g3316.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Possible lysine-specific histone demethylase 1.
Parent gene
- The parent gene g3316 is located on chr_3: 24518024..24543929 (- 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 | g3316 | g3316.t1 | TTS | g3316.t1 | 24517911 | 24517911 |
| chr_3 | g3316 | g3316.t1 | isoform | g3316.t1 | 24518024 | 24543929 |
| chr_3 | g3316 | g3316.t1 | exon | g3316.t1.exon1 | 24518024 | 24518223 |
| chr_3 | g3316 | g3316.t1 | cds | g3316.t1.CDS1 | 24518024 | 24518223 |
| chr_3 | g3316 | g3316.t1 | exon | g3316.t1.exon2 | 24519185 | 24519541 |
| chr_3 | g3316 | g3316.t1 | cds | g3316.t1.CDS2 | 24519185 | 24519541 |
| chr_3 | g3316 | g3316.t1 | exon | g3316.t1.exon3 | 24536010 | 24536243 |
| chr_3 | g3316 | g3316.t1 | cds | g3316.t1.CDS3 | 24536010 | 24536243 |
| chr_3 | g3316 | g3316.t1 | exon | g3316.t1.exon4 | 24542468 | 24542620 |
| chr_3 | g3316 | g3316.t1 | cds | g3316.t1.CDS4 | 24542468 | 24542620 |
| chr_3 | g3316 | g3316.t1 | exon | g3316.t1.exon5 | 24543836 | 24543929 |
| chr_3 | g3316 | g3316.t1 | cds | g3316.t1.CDS5 | 24543836 | 24543929 |
| chr_3 | g3316 | g3316.t1 | TSS | g3316.t1 | NA | NA |
Sequences
>g3316.t1 Gene=g3316 Length=1038
ATGAATCGGTTTGTGCCACTGCGTCAATCATGCAACGATGCAATTATCATGCAAGAACAC
ATCACATTGCTCCTTACTGCATTGCATTGCATCATTCTGAATGGATACTCATGCGTTCCT
ATTGCACTCAGTCGAGATCTTGATATACGTTTAAATACAGCCGTCAAGAAGATCCGCTAT
TGGGATGGAGGCGTTGAAGTAACGGCAGAAAATTTGAAGACCAATAATTCACAGGTCATT
CATAAAGCTGACATTGTTTTATCGACACTGACACTTGGAGTGCTGAAAATTGCCATTGCA
AAGGAATCAAATCAGTTAAACACTGTCCAGTTTGATCCACCACTACCACAGTGGAAACAA
ACAGCTATTGAACGACTTGGTTTTGGTAATCTCAACAAGGTTGTTCTGTGTTTCGATAAA
ATTTTTTGGGAACCGGACATTAATCTATTTGGACATGTTGGAAGCACAACAGCCAGTCGC
GGTGAACTTTTCTTGTTCTGGAACATTTATCAACTTCCTGTGCTTTTGGCACTCGTTGCC
GGTCAATCAGCATTCATTATGGAAAATGTTTCTGATGACGTAATTGTAGGCCGATGCATT
GCTGTATTGAAAGGCATTTTTGGTGACAAAATGGTTCCGCAACCAAAAGAAACAGTTGTA
ACTCGTTGGCGTGCAGATCCATATGCTCGTGGTTCATATAGTTATGTTTCAGTTGGCTCT
TCTGGCACTGATTATGATCTTTTGGCGTCACCTGTAAAACCGCACAGTGGAAAAGATGAA
AAGAATGCTGAAGGTGAAAATGAAGATGATTCAATTTTGCCACGATTATTCTTTGCTGGT
GAACACACGATTCGAAACTATCCTGCAACAGTACATGGAGCTTTGTTGAGTGGTTTACGC
GAAGCAGGACGAATTGCTGATTATTTTATTGGTAAGATCCCACAAGAGCCTGAAAAACCC
GATTCTGCAACCACAGCTACCGCAGATGATGACGACGTCATATTTTTAGATAATGAACCA
ACTTCATCGAGCAAGTAG
>g3316.t1 Gene=g3316 Length=345
MNRFVPLRQSCNDAIIMQEHITLLLTALHCIILNGYSCVPIALSRDLDIRLNTAVKKIRY
WDGGVEVTAENLKTNNSQVIHKADIVLSTLTLGVLKIAIAKESNQLNTVQFDPPLPQWKQ
TAIERLGFGNLNKVVLCFDKIFWEPDINLFGHVGSTTASRGELFLFWNIYQLPVLLALVA
GQSAFIMENVSDDVIVGRCIAVLKGIFGDKMVPQPKETVVTRWRADPYARGSYSYVSVGS
SGTDYDLLASPVKPHSGKDEKNAEGENEDDSILPRLFFAGEHTIRNYPATVHGALLSGLR
EAGRIADYFIGKIPQEPEKPDSATTATADDDDVIFLDNEPTSSSK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g3316.t1 | Gene3D | G3DSA:3.50.50.60 | - | 46 | 304 | 1.4E-61 |
| 8 | g3316.t1 | Gene3D | G3DSA:3.90.660.10 | - | 126 | 241 | 1.4E-61 |
| 7 | g3316.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 311 | 345 | - |
| 2 | g3316.t1 | PANTHER | PTHR10742 | FLAVIN MONOAMINE OXIDASE | 25 | 309 | 1.8E-94 |
| 3 | g3316.t1 | PANTHER | PTHR10742:SF397 | LYSINE-SPECIFIC HISTONE DEMETHYLASE 1A | 25 | 309 | 1.8E-94 |
| 1 | g3316.t1 | Pfam | PF01593 | Flavin containing amine oxidoreductase | 27 | 305 | 9.3E-76 |
| 10 | g3316.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 20 | - |
| 12 | g3316.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 21 | 43 | - |
| 11 | g3316.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 44 | 345 | - |
| 6 | g3316.t1 | SUPERFAMILY | SSF51905 | FAD/NAD(P)-binding domain | 23 | 309 | 6.48E-35 |
| 5 | g3316.t1 | SUPERFAMILY | SSF54373 | FAD-linked reductases, C-terminal domain | 127 | 235 | 3.47E-31 |
| 4 | g3316.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 21 | 43 | - |
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:0055114 | NA | NA |
| GO:0016491 | oxidoreductase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K11450 ([histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent 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.
