General information for g12953.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
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.t6 | TSS | g12953.t6 | 27134318 | 27134318 |
| chr_1 | g12953 | g12953.t6 | isoform | g12953.t6 | 27134389 | 27136149 |
| chr_1 | g12953 | g12953.t6 | exon | g12953.t6.exon1 | 27134389 | 27134410 |
| chr_1 | g12953 | g12953.t6 | exon | g12953.t6.exon2 | 27134639 | 27134785 |
| chr_1 | g12953 | g12953.t6 | cds | g12953.t6.CDS1 | 27134777 | 27134785 |
| chr_1 | g12953 | g12953.t6 | exon | g12953.t6.exon3 | 27134874 | 27135246 |
| chr_1 | g12953 | g12953.t6 | cds | g12953.t6.CDS2 | 27134874 | 27135246 |
| chr_1 | g12953 | g12953.t6 | exon | g12953.t6.exon4 | 27135523 | 27135853 |
| chr_1 | g12953 | g12953.t6 | cds | g12953.t6.CDS3 | 27135523 | 27135853 |
| chr_1 | g12953 | g12953.t6 | exon | g12953.t6.exon5 | 27135919 | 27136149 |
| chr_1 | g12953 | g12953.t6 | cds | g12953.t6.CDS4 | 27135919 | 27136147 |
| chr_1 | g12953 | g12953.t6 | TTS | g12953.t6 | NA | NA |
Sequences
>g12953.t6 Gene=g12953 Length=1104
AAATATTAGATTTAGGTTTAAGACAAATTCATCAGCACCACCGCCTTATCCACAACAAGG
CAATGCAATTCCAGCAAAGAGATTTAAACATGGTGAGGACCAGCAGCAGCAACCACCAAT
TGCACGTCCTCCATTCTATCTTACCCCGCAACAACTTCAAATGCTTCAGGCGTTGCAGAA
TACACCAAATCTTACGCCACAGCAACAAAATGCTTTGCAACAGCTGACACATCAATTTAA
ATTAATGCAACAACATCAACAGCAATTGAGATTACAGCAAGCACAGCTTCGTGGAGGTGG
ATTGCCAATTCGAGGTCAACCACCGCAAGCTCAACAATTTCCACAACAAAATCCAACAAA
TTTTCCAACACAGCCAATTGGTAATAGAACACCACAATCAGGAACTACTGCACAAACTGG
ATTTATGAATGATGGAAGTTTTTCACCTGCAACTGGTCATTCACAAGCTGGCATGCCATT
TAAATCAGCTGGTGGTTTTCAACAACAGCAAATCACATCGACAACGAACAATCAAGATTT
AAATGTAAGCGATCAAGAACTTCAAGCTTTGTTATCTCAACGTGATCTCACAACAACTTT
TGCTGAAAATATTTTAAAACAAATTGAAAATGAAGAGCCAATTGATTCAAAAACCAAATT
GCATGAAACACTCAATGTAGATGCCATTAATCAACGAAATAATAAATCACCAACGATAAA
ATGCGAAGCGACATCAACATCGACGCAGGCTCTTTTAAATAAACATGACATAAAATCAGA
GCCGGTTGTTAAAATTGAAAAATTGGTTGAGTTTGATAATAAAGTTGAATTCCATAATAA
AATGACAGCAAAGGAAGTTTTTGAGACAGTAAAAAGAATGGATAACAGTGAATGTCCATC
AACGTGTTCAGTTTTGGCACTTGATTTACCACCACCTAGTCCACCTGAAAATCCAACACC
ACACCGTCTCACACGTGATCAACTTCTTCCACCAACTCCATCAGTATTTCTAGAAAATAA
AAAACACGCGTTTAGTCCGCAGTTACAAGAATTTTGCTTAAAGCATCCAATTGCTGTTGT
TAGACAAATGGCATCAGCTTTAAA
>g12953.t6 Gene=g12953 Length=314
MLQALQNTPNLTPQQQNALQQLTHQFKLMQQHQQQLRLQQAQLRGGGLPIRGQPPQAQQF
PQQNPTNFPTQPIGNRTPQSGTTAQTGFMNDGSFSPATGHSQAGMPFKSAGGFQQQQITS
TTNNQDLNVSDQELQALLSQRDLTTTFAENILKQIENEEPIDSKTKLHETLNVDAINQRN
NKSPTIKCEATSTSTQALLNKHDIKSEPVVKIEKLVEFDNKVEFHNKMTAKEVFETVKRM
DNSECPSTCSVLALDLPPPSPPENPTPHRLTRDQLLPPTPSVFLENKKHAFSPQLQEFCL
KHPIAVVRQMASAL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g12953.t6 | Gene3D | G3DSA:2.60.120.650 | Cupin | 241 | 314 | 0 |
| 1 | g12953.t6 | PANTHER | PTHR14017 | LYSINE-SPECIFIC DEMETHYLASE | 2 | 314 | 0 |
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. There were no conditions that were differentially expressed