General information for g6693.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been not been annotated.
Parent gene
- The parent gene g6693 is located on chr_2: 18088837..18089172 (- 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 | g6693 | g6693.t1 | TTS | g6693.t1 | 18088813 | 18088813 |
| chr_2 | g6693 | g6693.t1 | isoform | g6693.t1 | 18088837 | 18089172 |
| chr_2 | g6693 | g6693.t1 | exon | g6693.t1.exon1 | 18088837 | 18089066 |
| chr_2 | g6693 | g6693.t1 | cds | g6693.t1.CDS1 | 18088837 | 18089066 |
| chr_2 | g6693 | g6693.t1 | exon | g6693.t1.exon2 | 18089124 | 18089172 |
| chr_2 | g6693 | g6693.t1 | cds | g6693.t1.CDS2 | 18089124 | 18089172 |
| chr_2 | g6693 | g6693.t1 | TSS | g6693.t1 | 18089245 | 18089245 |
Sequences
>g6693.t1 Gene=g6693 Length=279
ATGGCTCAAAATGTGACACCAACAAATCAGTCAACCTTATTGCCATTGGAACTTGTTGAT
AAATGCATTGGCTCTCGTATACATATTTTAATGAAAAATGATAAAGAAATGAGCGGCACA
CTCTTGGGATTTGATGATTTTGTAAACATGTTACTTGAAGATGTTACTGAGTTTGAGAAC
ACACCCGAAGGAAAAAGAATTACAAAATTGGATCAAATTCTTTTAAATGGAAATAACATT
ACAATGCTTGTTCCTGGTGGCTTTGATATGTCAGAATAA
>g6693.t1 Gene=g6693 Length=92
MAQNVTPTNQSTLLPLELVDKCIGSRIHILMKNDKEMSGTLLGFDDFVNMLLEDVTEFEN
TPEGKRITKLDQILLNGNNITMLVPGGFDMSE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g6693.t1 | CDD | cd01732 | LSm5 | 12 | 87 | 0 |
| 6 | g6693.t1 | Gene3D | G3DSA:2.30.30.100 | - | 14 | 89 | 0 |
| 2 | g6693.t1 | PANTHER | PTHR20971:SF2 | U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM5 | 1 | 87 | 0 |
| 3 | g6693.t1 | PANTHER | PTHR20971 | U6 SNRNA-ASSOCIATED PROTEIN | 1 | 87 | 0 |
| 1 | g6693.t1 | Pfam | PF01423 | LSM domain | 18 | 85 | 0 |
| 5 | g6693.t1 | SMART | SM00651 | Sm3 | 17 | 85 | 0 |
| 4 | g6693.t1 | SUPERFAMILY | SSF50182 | Sm-like ribonucleoproteins | 12 | 85 | 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 transcript has been annotated with K12624 (U6 snRNA-associated Sm-like protein LSm5)
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.
