General information for g7572.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been not been annotated.
Parent gene
- The parent gene g7572 is located on chr_2: 24607303..24607644 (- 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 | g7572 | g7572.t1 | TTS | g7572.t1 | 24607241 | 24607241 |
| chr_2 | g7572 | g7572.t1 | isoform | g7572.t1 | 24607303 | 24607644 |
| chr_2 | g7572 | g7572.t1 | exon | g7572.t1.exon1 | 24607303 | 24607454 |
| chr_2 | g7572 | g7572.t1 | cds | g7572.t1.CDS1 | 24607303 | 24607454 |
| chr_2 | g7572 | g7572.t1 | exon | g7572.t1.exon2 | 24607554 | 24607644 |
| chr_2 | g7572 | g7572.t1 | cds | g7572.t1.CDS2 | 24607554 | 24607644 |
| chr_2 | g7572 | g7572.t1 | TSS | g7572.t1 | 24607722 | 24607722 |
Sequences
>g7572.t1 Gene=g7572 Length=243
ATGTCTCGTAAAGAAGCGCTTTCACAATTCATCAATCAAATTCATGGCCGTGCAGTCGTC
GTAAAATTAAATAGCGGTGTTGATTATCGTGGTGTGCTTGCATGTCTCGATGGGTACATG
AATATTGCATTGGATCAAACTGAAGAATACCAAAATGGACAACTCAAGAACAAATATGGA
GATGCGTTCATTCGAGGCAATAACGTTCTTTACATTAGCACGAGTAAACTTGTAAAGAAG
TGA
>g7572.t1 Gene=g7572 Length=80
MSRKEALSQFINQIHGRAVVVKLNSGVDYRGVLACLDGYMNIALDQTEEYQNGQLKNKYG
DAFIRGNNVLYISTSKLVKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g7572.t1 | CDD | cd01726 | LSm6 | 8 | 73 | 0 |
| 6 | g7572.t1 | Gene3D | G3DSA:2.30.30.100 | - | 1 | 77 | 0 |
| 2 | g7572.t1 | PANTHER | PTHR11021:SF1 | U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM6 | 1 | 76 | 0 |
| 3 | g7572.t1 | PANTHER | PTHR11021 | SMALL NUCLEAR RIBONUCLEOPROTEIN F SNRNP-F | 1 | 76 | 0 |
| 7 | g7572.t1 | PIRSF | PIRSF006609 | snRNP_SmF | 2 | 80 | 0 |
| 1 | g7572.t1 | Pfam | PF01423 | LSM domain | 10 | 73 | 0 |
| 5 | g7572.t1 | SMART | SM00651 | Sm3 | 9 | 74 | 0 |
| 4 | g7572.t1 | SUPERFAMILY | SSF50182 | Sm-like ribonucleoproteins | 8 | 74 | 0 |
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:0000398 | mRNA splicing, via spliceosome | BP |
KEGG
Orthology
- This transcript has been annotated with K12625 (U6 snRNA-associated Sm-like protein LSm6)
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.
