General information for g445.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been not been annotated.
Parent gene
- The parent gene g445 is located on chr_3: 3376061..3376414 (- 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 | g445 | g445.t1 | TTS | g445.t1 | 3375874 | 3375874 |
| chr_3 | g445 | g445.t1 | isoform | g445.t1 | 3376061 | 3376414 |
| chr_3 | g445 | g445.t1 | exon | g445.t1.exon1 | 3376061 | 3376266 |
| chr_3 | g445 | g445.t1 | cds | g445.t1.CDS1 | 3376061 | 3376266 |
| chr_3 | g445 | g445.t1 | exon | g445.t1.exon2 | 3376330 | 3376414 |
| chr_3 | g445 | g445.t1 | cds | g445.t1.CDS2 | 3376330 | 3376414 |
| chr_3 | g445 | g445.t1 | TSS | g445.t1 | 3376480 | 3376480 |
Sequences
>g445.t1 Gene=g445 Length=291
ATGTCTGGGAGTTTAGAATCATTTGTAGGACAATCAGTAATGATTATAAGTTGCGATGGA
AGGTGTTTTAGTGGCACATTAAAAGGCTTTGATCAATTAATAAATTTAATTCTTGTCGAT
ACGCATGAAAGAATATACTCAACAACTGCCGGAATGGAGCAAATAAATCTCGGGTTAAAA
ATCATTCGTGGTGATAATGTAGCAGTAATTGGATTAATCGATGAAGCGGTAGAACAAGAA
ATTGATTATCAGAAAATTCGAGGTGAACAACTTAATCCTGTTGTCCATTAA
>g445.t1 Gene=g445 Length=96
MSGSLESFVGQSVMIISCDGRCFSGTLKGFDQLINLILVDTHERIYSTTAGMEQINLGLK
IIRGDNVAVIGLIDEAVEQEIDYQKIRGEQLNPVVH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g445.t1 | CDD | cd01727 | LSm8 | 2 | 92 | 0 |
| 6 | g445.t1 | Gene3D | G3DSA:2.30.30.100 | - | 3 | 94 | 0 |
| 2 | g445.t1 | PANTHER | PTHR15588:SF9 | U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM8 | 1 | 96 | 0 |
| 3 | g445.t1 | PANTHER | PTHR15588 | LSM1 | 1 | 96 | 0 |
| 1 | g445.t1 | Pfam | PF01423 | LSM domain | 5 | 71 | 0 |
| 5 | g445.t1 | SMART | SM00651 | Sm3 | 3 | 72 | 0 |
| 4 | g445.t1 | SUPERFAMILY | SSF50182 | Sm-like ribonucleoproteins | 3 | 79 | 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 |
| GO:0005688 | U6 snRNP | CC |
| GO:0046540 | U4/U6 x U5 tri-snRNP complex | CC |
KEGG
Orthology
- This transcript has been annotated with K12627 (U6 snRNA-associated Sm-like protein LSm8)
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.
