General information for g10111.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative U6 snRNA-associated Sm-like protein LSm1.
Parent gene
- The parent gene g10111 is located on chr_1: 7481617..7482070 (- 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 | g10111 | g10111.t1 | TTS | g10111.t1 | 7481414 | 7481414 |
| chr_1 | g10111 | g10111.t1 | isoform | g10111.t1 | 7481617 | 7482070 |
| chr_1 | g10111 | g10111.t1 | exon | g10111.t1.exon1 | 7481617 | 7481879 |
| chr_1 | g10111 | g10111.t1 | cds | g10111.t1.CDS1 | 7481617 | 7481879 |
| chr_1 | g10111 | g10111.t1 | exon | g10111.t1.exon2 | 7481938 | 7482070 |
| chr_1 | g10111 | g10111.t1 | cds | g10111.t1.CDS2 | 7481938 | 7482070 |
| chr_1 | g10111 | g10111.t1 | TSS | g10111.t1 | 7482143 | 7482143 |
Sequences
>g10111.t1 Gene=g10111 Length=396
ATGGAGAATACGGCACATTTACTGAATGAAATAGATAAAAAACTAATGATATTACTTAGA
GATGGTAGAACTTTAATTGGATATCTTCGTTCAGTAGATCAATTTGCGAATTTAGTGCTG
CATCGAGCAATCGAAAGAATTCATGTCGGTACTCAATATGGAGATATGGAACGTGGTGTA
TTTATAATACGTGGCGAAAATGTAGTATTACTTGGTGAAATTGATCGAGAGAAAGAAGAA
CAACTTAATAGCAAATTAACACAAGTTTCAGTAGAAGAAATTCTTGATGCACAACGAAGA
GAAATTGAATCAAAGCAGGAAAAGAATGCAATACTTCGACAACGTTTAAAACAACGAGGA
ATCAATAATAACCCATTGCTCGAAGATAATGAGTAA
>g10111.t1 Gene=g10111 Length=131
MENTAHLLNEIDKKLMILLRDGRTLIGYLRSVDQFANLVLHRAIERIHVGTQYGDMERGV
FIIRGENVVLLGEIDREKEEQLNSKLTQVSVEEILDAQRREIESKQEKNAILRQRLKQRG
INNNPLLEDNE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g10111.t1 | CDD | cd01728 | LSm1 | 4 | 74 | 9.40653E-39 |
| 7 | g10111.t1 | Coils | Coil | Coil | 95 | 115 | - |
| 6 | g10111.t1 | Gene3D | G3DSA:2.30.30.100 | - | 4 | 130 | 7.7E-38 |
| 2 | g10111.t1 | PANTHER | PTHR15588:SF8 | U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM1 | 3 | 125 | 3.6E-48 |
| 3 | g10111.t1 | PANTHER | PTHR15588 | LSM1 | 3 | 125 | 3.6E-48 |
| 1 | g10111.t1 | Pfam | PF01423 | LSM domain | 8 | 72 | 6.3E-16 |
| 5 | g10111.t1 | SMART | SM00651 | Sm3 | 5 | 73 | 3.1E-15 |
| 4 | g10111.t1 | SUPERFAMILY | SSF50182 | Sm-like ribonucleoproteins | 7 | 93 | 2.86E-19 |
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:0000956 | nuclear-transcribed mRNA catabolic process | BP |
KEGG
Orthology
- This transcript has been annotated with K12620 (U6 snRNA-associated Sm-like protein LSm1)
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.
