General information for g11624.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Sm-like protein LSM3B.
Parent gene
- The parent gene g11624 is located on chr_1: 17488811..17489329 (+ 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 | g11624 | g11624.t1 | TSS | g11624.t1 | 17488680 | 17488680 |
| chr_1 | g11624 | g11624.t1 | isoform | g11624.t1 | 17488788 | 17489214 |
| chr_1 | g11624 | g11624.t1 | exon | g11624.t1.exon1 | 17488788 | 17488805 |
| chr_1 | g11624 | g11624.t1 | cds | g11624.t1.CDS1 | 17488788 | 17488805 |
| chr_1 | g11624 | g11624.t1 | exon | g11624.t1.exon2 | 17488867 | 17488971 |
| chr_1 | g11624 | g11624.t1 | cds | g11624.t1.CDS2 | 17488867 | 17488971 |
| chr_1 | g11624 | g11624.t1 | exon | g11624.t1.exon3 | 17489035 | 17489214 |
| chr_1 | g11624 | g11624.t1 | cds | g11624.t1.CDS3 | 17489035 | 17489214 |
| chr_1 | g11624 | g11624.t1 | TTS | g11624.t1 | 17489319 | 17489319 |
Sequences
>g11624.t1 Gene=g11624 Length=303
ATGGCTGAAGAAGAACAACTTCCAATTCCTGTAAAAGAACCGCTTGATTTGATCAGATTA
AGTTTGGATGAAAAGATTTATGTCAAACTACGCAATGAGAGAGAGCTGCGAGGTGTTCTT
CATGCATTTGACCAGCATCTTAACATAATTCTCTCTGAAGCCGAAGAGACAATAACACAG
ATTGAAATTGATGAAGAGACCTATGAGGAAGTATATAAGACTACTAAAAGAACAATTCCA
TTTCTTTTTATCAGAGGCGATGCTGTAATCCTTGTTTCACCAAATTCAAGCAAAGTTTTT
TAA
>g11624.t1 Gene=g11624 Length=100
MAEEEQLPIPVKEPLDLIRLSLDEKIYVKLRNERELRGVLHAFDQHLNIILSEAEETITQ
IEIDEETYEEVYKTTKRTIPFLFIRGDAVILVSPNSSKVF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g11624.t1 | CDD | cd01730 | LSm3 | 13 | 94 | 2.64987E-51 |
| 7 | g11624.t1 | Coils | Coil | Coil | 51 | 71 | - |
| 6 | g11624.t1 | Gene3D | G3DSA:2.30.30.100 | - | 5 | 97 | 9.7E-30 |
| 2 | g11624.t1 | PANTHER | PTHR13110 | U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM3 | 1 | 95 | 3.4E-41 |
| 3 | g11624.t1 | PANTHER | PTHR13110:SF13 | U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM3 | 1 | 95 | 3.4E-41 |
| 1 | g11624.t1 | Pfam | PF01423 | LSM domain | 18 | 94 | 4.9E-20 |
| 5 | g11624.t1 | SMART | SM00651 | Sm3 | 16 | 94 | 2.3E-20 |
| 4 | g11624.t1 | SUPERFAMILY | SSF50182 | Sm-like ribonucleoproteins | 13 | 96 | 7.55E-23 |
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:0003723 | RNA binding | MF |
| GO:0000398 | mRNA splicing, via spliceosome | BP |
| GO:0000956 | nuclear-transcribed mRNA catabolic process | BP |
KEGG
Orthology
- This transcript has been annotated with K12622 (U6 snRNA-associated Sm-like protein LSm3)
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.
