General information for g6156.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative U6 snRNA-associated Sm-like protein LSm4.
Parent gene
- The parent gene g6156 is located on chr_2: 14631563..14632149 (- 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 | g6156 | g6156.t1 | TTS | g6156.t1 | 14631460 | 14631460 |
| chr_2 | g6156 | g6156.t1 | isoform | g6156.t1 | 14631563 | 14632149 |
| chr_2 | g6156 | g6156.t1 | exon | g6156.t1.exon1 | 14631563 | 14631817 |
| chr_2 | g6156 | g6156.t1 | cds | g6156.t1.CDS1 | 14631563 | 14631817 |
| chr_2 | g6156 | g6156.t1 | exon | g6156.t1.exon2 | 14631884 | 14631982 |
| chr_2 | g6156 | g6156.t1 | cds | g6156.t1.CDS2 | 14631884 | 14631982 |
| chr_2 | g6156 | g6156.t1 | exon | g6156.t1.exon3 | 14632045 | 14632086 |
| chr_2 | g6156 | g6156.t1 | cds | g6156.t1.CDS3 | 14632045 | 14632086 |
| chr_2 | g6156 | g6156.t1 | exon | g6156.t1.exon4 | 14632147 | 14632149 |
| chr_2 | g6156 | g6156.t1 | cds | g6156.t1.CDS4 | 14632147 | 14632149 |
| chr_2 | g6156 | g6156.t1 | TSS | g6156.t1 | 14632224 | 14632224 |
Sequences
>g6156.t1 Gene=g6156 Length=399
ATGTTACCGCTATCACTATTAAAAACTGCTCAATCACACCCAATGCTTGTTGAGCTAAAG
AATGGTGAAACTTATAATGGACATCTTGTAAGTTGTGATACATGGATGAATATTAACTTA
CGAGAAGTTATTTGCACATCAAAGGATGGCGATAAGTTTTGGAGAATGAATGAATGCTAT
ATTCGTGGTAGCACAATCAAATATCTTCGTATTCCCGATGAAGTCATTGATTTAGTAAAA
GAAGACATTCAAGCTAAAGCAAAGAATCGTAATCAAAATCAGAACCAAAATCGTAACAAT
AACAACAACCAGCAAAATCGCGGAAATAAGAACAACCCAAACCAGCATCGTCCAAATCCA
AATCGTAATCGGAATAACGTCAATATCAATAAGAATTGA
>g6156.t1 Gene=g6156 Length=132
MLPLSLLKTAQSHPMLVELKNGETYNGHLVSCDTWMNINLREVICTSKDGDKFWRMNECY
IRGSTIKYLRIPDEVIDLVKEDIQAKAKNRNQNQNQNRNNNNNQQNRGNKNNPNQHRPNP
NRNRNNVNINKN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g6156.t1 | CDD | cd01723 | LSm4 | 2 | 77 | 1.58003E-55 |
| 6 | g6156.t1 | Coils | Coil | Coil | 84 | 104 | - |
| 5 | g6156.t1 | Gene3D | G3DSA:2.30.30.100 | - | 1 | 83 | 2.8E-37 |
| 9 | g6156.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 86 | 132 | - |
| 10 | g6156.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 88 | 132 | - |
| 2 | g6156.t1 | PANTHER | PTHR23338:SF16 | U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM4 | 1 | 123 | 3.0E-55 |
| 3 | g6156.t1 | PANTHER | PTHR23338 | SMALL NUCLEAR RIBONUCLEOPROTEIN SM | 1 | 123 | 3.0E-55 |
| 1 | g6156.t1 | Pfam | PF01423 | LSM domain | 6 | 69 | 8.1E-16 |
| 8 | g6156.t1 | SMART | SM00651 | Sm3 | 5 | 71 | 3.2E-18 |
| 4 | g6156.t1 | SUPERFAMILY | SSF50182 | Sm-like ribonucleoproteins | 3 | 118 | 3.78E-31 |
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:0006396 | RNA processing | BP |
| GO:0000398 | mRNA splicing, via spliceosome | BP |
| GO:0000956 | nuclear-transcribed mRNA catabolic process | BP |
KEGG
Orthology
- This transcript has been annotated with K12623 (U6 snRNA-associated Sm-like protein LSm4)
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.
