General information for g7931.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative U6 snRNA-associated Sm-like protein LSm2.
Parent gene
- The parent gene g7931 is located on chr_2: 27113157..27113783 (- 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 | g7931 | g7931.t1 | isoform | g7931.t1 | 27113157 | 27113783 |
| chr_2 | g7931 | g7931.t1 | exon | g7931.t1.exon1 | 27113157 | 27113170 |
| chr_2 | g7931 | g7931.t1 | cds | g7931.t1.CDS1 | 27113157 | 27113170 |
| chr_2 | g7931 | g7931.t1 | TTS | g7931.t1 | 27113224 | 27113224 |
| chr_2 | g7931 | g7931.t1 | exon | g7931.t1.exon2 | 27113232 | 27113251 |
| chr_2 | g7931 | g7931.t1 | cds | g7931.t1.CDS2 | 27113232 | 27113251 |
| chr_2 | g7931 | g7931.t1 | exon | g7931.t1.exon3 | 27113328 | 27113414 |
| chr_2 | g7931 | g7931.t1 | cds | g7931.t1.CDS3 | 27113328 | 27113414 |
| chr_2 | g7931 | g7931.t1 | exon | g7931.t1.exon4 | 27113469 | 27113600 |
| chr_2 | g7931 | g7931.t1 | cds | g7931.t1.CDS4 | 27113469 | 27113600 |
| chr_2 | g7931 | g7931.t1 | exon | g7931.t1.exon5 | 27113659 | 27113726 |
| chr_2 | g7931 | g7931.t1 | cds | g7931.t1.CDS5 | 27113659 | 27113726 |
| chr_2 | g7931 | g7931.t1 | exon | g7931.t1.exon6 | 27113781 | 27113783 |
| chr_2 | g7931 | g7931.t1 | cds | g7931.t1.CDS6 | 27113781 | 27113783 |
| chr_2 | g7931 | g7931.t1 | TSS | g7931.t1 | 27113846 | 27113846 |
Sequences
>g7931.t1 Gene=g7931 Length=324
ATGTTATTTTATTCATTTTTTAAATCACTTGTCGGAAAAGATGTCATTGTAGAGCTAAAA
AATGATTTGTGTATATCAGGAACTCTTCATAGTGTCGACCAGTATCTTAATATTAAACTA
ACAGACATCAGTGTAACAGATCCAGAAAAATATCCACATATGCTCAGTGTTAAAAATTGC
TTCATTCGTGGTTCAGTCGTAAGGTATGTTCAGTTACCTGCTGATGAGATTGATACTCAG
ATTCTTCAAGATGCATCAAGAAAGGAGAGTACAACAAACTCAAATACGCGATTATATAAA
GTAAAAGAATGTATCATCGACTAG
>g7931.t1 Gene=g7931 Length=107
MLFYSFFKSLVGKDVIVELKNDLCISGTLHSVDQYLNIKLTDISVTDPEKYPHMLSVKNC
FIRGSVVRYVQLPADEIDTQILQDASRKESTTNSNTRLYKVKECIID
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g7931.t1 | CDD | cd01725 | LSm2 | 2 | 89 | 3.94709E-61 |
| 5 | g7931.t1 | Coils | Coil | Coil | 106 | 107 | - |
| 4 | g7931.t1 | Gene3D | G3DSA:2.30.30.100 | - | 1 | 96 | 9.2E-37 |
| 2 | g7931.t1 | PANTHER | PTHR13829 | SNRNP CORE PROTEIN FAMILY MEMBER | 1 | 90 | 3.2E-45 |
| 6 | g7931.t1 | PIRSF | PIRSF016394 | Lsm2 | 1 | 95 | 1.4E-52 |
| 1 | g7931.t1 | Pfam | PF01423 | LSM domain | 6 | 71 | 2.7E-17 |
| 8 | g7931.t1 | SMART | SM00651 | Sm3 | 5 | 72 | 3.3E-18 |
| 3 | g7931.t1 | SUPERFAMILY | SSF50182 | Sm-like ribonucleoproteins | 3 | 91 | 6.29E-25 |
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:0006397 | mRNA processing | BP |
KEGG
Orthology
- This transcript has been annotated with K12621 (U6 snRNA-associated Sm-like protein LSm2)
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.
