General information for g11852.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Small nuclear ribonucleoprotein Sm D3.
Parent gene
- The parent gene g11852 is located on chr_1: 18741771..18742330 (+ 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 | g11852 | g11852.t1 | TSS | g11852.t1 | 18741698 | 18741698 |
| chr_1 | g11852 | g11852.t1 | isoform | g11852.t1 | 18741771 | 18742330 |
| chr_1 | g11852 | g11852.t1 | exon | g11852.t1.exon1 | 18741771 | 18741838 |
| chr_1 | g11852 | g11852.t1 | cds | g11852.t1.CDS1 | 18741771 | 18741838 |
| chr_1 | g11852 | g11852.t1 | exon | g11852.t1.exon2 | 18741914 | 18742091 |
| chr_1 | g11852 | g11852.t1 | cds | g11852.t1.CDS2 | 18741914 | 18742091 |
| chr_1 | g11852 | g11852.t1 | exon | g11852.t1.exon3 | 18742148 | 18742330 |
| chr_1 | g11852 | g11852.t1 | cds | g11852.t1.CDS3 | 18742148 | 18742330 |
| chr_1 | g11852 | g11852.t1 | TTS | g11852.t1 | 18742453 | 18742453 |
Sequences
>g11852.t1 Gene=g11852 Length=429
ATGTCGATTGGTGTACCAATTAAAGTTCTTCATGAAGCTGAAGGTCATATTGTTACATGT
GAAACAATTACCGGTGAAGTATATCGAGGTAAACTCATTGAAGCTGAAGATAATATGAAT
TGTCAAATGACTCAGATTACAGTCACATATAGAGATGGAAGAATGGCAAATTTAGAAAAC
GTTTACATTCGTGGATCAAAAATTAGATTCATGATTCTACCGGATATGCTAAAGAATGCA
CCAATGTTTAAAAAGCAAACAAAAGCAGGGACGGCAGGAAGAGGAAAGAGTGCGATATTA
AGAGCACAAGCTGCAAGAGGCAGAGGAAGAGGAAATCAACCTGGGTCAAAACCGGGAGGT
TCTGGTGCTGGTTCAAAACAATGGCAGCAAGGTGGACCGTCTGGCGGCAGAGGACGTGGT
GGTATTTAA
>g11852.t1 Gene=g11852 Length=142
MSIGVPIKVLHEAEGHIVTCETITGEVYRGKLIEAEDNMNCQMTQITVTYRDGRMANLEN
VYIRGSKIRFMILPDMLKNAPMFKKQTKAGTAGRGKSAILRAQAARGRGRGNQPGSKPGG
SGAGSKQWQQGGPSGGRGRGGI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g11852.t1 | CDD | cd01721 | Sm_D3 | 6 | 75 | 3.00388E-47 |
| 8 | g11852.t1 | Gene3D | G3DSA:2.30.30.100 | - | 1 | 84 | 8.8E-32 |
| 6 | g11852.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 85 | 142 | - |
| 7 | g11852.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 118 | 132 | - |
| 2 | g11852.t1 | PANTHER | PTHR23338:SF17 | SMALL NUCLEAR RIBONUCLEOPROTEIN SM D3 | 1 | 111 | 7.0E-51 |
| 3 | g11852.t1 | PANTHER | PTHR23338 | SMALL NUCLEAR RIBONUCLEOPROTEIN SM | 1 | 111 | 7.0E-51 |
| 1 | g11852.t1 | Pfam | PF01423 | LSM domain | 9 | 72 | 4.5E-14 |
| 5 | g11852.t1 | SMART | SM00651 | Sm3 | 8 | 73 | 3.1E-15 |
| 4 | g11852.t1 | SUPERFAMILY | SSF50182 | Sm-like ribonucleoproteins | 6 | 122 | 2.01E-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:0006396 | RNA processing | BP |
| GO:0005681 | spliceosomal complex | CC |
| GO:0000387 | spliceosomal snRNP assembly | BP |
KEGG
Orthology
- This transcript has been annotated with K11088 (small nuclear ribonucleoprotein D3)
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.
