General information for g8195.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Small nuclear ribonucleoprotein Sm D2.
Parent gene
- The parent gene g8195 is located on chr_2: 29032915..29033953 (+ 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 | g8195 | g8195.t1 | TSS | g8195.t1 | 29032379 | 29032379 |
| chr_2 | g8195 | g8195.t1 | isoform | g8195.t1 | 29032444 | 29032915 |
| chr_2 | g8195 | g8195.t1 | exon | g8195.t1.exon1 | 29032444 | 29032447 |
| chr_2 | g8195 | g8195.t1 | cds | g8195.t1.CDS1 | 29032444 | 29032447 |
| chr_2 | g8195 | g8195.t1 | exon | g8195.t1.exon2 | 29032554 | 29032915 |
| chr_2 | g8195 | g8195.t1 | cds | g8195.t1.CDS2 | 29032554 | 29032915 |
| chr_2 | g8195 | g8195.t1 | TTS | g8195.t1 | 29032937 | 29032937 |
Sequences
>g8195.t1 Gene=g8195 Length=366
ATGTCGCTTGCTATGAAGCCGAAATCTGAAATGACACCAGAAGAGTTACAAAAGCTTGAA
GAAGAAGAATTTAATACGGGACCATTAAGTGTTCTTACTCAATCTGTCAAAAACAACACT
CAAGTTTTAATTAATTGCAGAAACAACAAGAAACTTCTTGGTCGTGTTAAAGCATTTGAT
CGTCATTGTAATATGGTATTGGAAAATGTTAAAGAAATGTGGACAGAAGTTCCAAAAAGC
GGTAAAGGAAAAAAAAAAGTTAAACCAGTTAGTAAAGATAGATACATCAGTAAAATGTTC
TTACGAGGAGATTCTGTTGTTCTTGTGCTTAGAAATCCACTCGCTGCTCAAGCTGCAACA
AAATAA
>g8195.t1 Gene=g8195 Length=121
MSLAMKPKSEMTPEELQKLEEEEFNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFD
RHCNMVLENVKEMWTEVPKSGKGKKKVKPVSKDRYISKMFLRGDSVVLVLRNPLAAQAAT
K
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g8195.t1 | CDD | cd01720 | Sm_D2 | 24 | 113 | 0 |
| 5 | g8195.t1 | Gene3D | G3DSA:2.30.30.100 | - | 1 | 115 | 0 |
| 2 | g8195.t1 | PANTHER | PTHR12777 | SMALL NUCLEAR RIBONUCLEOPROTEIN SM D2 | 6 | 113 | 0 |
| 1 | g8195.t1 | Pfam | PF01423 | LSM domain | 37 | 109 | 0 |
| 4 | g8195.t1 | SMART | SM00651 | Sm3 | 32 | 111 | 0 |
| 3 | g8195.t1 | SUPERFAMILY | SSF50182 | Sm-like ribonucleoproteins | 27 | 112 | 0 |
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:0030532 | small nuclear ribonucleoprotein complex | CC |
| GO:0008380 | RNA splicing | BP |
KEGG
Orthology
- This transcript has been annotated with K11096 (small nuclear ribonucleoprotein D2)
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.
