General information for g8565.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Small nuclear ribonucleoprotein Sm D1.
Parent gene
- The parent gene g8565 is located on chr_2: 31361799..31362296 (+ 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 | g8565 | g8565.t1 | TSS | g8565.t1 | 31361718 | 31361718 |
| chr_2 | g8565 | g8565.t1 | isoform | g8565.t1 | 31361786 | 31362296 |
| chr_2 | g8565 | g8565.t1 | exon | g8565.t1.exon1 | 31361786 | 31361799 |
| chr_2 | g8565 | g8565.t1 | cds | g8565.t1.CDS1 | 31361786 | 31361799 |
| chr_2 | g8565 | g8565.t1 | exon | g8565.t1.exon2 | 31361863 | 31362167 |
| chr_2 | g8565 | g8565.t1 | cds | g8565.t1.CDS2 | 31361863 | 31362167 |
| chr_2 | g8565 | g8565.t1 | exon | g8565.t1.exon3 | 31362226 | 31362296 |
| chr_2 | g8565 | g8565.t1 | cds | g8565.t1.CDS3 | 31362226 | 31362296 |
| chr_2 | g8565 | g8565.t1 | TTS | g8565.t1 | 31362428 | 31362428 |
Sequences
>g8565.t1 Gene=g8565 Length=390
ATGAAACTAGTAAGATTTTTAATGAAGTTAAGTCACGAAACAGTGACTATTGAATTGAAA
AATGGAACACAAGTTTATGGTACAATAACCGGAGTGGATGTCGCTATGAACACTCATTTA
AAAGCAGTCAAAATGACAATCAAAAACCGAAATCCTGTTCAGCTCGAATCATTGAGCATT
CGTGGTAATAATATTCGATATTTTATTCTACCCGATTCGCTTCCTCTTGAAACAATGCTT
GTTGATGATACACCAAAAACAAAAGCAAAGAAAAAAGATGGAAAAGTTGGTTCGCGCGGA
AGAGGAAGAAGTGTTAGAGGTCGTGGAAGAGGAGGTCCGAGAGGAGGTGGAACTGGCGGA
CCAAGAGGTGGTGGAAGAGGCAAACGCTAA
>g8565.t1 Gene=g8565 Length=129
MKLVRFLMKLSHETVTIELKNGTQVYGTITGVDVAMNTHLKAVKMTIKNRNPVQLESLSI
RGNNIRYFILPDSLPLETMLVDDTPKTKAKKKDGKVGSRGRGRSVRGRGRGGPRGGGTGG
PRGGGRGKR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g8565.t1 | CDD | cd01724 | Sm_D1 | 2 | 85 | 1.54194E-55 |
| 8 | g8565.t1 | Gene3D | G3DSA:2.30.30.100 | - | 1 | 85 | 4.5E-36 |
| 6 | g8565.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 80 | 129 | - |
| 7 | g8565.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 92 | 108 | - |
| 2 | g8565.t1 | PANTHER | PTHR23338:SF52 | SMALL NUCLEAR RIBONUCLEOPROTEIN SM D1 | 1 | 108 | 2.5E-56 |
| 3 | g8565.t1 | PANTHER | PTHR23338 | SMALL NUCLEAR RIBONUCLEOPROTEIN SM | 1 | 108 | 2.5E-56 |
| 1 | g8565.t1 | Pfam | PF01423 | LSM domain | 5 | 69 | 6.6E-19 |
| 5 | g8565.t1 | SMART | SM00651 | Sm3 | 5 | 70 | 3.7E-18 |
| 4 | g8565.t1 | SUPERFAMILY | SSF50182 | Sm-like ribonucleoproteins | 4 | 125 | 1.29E-26 |
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:0000387 | spliceosomal snRNP assembly | BP |
KEGG
Orthology
- This transcript has been annotated with K11087 (small nuclear ribonucleoprotein D1)
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.
