General information for g8565.t4
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.t4 | TSS | g8565.t4 | 31361718 | 31361718 |
| chr_2 | g8565 | g8565.t4 | isoform | g8565.t4 | 31361786 | 31362296 |
| chr_2 | g8565 | g8565.t4 | exon | g8565.t4.exon1 | 31361786 | 31362167 |
| chr_2 | g8565 | g8565.t4 | cds | g8565.t4.CDS1 | 31361870 | 31362167 |
| chr_2 | g8565 | g8565.t4 | exon | g8565.t4.exon2 | 31362226 | 31362296 |
| chr_2 | g8565 | g8565.t4 | cds | g8565.t4.CDS2 | 31362226 | 31362296 |
| chr_2 | g8565 | g8565.t4 | TTS | g8565.t4 | 31362428 | 31362428 |
Sequences
>g8565.t4 Gene=g8565 Length=453
ATGAAACTAGTAAGGTAAATATAATTATTCTAATAACTAAAATATAAAAATAAAATAGTT
TACATCATTTATTGCAGATTTTTAATGAAGTTAAGTCACGAAACAGTGACTATTGAATTG
AAAAATGGAACACAAGTTTATGGTACAATAACCGGAGTGGATGTCGCTATGAACACTCAT
TTAAAAGCAGTCAAAATGACAATCAAAAACCGAAATCCTGTTCAGCTCGAATCATTGAGC
ATTCGTGGTAATAATATTCGATATTTTATTCTACCCGATTCGCTTCCTCTTGAAACAATG
CTTGTTGATGATACACCAAAAACAAAAGCAAAGAAAAAAGATGGAAAAGTTGGTTCGCGC
GGAAGAGGAAGAAGTGTTAGAGGTCGTGGAAGAGGAGGTCCGAGAGGAGGTGGAACTGGC
GGACCAAGAGGTGGTGGAAGAGGCAAACGCTAA
>g8565.t4 Gene=g8565 Length=122
MKLSHETVTIELKNGTQVYGTITGVDVAMNTHLKAVKMTIKNRNPVQLESLSIRGNNIRY
FILPDSLPLETMLVDDTPKTKAKKKDGKVGSRGRGRSVRGRGRGGPRGGGTGGPRGGGRG
KR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g8565.t4 | CDD | cd01724 | Sm_D1 | 1 | 78 | 1.12198E-50 |
| 8 | g8565.t4 | Gene3D | G3DSA:2.30.30.100 | - | 1 | 78 | 7.9E-32 |
| 6 | g8565.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 74 | 122 | - |
| 7 | g8565.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 85 | 101 | - |
| 2 | g8565.t4 | PANTHER | PTHR23338:SF52 | SMALL NUCLEAR RIBONUCLEOPROTEIN SM D1 | 1 | 101 | 6.2E-52 |
| 3 | g8565.t4 | PANTHER | PTHR23338 | SMALL NUCLEAR RIBONUCLEOPROTEIN SM | 1 | 101 | 6.2E-52 |
| 1 | g8565.t4 | Pfam | PF01423 | LSM domain | 2 | 62 | 1.5E-17 |
| 5 | g8565.t4 | SMART | SM00651 | Sm3 | 1 | 63 | 1.1E-13 |
| 4 | g8565.t4 | SUPERFAMILY | SSF50182 | Sm-like ribonucleoproteins | 2 | 118 | 6.95E-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:0000387 | spliceosomal snRNP assembly | BP |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
