General information for g10278.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been not been annotated.
Parent gene
- The parent gene g10278 is located on chr_1: 8612782..8613073 (- 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 | g10278 | g10278.t1 | TTS | g10278.t1 | 8612699 | 8612699 |
| chr_1 | g10278 | g10278.t1 | isoform | g10278.t1 | 8612782 | 8613073 |
| chr_1 | g10278 | g10278.t1 | exon | g10278.t1.exon1 | 8612782 | 8612980 |
| chr_1 | g10278 | g10278.t1 | cds | g10278.t1.CDS1 | 8612782 | 8612980 |
| chr_1 | g10278 | g10278.t1 | exon | g10278.t1.exon2 | 8613042 | 8613073 |
| chr_1 | g10278 | g10278.t1 | cds | g10278.t1.CDS2 | 8613042 | 8613073 |
| chr_1 | g10278 | g10278.t1 | TSS | g10278.t1 | 8613209 | 8613209 |
Sequences
>g10278.t1 Gene=g10278 Length=231
ATGTCGAAAGCTCATCCTCCAGAATTGAAAAAATATATGGACAAAAAGTTATCACTCAAA
TTAAATGGAGGAAGATGTGTACAAGGTATTTTGCGAGGTTTTGATCCATTCATGAATGTT
GTAGTTGATGAAGCAAACGAAGTTAGTAAGGACGGAAAAAAGAGCGACATCGGAATGGTT
GTCATTAGAGGAAACAGTATAATAATGGTAGAAGCATTAGAGCGGATATAA
>g10278.t1 Gene=g10278 Length=76
MSKAHPPELKKYMDKKLSLKLNGGRCVQGILRGFDPFMNVVVDEANEVSKDGKKSDIGMV
VIRGNSIIMVEALERI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g10278.t1 | CDD | cd01719 | Sm_G | 5 | 74 | 0 |
| 6 | g10278.t1 | Gene3D | G3DSA:2.30.30.100 | - | 1 | 76 | 0 |
| 2 | g10278.t1 | PANTHER | PTHR10553:SF26 | SMALL NUCLEAR RIBONUCLEOPROTEIN G-RELATED | 1 | 76 | 0 |
| 3 | g10278.t1 | PANTHER | PTHR10553 | SMALL NUCLEAR RIBONUCLEOPROTEIN | 1 | 76 | 0 |
| 7 | g10278.t1 | PIRSF | PIRSF037188 | Lsm7 | 3 | 75 | 0 |
| 1 | g10278.t1 | Pfam | PF01423 | LSM domain | 8 | 71 | 0 |
| 5 | g10278.t1 | SMART | SM00651 | Sm3 | 7 | 72 | 0 |
| 4 | g10278.t1 | SUPERFAMILY | SSF50182 | Sm-like ribonucleoproteins | 7 | 74 | 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:0005681 | spliceosomal complex | CC |
| GO:0000387 | spliceosomal snRNP assembly | BP |
KEGG
Orthology
- This transcript has been annotated with K11099 (small nuclear ribonucleoprotein G)
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.
