General information for g7768.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Survival of motor neuron-related-splicing factor 30.
Parent gene
- The parent gene g7768 is located on chr_2: 25873401..25874008 (+ 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 | g7768 | g7768.t1 | TSS | g7768.t1 | 25873160 | 25873160 |
| chr_2 | g7768 | g7768.t1 | isoform | g7768.t1 | 25873218 | 25874008 |
| chr_2 | g7768 | g7768.t1 | exon | g7768.t1.exon1 | 25873218 | 25873323 |
| chr_2 | g7768 | g7768.t1 | cds | g7768.t1.CDS1 | 25873218 | 25873323 |
| chr_2 | g7768 | g7768.t1 | exon | g7768.t1.exon2 | 25873383 | 25874008 |
| chr_2 | g7768 | g7768.t1 | cds | g7768.t1.CDS2 | 25873383 | 25874008 |
| chr_2 | g7768 | g7768.t1 | TTS | g7768.t1 | 25874055 | 25874055 |
Sequences
>g7768.t1 Gene=g7768 Length=732
ATGGCAGACGAGCTGAGTAATTATAAATTGCAATTACAACAAGTTGAAGTAGCTCTTCTC
ACAGATCCCGATAATGCAGAATTGTTGAAATTAAAGGAGGATATAGAACAATTAATTGAA
CTACAAAAGGATTTAATTCGAACGCAAGAAGCTGAATCTAAAAAGTATATCGAGCCAACA
ATTGGTCCAGCAGCAACAACATCTTCAAATTATTACAAAGAACAGAAATCAAAAAATCCT
TTAAAAATATGGAAAGTTGGAGATAAATGTATGGCTCGTGATGCGACAAACGGACAATAT
TATGAAGCAACAATTGAATCAATTAGTGACGATGGTGATGCTCAAGTTATTTTCGATGCA
TATCAAAATCGCGGTCAATCTCATGTCAAAGATTTAAAAGAGTACAAAGTGCGAGTTGAA
GTATTTTCATCTGCAAATAGCCTGAAGCGATCGAAAGCAGCTCGACCTAATCATAAAGAA
TATTTGAAAAAGAAGAAACTAAAGAAGCAAGCTCGATTAACAGAGTTGGAAGAGGAACGT
GAGAAAGAGAAGAACAAATGGTTAAATTTCAATAACAAAACTAATAAGAAATCGATTAAC
AAACAGCAATCTATATTTCAATCACCTGAATTTGGTCGAGTTGGTATCGGCACTTTAAAA
ACCAATGCAAATGATGTTCCACTTCCCAATAATTTTCAAGCTTCTCGCGATATTCATAAG
CGTAAAATGTAA
>g7768.t1 Gene=g7768 Length=243
MADELSNYKLQLQQVEVALLTDPDNAELLKLKEDIEQLIELQKDLIRTQEAESKKYIEPT
IGPAATTSSNYYKEQKSKNPLKIWKVGDKCMARDATNGQYYEATIESISDDGDAQVIFDA
YQNRGQSHVKDLKEYKVRVEVFSSANSLKRSKAARPNHKEYLKKKKLKKQARLTELEEER
EKEKNKWLNFNNKTNKKSINKQQSIFQSPEFGRVGIGTLKTNANDVPLPNNFQASRDIHK
RKM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g7768.t1 | CDD | cd04508 | TUDOR | 87 | 134 | 8.3048E-9 |
| 6 | g7768.t1 | Coils | Coil | Coil | 28 | 52 | - |
| 7 | g7768.t1 | Coils | Coil | Coil | 159 | 193 | - |
| 5 | g7768.t1 | Gene3D | G3DSA:2.30.30.140 | - | 73 | 135 | 8.8E-12 |
| 2 | g7768.t1 | PANTHER | PTHR13681 | SURVIVAL OF MOTOR NEURON-RELATED-SPLICING FACTOR 30-RELATED | 2 | 218 | 1.2E-22 |
| 3 | g7768.t1 | PANTHER | PTHR13681:SF26 | SURVIVAL OF MOTOR NEURON-RELATED-SPLICING FACTOR 30 | 2 | 218 | 1.2E-22 |
| 1 | g7768.t1 | Pfam | PF06003 | Survival motor neuron protein (SMN) | 71 | 216 | 1.1E-6 |
| 10 | g7768.t1 | ProSiteProfiles | PS50304 | Tudor domain profile. | 83 | 142 | 11.772 |
| 9 | g7768.t1 | SMART | SM00333 | TUDOR_7 | 82 | 140 | 1.3E-4 |
| 4 | g7768.t1 | SUPERFAMILY | SSF63748 | Tudor/PWWP/MBT | 83 | 133 | 1.2E-8 |
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:0006397 | mRNA processing | BP |
| GO:0005634 | nucleus | CC |
| GO:0003723 | RNA binding | MF |
| GO:0005737 | cytoplasm | CC |
KEGG
Orthology
- This transcript has been annotated with K12839 (survival of motor neuron-related-splicing factor 30)
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.
