General information for g6668.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Pre-mRNA-splicing factor 38.
Parent gene
- The parent gene g6668 is located on chr_2: 18012755..18013781 (- 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 | g6668 | g6668.t2 | isoform | g6668.t2 | 18007556 | 18013654 |
| chr_2 | g6668 | g6668.t2 | exon | g6668.t2.exon1 | 18007556 | 18007571 |
| chr_2 | g6668 | g6668.t2 | exon | g6668.t2.exon2 | 18007784 | 18007921 |
| chr_2 | g6668 | g6668.t2 | exon | g6668.t2.exon3 | 18008199 | 18008255 |
| chr_2 | g6668 | g6668.t2 | exon | g6668.t2.exon4 | 18008315 | 18008435 |
| chr_2 | g6668 | g6668.t2 | exon | g6668.t2.exon5 | 18008500 | 18008661 |
| chr_2 | g6668 | g6668.t2 | exon | g6668.t2.exon6 | 18008718 | 18008886 |
| chr_2 | g6668 | g6668.t2 | cds | g6668.t2.CDS1 | 18008759 | 18008886 |
| chr_2 | g6668 | g6668.t2 | exon | g6668.t2.exon7 | 18013408 | 18013654 |
| chr_2 | g6668 | g6668.t2 | cds | g6668.t2.CDS2 | 18013408 | 18013654 |
| chr_2 | g6668 | g6668.t2 | TSS | g6668.t2 | 18013742 | 18013742 |
| chr_2 | g6668 | g6668.t2 | TTS | g6668.t2 | NA | NA |
Sequences
>g6668.t2 Gene=g6668 Length=910
ATGGCAAATAGAACGTTAAAAGATGCAAAAAATGTGCACGGTACAAATCCACAATACCTC
ATTGAAAAAATCATCAGATCAAGAATTTATGATTCCCAGTATTGGAAAGAATCTTGCTTC
GCGCTTACTGCAGAGTTAATGGTTGACAAAGCCATGGAATTACGCTATATCGGAGGTGTT
TTTGGTGGCAATATTAAACCAACACCATTTATTTGCCTAATACTAAAATTTCTTCAAATT
CAACCAGAATCTGCAGGGTCAAAGAAAACTTCTAATTCTTCTATCTGGAACTTGTCATTG
ACCTTAGCAACAGACACTCCAAAAACTTCTAGAACTCTATTTGATGCTTTTGCTTCATAT
TTTTTCCCAGAATGAGTTTCAAGTGTGACATCTCCATTATTCAATCCCCAATGTCTCCAT
TTAAAAGCAACAACTGGTGGTCCACTATAAACCTTAATAACTTCCCATGAAAATGCACGT
AATGCTCTTTTAAAAAGTTTGTGTGAATCCAAGAAATTTAATTCACTTGCTTTGTATAAT
TCAGTATCACCAATTAATGCATTATACGTTCCAAGCTTAAGCATATTTTCAACATCATTC
CAAGCTTTACCATTGACAGAAAAACGATATTTTTCAGGATTAATTGTTCTAATTTGATCT
TTACGAAGCTTATGAGACATTTCCTTTTCCCAATTCTTAACCAAGTTTGATACTAAAAAT
TCAAGCGATCCTTCTTCATGATTAACTGTTTTCTCTCTTCTTCAAAATATTTGTTAGCTT
TGGAATAATCAGGAATGATATTATAACGCCATTCATGATCTTTGTCTTTCAAAACTGCAT
TTGGATCAAGCATGAAATCTGGGAGTGACATGTTGAAATTTTTCTATAAAAAAGATTTTT
TTTATTGATC
>g6668.t2 Gene=g6668 Length=124
MANRTLKDAKNVHGTNPQYLIEKIIRSRIYDSQYWKESCFALTAELMVDKAMELRYIGGV
FGGNIKPTPFICLILKFLQIQPESAGSKKTSNSSIWNLSLTLATDTPKTSRTLFDAFASY
FFPE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g6668.t2 | PANTHER | PTHR23142 | UNCHARACTERIZED | 1 | 84 | 0 |
| 3 | g6668.t2 | PANTHER | PTHR23142:SF7 | PRE-MRNA-SPLICING FACTOR 38A | 1 | 84 | 0 |
| 1 | g6668.t2 | Pfam | PF03371 | PRP38 family | 10 | 84 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
