General information for g6668.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t3 | TTS | g6668.t3 | 18012554 | 18012554 |
| chr_2 | g6668 | g6668.t3 | isoform | g6668.t3 | 18012755 | 18013781 |
| chr_2 | g6668 | g6668.t3 | exon | g6668.t3.exon1 | 18012755 | 18013695 |
| chr_2 | g6668 | g6668.t3 | cds | g6668.t3.CDS1 | 18012755 | 18013654 |
| chr_2 | g6668 | g6668.t3 | TSS | g6668.t3 | 18013742 | 18013742 |
| chr_2 | g6668 | g6668.t3 | exon | g6668.t3.exon2 | 18013764 | 18013781 |
Sequences
>g6668.t3 Gene=g6668 Length=959
GTATAAAAAATAACAGAGGAAAAGATTGATGAAAATAATTTTAATCACTATAATTTAAGA
TGGCAAATAGAACGTTAAAAGATGCAAAAAATGTGCACGGTACAAATCCACAATACCTCA
TTGAAAAAATCATCAGATCAAGAATTTATGATTCCCAGTATTGGAAAGAATCTTGCTTCG
CGCTTACTGCAGAGTTAATGGTTGACAAAGCCATGGAATTACGCTATATCGGAGGTGTTT
TTGGTGGCAATATTAAACCAACACCATTTATTTGCCTAATACTAAAATTTCTTCAAATTC
AACCAGAAAAGGACATTGTAATTGAGTTCATTAAAAATGAGGAATTCAAATATGTAAGAG
CTCTTGGTGCATTTTATTTGAGACTTACAGCTTCTGCTGTTGACTGTTACAAATATTTGG
AACCACTTTATAATGACTATCGTAAATTAAGGCGACAAAATAGAATGGGGCATTATGAGA
TTATACACATGGACGAATTTATTGATGAACTTTTAAGAGAAGAACGCGTTTGTGATGTTA
TTCTTCCTCGTATTCAAAAAAGACACGTTTTAGAAGAAAATGGTGACTTGGAACCAAAAG
TATCACTACTTGATGACGATTTGGATGAAGAAATGCCAAGTGAAGATGAAGAAGAGCAAT
TACAACAACTAAAGAAAACTGATAATTCAAAGCATCAGAGTAGCAAAGACTCAGAACGTC
GCAGAAGTAGATCTTTATCACGTGAAAGACACAAAAAATCAAAAGATTATAGACGAGATG
ATTCACCATTGAGGAAGAAATATCGTGATGAAAGAAGAGAGCGTGACAAAAAAAGATCAC
CAGATAGAGAACGACGTCGATCCAGATCTAGATCTACTGAAAGAACAAGACATAACAGAG
ATGATAGAAGTTATTATAAAAGAGATAGAAGTTATGAACGCGACAGACGTCGTTATTAA
>g6668.t3 Gene=g6668 Length=299
MANRTLKDAKNVHGTNPQYLIEKIIRSRIYDSQYWKESCFALTAELMVDKAMELRYIGGV
FGGNIKPTPFICLILKFLQIQPEKDIVIEFIKNEEFKYVRALGAFYLRLTASAVDCYKYL
EPLYNDYRKLRRQNRMGHYEIIHMDEFIDELLREERVCDVILPRIQKRHVLEENGDLEPK
VSLLDDDLDEEMPSEDEEEQLQQLKKTDNSKHQSSKDSERRRSRSLSRERHKKSKDYRRD
DSPLRKKYRDERRERDKKRSPDRERRRSRSRSTERTRHNRDDRSYYKRDRSYERDRRRY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g6668.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 190 | 299 | - |
| 6 | g6668.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 198 | 224 | - |
| 7 | g6668.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 233 | 299 | - |
| 3 | g6668.t3 | PANTHER | PTHR23142 | UNCHARACTERIZED | 1 | 295 | 1.2E-112 |
| 4 | g6668.t3 | PANTHER | PTHR23142:SF7 | PRE-MRNA-SPLICING FACTOR 38A | 1 | 295 | 1.2E-112 |
| 1 | g6668.t3 | Pfam | PF03371 | PRP38 family | 10 | 174 | 3.0E-64 |
| 2 | g6668.t3 | Pfam | PF12871 | Pre-mRNA-splicing factor 38-associated hydrophilic C-term | 179 | 275 | 9.3E-7 |
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 transcript has been annotated with K12849 (pre-mRNA-splicing factor 38A)
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.
