General information for g4844.t1
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 g4844 is located on chr_2: 5264579..5265322 (- 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 | g4844 | g4844.t1 | isoform | g4844.t1 | 5264579 | 5265322 |
| chr_2 | g4844 | g4844.t1 | exon | g4844.t1.exon1 | 5264579 | 5265322 |
| chr_2 | g4844 | g4844.t1 | cds | g4844.t1.CDS1 | 5264579 | 5265322 |
| chr_2 | g4844 | g4844.t1 | TSS | g4844.t1 | NA | NA |
| chr_2 | g4844 | g4844.t1 | TTS | g4844.t1 | NA | NA |
Sequences
>g4844.t1 Gene=g4844 Length=744
ATGGCAAATAGAACACTAAAAGGATCAAAAAATATTCATGGACAAGATCCTCAACATCTC
GTTGAAAAAATAATAAGAACAAGAATCTATGATAGTAATTATTGGAAGGAAAATTGTTTT
GATCTCACTGCTGAATTAATGATTGATAAAGCAATTGAATTAAAGTATATTGGAGGAGTT
TATGGTGCTAATATCAAACCTACACCATTTATTTGCTTGATTTTAAAATTACTGCAAATT
CAGCCTGAAAAAGATATCATAATTGAGTTCATAAAAAATGAAGATTTTAAATATATCAGA
GCTCTTGGTGCTTTTTATTTGCGATTAACAGCACCTGCAATTGAATGCTATAAATATCTA
GAGCCACTTTACAATGATTATCGCAAACTAAGAAGACAAAATCGTATGGGACATTATGAA
ATTGTTTATATGGATGAATTTATTGACGAATTGTTGATAAAAGATCGAGTTTGTGATGTG
ATTTTACCTCGTATTCAGAAAAGACAAGTGCTAGAAGAGAATGGTGAGCTTGAACAAAGA
GTCACAACATTAAATGATTTAAACGAAAGTGAAAATGAGCAGCAAGGAAACAAATCTCGT
CGTAGAAGTAGCAGTTCAGAAGATGAAACAAGAAGATCTCATATTCGTCATCAAAGAGAT
TCACCATTAAGAAAGAAATATCGTAAAGAAAAGTATGAACGTGATAGAGAAAGACAACGA
CCAAGATCCAATGAAAGAAAATGA
>g4844.t1 Gene=g4844 Length=247
MANRTLKGSKNIHGQDPQHLVEKIIRTRIYDSNYWKENCFDLTAELMIDKAIELKYIGGV
YGANIKPTPFICLILKLLQIQPEKDIIIEFIKNEDFKYIRALGAFYLRLTAPAIECYKYL
EPLYNDYRKLRRQNRMGHYEIVYMDEFIDELLIKDRVCDVILPRIQKRQVLEENGELEQR
VTTLNDLNESENEQQGNKSRRRSSSSEDETRRSHIRHQRDSPLRKKYRKEKYERDRERQR
PRSNERK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g4844.t1 | Coils | Coil | Coil | 167 | 194 | - |
| 5 | g4844.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 181 | 247 | - |
| 6 | g4844.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 193 | 216 | - |
| 4 | g4844.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 225 | 247 | - |
| 2 | g4844.t1 | PANTHER | PTHR23142 | UNCHARACTERIZED | 1 | 245 | 2.4E-96 |
| 3 | g4844.t1 | PANTHER | PTHR23142:SF7 | PRE-MRNA-SPLICING FACTOR 38A | 1 | 245 | 2.4E-96 |
| 1 | g4844.t1 | Pfam | PF03371 | PRP38 family | 10 | 174 | 6.5E-65 |
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. There were no conditions that were differentially expressed