General information for g12931.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Pre-mRNA-splicing factor Slu7.
Parent gene
- The parent gene g12931 is located on chr_1: 26979735..26981283 (+ 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 | g12931 | g12931.t4 | isoform | g12931.t4 | 26978803 | 26979735 |
| chr_1 | g12931 | g12931.t4 | exon | g12931.t4.exon1 | 26978803 | 26979442 |
| chr_1 | g12931 | g12931.t4 | cds | g12931.t4.CDS1 | 26978803 | 26979442 |
| chr_1 | g12931 | g12931.t4 | exon | g12931.t4.exon2 | 26979511 | 26979735 |
| chr_1 | g12931 | g12931.t4 | cds | g12931.t4.CDS2 | 26979511 | 26979515 |
| chr_1 | g12931 | g12931.t4 | TTS | g12931.t4 | 26979790 | 26979790 |
| chr_1 | g12931 | g12931.t4 | TSS | g12931.t4 | NA | NA |
Sequences
>g12931.t4 Gene=g12931 Length=865
GATTTAGAATTTGGCGGTGAGAATTTTGTTCGTTTTACTGGCGACACACAGAAACATGCA
ACTGCACAATTGTTTGCATGGGAAGCATCTAGCAAGGGCGTTGATGTGCATGTTCTTGCT
GAACCAACAAAATTAGAGTTGCTGCAAAAAGAATATGAGAAAAAGAAAGAAGAACTCAAA
ACTAGCGTTAAAAGTAATGTGCTAGAAAAGTATGGAGGAGAAGAACATTTGGAAGCACCG
CCAAGGCAACTTTTGCTTGCACAGACTGAGCAATACGTTGAATATGCTAGAGATGGACGA
ATAATTAAAGGTGCCGAGAAAGTGATTATTCGAAGTCGTTATGAGGAGGACGTTTATATC
AACAATCACACGACTGTATTTGGTTCATATTGGAATAACGGAAAATGGGGATACAAATGC
TGCAAATCGTTTGTCAAAAATTCATGGTGTGTTAAAAGTTCAGTAGGAGCTGAAATTGCA
GAAGGTGAATCAACTGAAATTCCATCGACAAGTGGTTGGTCGAGTAATAAGGAAAAAGTT
GCTGAACAAAACAAATCAGATTCAGAACATGAAGAAAGTGAGAAATCATCAAGTGAAAAG
AAAAAAGAATCGTCAGAGTCAGATTCAGATGATTCAAGTAGATAAGCGTGCTGAAAAGAA
AGAAAAAGATAAATTGCAAGAAGCTCTTGAAGCTGAAGACAAACGAATAAAAGAATATGA
CGAAATGATGACCATTGATGAACGAAAACGAAAATATAATAGTATGTATGAAGCAAAAGC
ACCAACTGAAGAAGAAATGGAGGCTTATTATATCAAGAGGGCAAGAGAAGAAGATCCTAT
GATGCAATTCATGAAGAATAAGTGA
>g12931.t4 Gene=g12931 Length=214
DLEFGGENFVRFTGDTQKHATAQLFAWEASSKGVDVHVLAEPTKLELLQKEYEKKKEELK
TSVKSNVLEKYGGEEHLEAPPRQLLLAQTEQYVEYARDGRIIKGAEKVIIRSRYEEDVYI
NNHTTVFGSYWNNGKWGYKCCKSFVKNSWCVKSSVGAEIAEGESTEIPSTSGWSSNKEKV
AEQNKSDSEHEESEKSSSEKKKESSESDSDDSSR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g12931.t4 | Coils | Coil | Coil | 45 | 65 | - |
| 4 | g12931.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 160 | 214 | - |
| 6 | g12931.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 164 | 179 | - |
| 5 | g12931.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 180 | 214 | - |
| 2 | g12931.t4 | PANTHER | PTHR12942:SF2 | PRE-MRNA-SPLICING FACTOR SLU7 | 3 | 203 | 3.1E-65 |
| 3 | g12931.t4 | PANTHER | PTHR12942 | STEP II SPLICING FACTOR SLU7 | 3 | 203 | 3.1E-65 |
| 1 | g12931.t4 | Pfam | PF11708 | Pre-mRNA splicing Prp18-interacting factor | 4 | 129 | 4.9E-51 |
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:0000386 | second spliceosomal transesterification activity | MF |
| GO:0000398 | mRNA splicing, via spliceosome | BP |
| GO:0030628 | pre-mRNA 3’-splice site binding | MF |
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.
