General information for g12931.t1
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.t1 | TSS | g12931.t1 | 26977760 | 26977760 |
| chr_1 | g12931 | g12931.t1 | isoform | g12931.t1 | 26977863 | 26979735 |
| chr_1 | g12931 | g12931.t1 | exon | g12931.t1.exon1 | 26977863 | 26978025 |
| chr_1 | g12931 | g12931.t1 | cds | g12931.t1.CDS1 | 26977863 | 26978025 |
| chr_1 | g12931 | g12931.t1 | exon | g12931.t1.exon2 | 26978086 | 26978142 |
| chr_1 | g12931 | g12931.t1 | cds | g12931.t1.CDS2 | 26978086 | 26978142 |
| chr_1 | g12931 | g12931.t1 | exon | g12931.t1.exon3 | 26978198 | 26979735 |
| chr_1 | g12931 | g12931.t1 | cds | g12931.t1.CDS3 | 26978198 | 26979735 |
| chr_1 | g12931 | g12931.t1 | TTS | g12931.t1 | 26979790 | 26979790 |
Sequences
>g12931.t1 Gene=g12931 Length=1758
ATGAATGCTCCACGTATACCGATATCACAATTATTGACCGATAAGGATAAATCGGAATCA
ACAGATGAGCCAACGAAAAAAACTAGAGAAGATTGGAGAAAACAAAAAGAACTTGAAGAA
GCGAGAAAAGCTGGTCAAGCACCCGCTGCTGTTGATGAAGAAGGCAAAGACATCAATCCA
CATATTCCACAATACATTTCTTCAGCACCATGGTATTATGGATCAAGTGGGCCAACATTA
AAACATCAGAGACCACAAGAAGAAAAGCAAAAGCAATATTCAGGAGTTGATGAATGGTAT
AAGAAAGGAGTTGATAAAAGCAAAGTTGCTACGAAATTTAGAAAAGGAGCATGTGAGAAT
TGTGGTGCAATGACTCATAAGAGAAAAGATTGTCTTGAGAGACCAAGAAAGGTCGGTGCA
AAATTTACAAATGCACAAATTGCATACGATGAATTTGAACAGCCAGATCTGAAACCAGAT
TTTGATGGGAAAAGAGATCGTTGGGCAGGCTATGATCCTTCAAATCATCGTGAGATTGTT
GAAGAATATCAGAAAATTGAAGAAGCAAAACGGCAATTAAAAGCTGAAAAATTGAAAGAA
GACCCAAATGCAGAATCATCGAGTGAAGATGATGAGGATAAATATGCAGATGGTGTAGAC
ATGCCTGGTACAAAAGTAGACAGTAAACAGCGTATCATTGTGAGAAATTTGCGTATTCGT
GAAGATACAGCTAAATATTTGAGGAATCTTGATCCTAATTCAGCTTTTTATGATCCAAAA
ACTCGTTCTATGCGTGAAAATCCCAATCCAAATAAAAATCCTGAAGATTTAGAATTTGGC
GGTGAGAATTTTGTTCGTTTTACTGGCGACACACAGAAACATGCAACTGCACAATTGTTT
GCATGGGAAGCATCTAGCAAGGGCGTTGATGTGCATGTTCTTGCTGAACCAACAAAATTA
GAGTTGCTGCAAAAAGAATATGAGAAAAAGAAAGAAGAACTCAAAACTAGCGTTAAAAGT
AATGTGCTAGAAAAGTATGGAGGAGAAGAACATTTGGAAGCACCGCCAAGGCAACTTTTG
CTTGCACAGACTGAGCAATACGTTGAATATGCTAGAGATGGACGAATAATTAAAGGTGCC
GAGAAAGTGATTATTCGAAGTCGTTATGAGGAGGACGTTTATATCAACAATCACACGACT
GTATTTGGTTCATATTGGAATAACGGAAAATGGGGATACAAATGCTGCAAATCGTTTGTC
AAAAATTCATGGTGTGTTAAAAGTTCAGTAGGAGCTGAAATTGCAGAAGGTGAATCAACT
GAAATTCCATCGACAAGTGGTTGGTCGAGTAATAAGGAAAAAGTTGCTGAACAAAACAAA
TCAGATTCAGAACATGAAGAAAGTGAGAAATCATCAAGTGAAAAGAAAAAAGAATCGTCA
GAGTCAGATTCAGATGATTCAAGTAGTGAAGAAGAAAGAAAAAGAAAATCTAAAAAGCGT
GACAAAAAACGTAAAAAGAAGAAGAAGCAAAAGGATAAGCGTGCTGAAAAGAAAGAAAAA
GATAAATTGCAAGAAGCTCTTGAAGCTGAAGACAAACGAATAAAAGAATATGACGAAATG
ATGACCATTGATGAACGAAAACGAAAATATAATAGTATGTATGAAGCAAAAGCACCAACT
GAAGAAGAAATGGAGGCTTATTATATCAAGAGGGCAAGAGAAGAAGATCCTATGATGCAA
TTCATGAAGAATAAGTGA
>g12931.t1 Gene=g12931 Length=585
MNAPRIPISQLLTDKDKSESTDEPTKKTREDWRKQKELEEARKAGQAPAAVDEEGKDINP
HIPQYISSAPWYYGSSGPTLKHQRPQEEKQKQYSGVDEWYKKGVDKSKVATKFRKGACEN
CGAMTHKRKDCLERPRKVGAKFTNAQIAYDEFEQPDLKPDFDGKRDRWAGYDPSNHREIV
EEYQKIEEAKRQLKAEKLKEDPNAESSSEDDEDKYADGVDMPGTKVDSKQRIIVRNLRIR
EDTAKYLRNLDPNSAFYDPKTRSMRENPNPNKNPEDLEFGGENFVRFTGDTQKHATAQLF
AWEASSKGVDVHVLAEPTKLELLQKEYEKKKEELKTSVKSNVLEKYGGEEHLEAPPRQLL
LAQTEQYVEYARDGRIIKGAEKVIIRSRYEEDVYINNHTTVFGSYWNNGKWGYKCCKSFV
KNSWCVKSSVGAEIAEGESTEIPSTSGWSSNKEKVAEQNKSDSEHEESEKSSSEKKKESS
ESDSDDSSSEEERKRKSKKRDKKRKKKKKQKDKRAEKKEKDKLQEALEAEDKRIKEYDEM
MTIDERKRKYNSMYEAKAPTEEEMEAYYIKRAREEDPMMQFMKNK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g12931.t1 | Coils | Coil | Coil | 176 | 199 | - |
| 12 | g12931.t1 | Coils | Coil | Coil | 320 | 340 | - |
| 11 | g12931.t1 | Coils | Coil | Coil | 499 | 540 | - |
| 6 | g12931.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 61 | - |
| 5 | g12931.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 15 | 59 | - |
| 4 | g12931.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 193 | 223 | - |
| 3 | g12931.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 435 | 532 | - |
| 7 | g12931.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 439 | 454 | - |
| 8 | g12931.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 455 | 496 | - |
| 9 | g12931.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 497 | 513 | - |
| 10 | g12931.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 514 | 532 | - |
| 2 | g12931.t1 | PANTHER | PTHR12942 | STEP II SPLICING FACTOR SLU7 | 23 | 583 | 3.2E-198 |
| 1 | g12931.t1 | Pfam | PF11708 | Pre-mRNA splicing Prp18-interacting factor | 160 | 404 | 2.1E-104 |
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 transcript has been annotated with K12819 (pre-mRNA-processing factor SLU7)
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.
