General information for g12931.t3
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.t3 | TSS | g12931.t3 | 26977760 | 26977760 |
| chr_1 | g12931 | g12931.t3 | isoform | g12931.t3 | 26978198 | 26979735 |
| chr_1 | g12931 | g12931.t3 | exon | g12931.t3.exon1 | 26978198 | 26979439 |
| chr_1 | g12931 | g12931.t3 | cds | g12931.t3.CDS1 | 26978347 | 26979439 |
| chr_1 | g12931 | g12931.t3 | exon | g12931.t3.exon2 | 26979499 | 26979735 |
| chr_1 | g12931 | g12931.t3 | cds | g12931.t3.CDS2 | 26979499 | 26979515 |
| chr_1 | g12931 | g12931.t3 | TTS | g12931.t3 | 26979790 | 26979790 |
Sequences
>g12931.t3 Gene=g12931 Length=1479
GATCAAGTGGGCCAACATTAAAACATCAGAGACCACAAGAAGAAAAGCAAAAGCAATATT
CAGGAGTTGATGAATGGTATAAGAAAGGAGTTGATAAAAGCAAAGTTGCTACGAAATTTA
GAAAAGGAGCATGTGAGAATTGTGGTGCAATGACTCATAAGAGAAAAGATTGTCTTGAGA
GACCAAGAAAGGTCGGTGCAAAATTTACAAATGCACAAATTGCATACGATGAATTTGAAC
AGCCAGATCTGAAACCAGATTTTGATGGGAAAAGAGATCGTTGGGCAGGCTATGATCCTT
CAAATCATCGTGAGATTGTTGAAGAATATCAGAAAATTGAAGAAGCAAAACGGCAATTAA
AAGCTGAAAAATTGAAAGAAGACCCAAATGCAGAATCATCGAGTGAAGATGATGAGGATA
AATATGCAGATGGTGTAGACATGCCTGGTACAAAAGTAGACAGTAAACAGCGTATCATTG
TGAGAAATTTGCGTATTCGTGAAGATACAGCTAAATATTTGAGGAATCTTGATCCTAATT
CAGCTTTTTATGATCCAAAAACTCGTTCTATGCGTGAAAATCCCAATCCAAATAAAAATC
CTGAAGATTTAGAATTTGGCGGTGAGAATTTTGTTCGTTTTACTGGCGACACACAGAAAC
ATGCAACTGCACAATTGTTTGCATGGGAAGCATCTAGCAAGGGCGTTGATGTGCATGTTC
TTGCTGAACCAACAAAATTAGAGTTGCTGCAAAAAGAATATGAGAAAAAGAAAGAAGAAC
TCAAAACTAGCGTTAAAAGTAATGTGCTAGAAAAGTATGGAGGAGAAGAACATTTGGAAG
CACCGCCAAGGCAACTTTTGCTTGCACAGACTGAGCAATACGTTGAATATGCTAGAGATG
GACGAATAATTAAAGGTGCCGAGAAAGTGATTATTCGAAGTCGTTATGAGGAGGACGTTT
ATATCAACAATCACACGACTGTATTTGGTTCATATTGGAATAACGGAAAATGGGGATACA
AATGCTGCAAATCGTTTGTCAAAAATTCATGGTGTGTTAAAAGTTCAGTAGGAGCTGAAA
TTGCAGAAGGTGAATCAACTGAAATTCCATCGACAAGTGGTTGGTCGAGTAATAAGGAAA
AAGTTGCTGAACAAAACAAATCAGATTCAGAACATGAAGAAAGTGAGAAATCATCAAGTG
AAAAGAAAAAAGAATCGTCAGAGTCAGATTCAGATGATTCAAAAGAAGCAAAAGGATAAG
CGTGCTGAAAAGAAAGAAAAAGATAAATTGCAAGAAGCTCTTGAAGCTGAAGACAAACGA
ATAAAAGAATATGACGAAATGATGACCATTGATGAACGAAAACGAAAATATAATAGTATG
TATGAAGCAAAAGCACCAACTGAAGAAGAAATGGAGGCTTATTATATCAAGAGGGCAAGA
GAAGAAGATCCTATGATGCAATTCATGAAGAATAAGTGA
>g12931.t3 Gene=g12931 Length=369
MTHKRKDCLERPRKVGAKFTNAQIAYDEFEQPDLKPDFDGKRDRWAGYDPSNHREIVEEY
QKIEEAKRQLKAEKLKEDPNAESSSEDDEDKYADGVDMPGTKVDSKQRIIVRNLRIREDT
AKYLRNLDPNSAFYDPKTRSMRENPNPNKNPEDLEFGGENFVRFTGDTQKHATAQLFAWE
ASSKGVDVHVLAEPTKLELLQKEYEKKKEELKTSVKSNVLEKYGGEEHLEAPPRQLLLAQ
TEQYVEYARDGRIIKGAEKVIIRSRYEEDVYINNHTTVFGSYWNNGKWGYKCCKSFVKNS
WCVKSSVGAEIAEGESTEIPSTSGWSSNKEKVAEQNKSDSEHEESEKSSSEKKKESSESD
SDDSKEAKG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g12931.t3 | Coils | Coil | Coil | 53 | 76 | - |
| 10 | g12931.t3 | Coils | Coil | Coil | 197 | 217 | - |
| 4 | g12931.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 30 | 53 | - |
| 7 | g12931.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 70 | 100 | - |
| 6 | g12931.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 312 | 369 | - |
| 8 | g12931.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 316 | 331 | - |
| 5 | g12931.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 332 | 369 | - |
| 2 | g12931.t3 | PANTHER | PTHR12942:SF2 | PRE-MRNA-SPLICING FACTOR SLU7 | 1 | 358 | 2.9E-136 |
| 3 | g12931.t3 | PANTHER | PTHR12942 | STEP II SPLICING FACTOR SLU7 | 1 | 358 | 2.9E-136 |
| 1 | g12931.t3 | Pfam | PF11708 | Pre-mRNA splicing Prp18-interacting factor | 37 | 281 | 6.3E-105 |
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. There were no conditions that were differentially expressed