BtaINT0129697 @ bosTau6
Intron Retention
Gene
ENSBTAG00000016223 | SCRN1
Description
Bos taurus secernin 1 (SCRN1), mRNA. [Source:RefSeq mRNA;Acc:NM_001110803]
Coordinates
chr4:66832884-66834251:+
Coord C1 exon
chr4:66832884-66833086
Coord A exon
chr4:66833087-66834056
Coord C2 exon
chr4:66834057-66834251
Length
970 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
GGACTTTGTATTCTTTACAGAGG
3' ss Score
6.28
Exon sequences
Seq C1 exon
GCTTGGTTTAGAGAGAGGGGCAACAGCTAAAGAAGCCTTAGACGTCATCGTCGCCTTGTTGGAAGAACATGGACAGGGTGGGAATTATTATGAAGATGCTAACTCCTGCCACAGCTTCCAAAGTGCATTTCTGATTGTGGACCGTGAGGAGGCGTGGGTGCTGGAGACTGTAGGGAAGTACTGGGCTGCAGAGAAGATCACAG
Seq A exon
GTGAGTGGGGGTGGCTGGTGGGGAGTTTCAAGGACAGGAAGAGCTAAGGCCATGGTGCCCAGACTTACAGACCTTCTCAGTGCTACATCTGCAGGCTCTAATGTGCTCCTCATTTCTGGGCACCCAAATACACACATATTTGCACATACATTCCATTATTTTAAAACAATTCATTATTGGGGATTCCCTGGTGGTCCGTCCAGTGGTTAGGACTACATTCTGTCATTGCCAGGTACCTGGGTTCAATCCCTGGTTAGGTTACTAAGATCCTACAAGCTGCACAGTGTGGCCTAAATAAATAAATACATAATTCATTATCAGGGTCACTGTGTTTTTCTAAATGTTGGGGCCTGAAAAAAAGTCTGAATGAAGAAGTCCCATAATTTAAAAATTAAAAAAACAAAAAACGTATATATTGATTTGAGCAGAGGGCGATAGTTAAGCGAGACTAAGCGACTTAGCAGCAGCAGCAGCAGCAACCTGGTGAGGAGAAATGTCTGGAGCTGCGACATTCATGAGTCTTGTTAGCAATACAGAGCCTCTTTCAAGGAACCTTTCACTTTTCTCGTGGGTAGTAAACGAGAATAATAATAAAATATTAAAATAAAATAAAATATTAATATTTTATTAAAATATTTTAATGGGTAGTAAATGAGAATAGTAATAAAATATTAATATTAAAATAAAATAAAATAAAAATAAAAACCTTTCACTTTTCTCTTGGGGTTTAGTTTGTCAGGTCAAGTGACTCACTCATTGAAAACGTGATAAAATGTGTCAGGGCTGCTCAAACCTTCTAGGAGATCTTAAAAGAAGACCAAGGACTTTATGTTTCTCTCTTCAGAAATGAAATTGATTCCTCCATATAGTTAGAGTCAAGTTGCAGGGGAGAGCTGCCCTGTAACATCCATTTCTTGATAAAGTCTCTATAAGTCTATGTCTAAATAGTTGGACTTTGTATTCTTTACAG
Seq C2 exon
AGGGAGTCAAGTGCATTTGCAATCAGCTTTCGCTCACGACTAAAATCGACGCAGAGCATCCGGAACTCAGGAGTTATGCTCAGAGTCAAGGTTGGTGGATGGGAGAGGACGAGTTTAATTTCTCTGAAGTTTTTTCTCCAGCTGATGACCATCTAACCTGCTGTTCAGGCAGAGACACCTTAGAAAAGCAAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000016223:ENSBTAT00000021588:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0357710=Peptidase_C69=FE(31.6=100)
A:
NA
C2:
PF0357710=Peptidase_C69=PD(26.5=86.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CATCGTCGCCTTGTTGGAAGA
R:
TCTAAGGTGTCTCTGCCTGAACA
Band lengths:
342-1312
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]