BtaINT0139140 @ bosTau6
Intron Retention
Gene
ENSBTAG00000014611 | SORL1
Description
Bos taurus sortilin-related receptor, L(DLR class) A repeats containing (SORL1), mRNA. [Source:RefSeq mRNA;Acc:NM_001192757]
Coordinates
chr15:32684991-32686991:+
Coord C1 exon
chr15:32684991-32685082
Coord A exon
chr15:32685083-32686744
Coord C2 exon
chr15:32686745-32686991
Length
1662 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGT
5' ss Score
10.24
3' ss Seq
TTTTCCCTGGTTTCGCCCAGGGT
3' ss Score
6.57
Exon sequences
Seq C1 exon
GTGGGGCATCCAGACGGCGACTTCCGCCTCACTATTGTCAATTCCTCTGTGCTCGATCGACCCAGGGCTCTGGTCCTCGTACCTCAAGATGG
Seq A exon
GTAAGTGTGGTCCCAGAGAAGATCCATGTGGGTCCAGGGCTGCCACAGATAGAGTCTCTTGGTAATGCAAACTGCTGGCCAAAAACTTGTTTCTTATCATTGTGGTTGAAATAATCTAGGACCTGCAAGTCTTGGAGCCGTAGCTTAGTCATCCTGGGCTGCACACTCCATCCCCTTTCTGTTAGCAAGCATCTCAGTCTGTAGGCACCCAGATGTCTTGCAGCTGTGGGGTGTTTCCCTAACAGAAAATAGTATTTAAAGTCTCTCTGGTCATAATCAGCCAGCCTTGCTTGAATATTGTAAGGAGCCTTTATCTTGAGTTTCACGTGTGATACAAATATTTAAACCATTCTTTCTTTTTCCTGCCCCCAGCTTGTGTTTTCTTACCAGCAATTTGCATGCAAACTGGAAAATGGGAAATGCAGAGGTGCTTCTCACTAATTTATTGCTAACTTAAGGAAACATACCTAAAAAGGGAAATTCTGGATTAGTCTTTCTAGCATTTGTGATTGAGAAATCAGTTTTTAAAAGAAAATTCTGAAAGTAACATATGCATTTGGTTAAAAATATTAAAAGAAAGTAGAAATTTATGAAATGAAAAATATTGGTTTCTTCTTTTCGCGTTCACATTTTCTAGGAGTAATCATGGTTGATATTTTCTTGTGTCTCATTCAGAGTTTATTTTTACCCATGTACTTGTGTACACCCTTTAACACACAGAGACACATATCCACACACATGCATCAAGGAGGATCATAGGATACTTACTATTCTGCATGCTTTAAAAATATTAATATGGTTGGAAGATTTTTTAATCTGAACGCATGTAGATCCTTAGACGTTTTATTGTTCTTTTCTATGTACCATAATGTAACAATTTACAGATTAATATTTTTGTGTGTATATACACACACACACACACTTAAATAGATATATATGTATGTGTGCACATCTACCTATATATGTATATTTTTTGCTAGTGTGGACAGTGGGCTTCCCAGGTGACTCAATGGTGAAGAATCCACATGCAATTCAGGAGACCTGGGTTTGATCCCTGGGTTAAGAAGATTCCCTGGAGAAGGAAATGGCAGCCTACTCCAGTATTCTTGCCTGGGAAGTCCCATGGACAGAGAAGCCTGGTAGGCTACTGTCCATGGGGTCGTAAAGAGTCTGACACAATTTAATGGCTAAACAGCAACAAATGTGAACAATGCTGATGATGAACATGTTTGTACACTCTCTTTGCATAACTTGATTCTATCCATAGATCAATTCCAGTAGAAGAATTTCTGGGTCAGGTAGTTAACTGGCTTTAAGTAGTATAATTAGAGATTACAATAACAAGGCCAAACTAACTGGCTGAATGCTTGGCACTTTGGAGGAGTATTTGAGCGTCCATCTCCCCATTCTTTCCCCAATGGCTTAGTGGTAAACAGTCTGCCTGCAGTGTAGGAGATGCAGGTTCCATCTCTGGGTAGGGAAGATCCCCTGGAGGAGGGCGTGGCAATCCACTCCAGTATTCTGGCCTGGAGAATCCCATGGACAGAGGAGCCTGGTAGGCTGTGGTCCATGGGATCTCAAAGAGTTGGACATGACTGAAGCGACTGAGCACGCACACTCCCCATTCTGATGGGATGTGTGTTTTTCCCTGGTTTCGCCCAG
Seq C2 exon
GGTGATGTTCTGGACCGACTGGGGGGACCTGAGGCCTGGCATTTACCGGAGCAACATGGATGGTTCAGCTGCCTACCGCCTTGTATCAGAGGATGTGAAGTGGCCCAACGGCATCGCCGTGGACGAGCAGTGGATCTACTGGACGGATGCCTACCTGGATTGTATTGAGCGGATCACTTTCAGTGGCCAGCAGCGCTCCGTCATCCTGGACAACCTCCCGCACCCCTACGCTATTGCTGTCTTTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000014611:ENSBTAT00000019457:19
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:
PF0005812=Ldl_recept_b=PD(63.4=83.9),PF0005812=Ldl_recept_b=PU(0.1=0.0)
A:
NA
C2:
PF0005812=Ldl_recept_b=WD(100=51.8),PF0005812=Ldl_recept_b=WD(100=48.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCATCCAGACGGCGACTTC
R:
GCAATAGCGTAGGGGTGCG
Band lengths:
324-1986
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development