BtaINT0039184 @ bosTau6
Intron Retention
Gene
ENSBTAG00000030424 | CLEC1A
Description
Bos taurus C-type lectin domain family 1, member A (CLEC1A), mRNA. [Source:RefSeq mRNA;Acc:NM_001076081]
Coordinates
chr5:100311612-100313495:+
Coord C1 exon
chr5:100311612-100311710
Coord A exon
chr5:100311711-100313318
Coord C2 exon
chr5:100313319-100313495
Length
1608 bp
Sequences
Splice sites
5' ss Seq
TGTGTAAGT
5' ss Score
7.65
3' ss Seq
CACTTGGTAATTTGATTTAGTTT
3' ss Score
3.88
Exon sequences
Seq C1 exon
AGCACCAGCGTCCCTCTTCTGCTTGGCGTCCAGTGGCCCTGATCCTGCTGACTCTCTGTTTGGTGCTGCTGATTGGCCTGGCAGCTCTGGGGCTTGTGT
Seq A exon
GTAAGTCCGCACTCTGACTTGGGGGAGGATCCTGGTTTCAAGGTTTGTCTAGGATAAGAAACACTCATTATTTTTTTTAACTTTGATTCTGGAGCCTGTGAATAAGTCCTTATTCGGATGAAACCCTGTAAATGATGAATATAGTGGAAGAAGCATTAAAATACAACAATCACTTTCCAGCTAAACATTTACATTCTGTTTGCGATAAGAAGGTTTTTGCCTGTTAATATATCAATATTTAACATCAGCAATTTTTAATGAATGTACACATCAGCCCTTTTCCATTTCACAAAAGACTACAGCTGCAGTGATTTTTGTTTCTGTCATTTATGGCTCAGTGGGCCATGCAGAGGGAAAGATTTAATTTATATCCAATCTCTTCAAGGTACAGAGAATAGACCAAGTCTTTAATCACTATAATATCTAATATTAAATATTATTTTTAAAAGGGGGGCTTCCCTGTGGCTCAGATGGTAAAAAATCTGCCTGCAATGCCAGAGACCTGGGTTTGATCCCTGGGTCTGGAAGATCCTCTGGAGAAGGGAATGGCAATCTATTTCCGAGAATATTTCAGTATTCTTTCCTGAAAAAGTCCATGGGCAGAGGAGCCTGGCGGGCTACAGTCCATGGAGTTGCAAAGAGTCAGACACGACTGAGCGACTAATACACACTCACACTCACACACAACTATTGTAATAAAGAAGTCCAAGAAGTTATATAATCATTTTGCAGAGACTTGTGGAAATCAAATAAAGAAGAATTCATGTATAAAAGTCTTTAATTTTCAAACTAGTAAGAATAAAGTTTAAAACTCAAAAACAAAAGGGGATAAATTTATTTCAACAGATGGGACCCTTTAACAATATGTCCTGAACAGTTGAAGAAAGTTGTTAACAGTAAAAGCAGGTTTTAATGTCAAAAATTTCATTTTTATAGGAAATTTTAGACCTTGTTTGTAATCTTAAATTAAATTTTTTTTTAAAAATGTATCTTAATGTTTCTACCCTGGCTCCCCAACTTTGATATAACTGTTGTTTTGCAGGCAATATTCTTTTCAGTGATAGAAAGTGACTCTCATGATTCATGGAGGATGTTTCTACTTAGATTTAGAAACTTGGAATTTAAAGCTAAGTTGAAATTTTCTAGCCTAGTCACATTGAGAAAATTACTTGTTCTCGCTGAGCCCAGTTTACAAAGCTATAAAATATAGAAATGATAATATTACTATGAATGTGATAAAAATATATGGTACATTGTCAATACTCAATATAATGATTAATAGATAAATGATGTATACTTTTAGGTTGAGTAATGGTTTGACAGTATACACAGAAAGATTTATTGAACAGTAAATATATTTAAGGAGTTTATCCCTGAAGCTGGGAACAGTTATTATAACTCTACATTTTCAGATAAGGAAATAGAGAAATTCATTTGCCCAGGGCAATACAATTTATTATAGCTAGAGTCCAAACTTGAATGTAGGCAATATGAGATCTCAGAGCCTGGGATCTCAAACAGCATACTGTTTTGTTTTCCCCAGGTGTAGACAATAGAAATAAAAGTGAAGAAATACTCTGTCCAGCCTCACTTGGTAATTTGATTTAG
Seq C2 exon
TTTTTCAGTTCTACCAGCTCTCCAACACTCAGCAAGACAGCATTTTGCAAAAGGAGGAAAAACTGGGGAATCTCTCCCGACAGCTGCAATCTCTCCGAACCCAAAACAGGAAACTTGCAGAAACTCTGCATCACGTGGCTGAGAAACTCTGTCGTGAGCTCTATAACAAAACTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000030424:ENSBTAT00000019328:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.118 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF083915=Ly49=PU(25.9=82.4),PF041569=IncA=PU(31.8=79.4),PF039189=CcmH=PU(25.3=61.8)
A:
NA
C2:
PF083915=Ly49=FE(54.6=100),PF041569=IncA=PD(67.1=95.0),PF039189=CcmH=FE(71.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGCGTCCCTCTTCTGCTTG
R:
TCCAGTTTTGTTATAGAGCTCACGA
Band lengths:
270-1878
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]