DreINT0048728 @ danRer10
Intron Retention
Gene
ENSDARG00000024032 | coch
Description
coagulation factor C homolog, cochlin (Limulus polyphemus) [Source:ZFIN;Acc:ZDB-GENE-030616-403]
Coordinates
chr17:28726698-28728867:-
Coord C1 exon
chr17:28728354-28728867
Coord A exon
chr17:28727237-28728353
Coord C2 exon
chr17:28726698-28727236
Length
1117 bp
Sequences
Splice sites
5' ss Seq
AGGGTATGT
5' ss Score
8.34
3' ss Seq
TTTTCTTCTTTCTTCAACAGGAA
3' ss Score
12.92
Exon sequences
Seq C1 exon
GCAGTGTGCAAGGACAATGAGTTCTTCACCTTCACCATGCCCAGTTGGTTCAGCACCAACAAGTTTGTAAAGCCACTAGCTCAAAAGCTTTGCTCCATCGATCAGATGCTTTGCAGCAAGACGTGCTACAACTCAGTGGATCTGGGCTTCCTGATCGATGGCTCCAGCAGTGTAGGTGACGGGAACTTCCGGCTGGTGCTGGACCTCCTTGTCTCTATCGCACGTAGCTTTGATATCTCCGACATTGGATCTCGCATTGGTGCTATCCAGTTTACCTATGACCAAAGGATGGAGTTCAACTTCAATGACCATGTCTTGAAAGATAATGCTCTAAGGGCCCTGCAGAAGATCCCATATATGAGCGGGGGAACAGCCACTGGAGATGCCATTAACTTTGCTGTGCGGAGTCTCTTTAAACCCCGCTCAAGCTCCAACAGGAAGTTTCTCATCATCATCACTGATGGACAATCTTACGATGATGTGAGAGTTCCAGCTATGGCTGCCCAAAGAGAGG
Seq A exon
GTATGTATTTTACTCACACAAGGGCATCTAAACTATCTCCAGGAGAGCCTCTGTTCTAGCAGACTTTAGCTCCTACACTTGAAAAGGGAATACATGTTTAGGATCACTAGAAATTTACAGGCAAGTATGTTGGAGCTGACATCTGTAGGACGATGACTCTTTCAAGAGCACGATTGGGCATCTTTGAATTGGCATTTCCTCTAGAATCGGGTAGTCAAAGTGGACAGCCACAGCCCTGAAGGGTTCTGATCAAACTCGGATTAAATCTGACCTGTCTGCCATTTAGGAGGTTGGTTAAGGTTGGAGTGGAACTCTTCAGGACTGTACCTCATTATAACCGAACTTGGCCATCCCTGGTTTTGAAGGGGAACTGTCCTGCAATAAATGAAATAAAAATCTGCAGACCAAAAAAGACTGCCGGACCTCCACAAGCAAGATTGGGCAAATCAGTACTGACCGCAGGAGTGTCTAAAGCAGGGGTCACCAATCTGTCGTGGAGGGCCGGTGTCCCTGCAGGGTTTAGCTCCAACTTGTCTCAACACACCTGCCTGGGTGTTTCAAGTATACCTAGTAAGACCTTGATTAGCTTGTTCAGGCGTGTTTGATTAGGGTTGGAGCTAAAATCTGCAGAACACCGGCCCTCCAGAAACAAGTTTGGTGACCCCTAGTCTAAACGTTCTTCAAGGACCATGGGTCTGCACAGTTAACTCTAACCTTAATAAAACACATCTGAAATAGTTAATCAATGTGCTTAGGCTCACTAGAAACCTCCTCGCAAGTGTGCTAAAGCTGGTTAAAGAGCTAGTTCTTCCTGGAGAAGTATTGGACAACCCTGATCTGAAACTAGGGATCCGTGGGGCTCTGAAGGTCCAGGGGGACCAACGAGATAAAAATGTTATTTGAAGTATAAGAAAGAGTTGCCAGCTAAATCTAGCTGTTTATTTATTTATTTTTTTTTACTGTGAAGGGCCCTGAGGTGGTGCAGGTACTGGTGGGGGACCTCATGGTCAGCAAGGATTAACAATGAGTGATCTTGAACATTCAGGAGCAAAAAAACAAAGGTGATATTATGTCTAATGTCATCCTGACCGTGATTTTTTTCTTCTTTCTTCAACAG
Seq C2 exon
GAATCACTGTTTACGCAGTGGGTGTTGCTTGGGCTCCTATGGAAGATCTGAAGGCGATGGCGTCTGAGCCCAAGGAGAGCCATGTGTTTTTCACTCGCGAGTTCACCGGGTTGGGACAGTTCCAGCAGCCCATCGTCCGGGGCATTTGCAGGGACTTCACAGAGTTCAATTAGACAATTTTGAGATTTTCTTGAGTGCAAGAATATGAAGAAATTCAACAAAAAAAAAAAGGTGTCAGAGTAAATAAGAAAACCACGTTTGTCTTTAGATTTGTAGAAAAAGGGATTTGAACGGTTTTGATATAAAGGAATTGATATGTTTGATCCAAAGGTTTTTACAGCTTTTTTGAGAATGTATCACACAGTATTGTATGTCAACTTCTCTATATGTGGAGAATGTAATTATTTGTGATTTGTAGTCTTTCTCTTTATGTTTCTGTTGAAAAAAACCAACAACACATTCTTTCGCTGCTTCTGGCAAGCCTTTTTTCCTGTGGAGGGGTCACTGTAACAAAAGGCTCTTTTAGAATAATTTCAGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000024032:ENSDART00000000948:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009223=VWA=PD(11.3=11.6),PF0009223=VWA=PU(73.5=72.7)
A:
NA
C2:
PF0009223=VWA=PD(25.9=75.9)
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:
GTGCTGGACCTCCTTGTCTCT
R:
AAGCAACACCCACTGCGTAAA
Band lengths:
349-1466
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]