RnoINT0042645 @ rn6
Intron Retention
Gene
ENSRNOG00000030719 | Csmd1
Description
CUB and Sushi multiple domains 1 [Source:RGD Symbol;Acc:1305103]
Coordinates
chr16:78572533-78578955:+
Coord C1 exon
chr16:78572533-78572721
Coord A exon
chr16:78572722-78578785
Coord C2 exon
chr16:78578786-78578955
Length
6064 bp
Sequences
Splice sites
5' ss Seq
TGGGTAGGT
5' ss Score
6.86
3' ss Seq
TAATGTCCCATTTATTTTAGCTG
3' ss Score
6.56
Exon sequences
Seq C1 exon
AATATGACCTAGAACCCTGTGATGACCCTGGAGTCCCTGCCTACAGTCGCAGAATTGGGTTCCAGTTCGGTGTGGGTGACACCCTGGCTTTCACCTGCTTCCAGGGATACCGCTTAGAAGGTGCAACCAAGCTTACCTGCCTGGGTGGGGGACGCCGAGTGTGGAGTGCACCTCTGCCAAGGTGTGTGG
Seq A exon
GTAGGTGGCCACACGCTTTCATTTCATTCATCCATGGGCAGTGGGTCAGGAAACAGAGAGAGGACTGGGCAGGAATGGCAGAGACTGGAACTGGAATAGACTGGACTAAGGGGAGCTACCTCACATTTGGAGCCTGACTTATATCATGTACGAACTGTGTATCTGTCAGCTAGAAGGTTGGAAGCTAGAAAAGGGAACCCAGTGACTCTGTAAAGGAAAAAAATAGTTTATGTTAAAAAAAAGAAAGAAAAAGAAAAATGGGGAAAAGGAAAATGCTAGAAGACATGCTATAGAAACACAAGTTCTACCATTGCTGAGAGCAACACTCTCTGTGATGACACTGGCAGTTCAGAGGAGTGGCTTTGTTGTCCCTGGGAGCCCTTCATTGCGGGTTTGTAGTGTGATCTAGCAAAGAAGCACCAGTAGTATTTGGGCTCAGAGTTAGCTGTGAGGAGGAGACAGCTTTTCTGCCATGAGGTGTAGCACAGTTCAGTTAACTTGCAAGGAGTTTCTGAGGACATAGATCTATCAGTGCAGAAGTTCAGAACAGTGGTACCATTCTCCTGTTGGGCATTGTGCTAGTCGGAGGGACTGGGGGACCAGAGCCACCATTACCACCTTTGTTTTAACATAAGACTTCTGTGAATCCTGAAGGCCTGGTCTGTTATTCCTGAGACAGAGACTGACAGCTGTCACTCAATCACAACACTCAGCAAATCAGCAGAGGTCTGCTCATGACCAGACATCCTAAAATGGAAACCATGTGAGAGACTGGCCATGTTTTCCCTAAGACTACTCTGTTTACAGAAGTGTATGAAAGGGTCATTCCAAAGTCCATGGCCACAAAACAGAGGCAGGCCTAGGATCCCTAAGAGAGACAGGTCATGAACCAGAAGCAGGCTTGGGATCCCTGAGAAAGACTAAATAACAAGAAATTCACAGAAGGTTAGCAGGATATGCCTATATTTCTCCACAGCTCTGAGTTTCTTTTATTCTAGGCATGACTTAGTACTTGTTTGGAGTCCAAAAGTCAATGCTGGCCTTTGCCTCCTCATGAGTCTCAGAGGATCAATACTCAACTGTAGACGAAATTAAATCATCATCAAAAGTGTTTTTCTTCCTCCTCTTTCTCTTCTTCCCTGCATTCTCATGCTGTGTTGAAAACACAAAGACTATCTAGACACTTCCAAAGTTCCAAAGACTATCTAGACACTGCTCTGTTTATGTTCTGAGAATTTCTCAGACTTCCCTAGGATGGAATCTCCATGTTTAAACACTTTCACAATTACAGTTTGAGTTTTCTGGGGAAACCCACTTAAATGAAATCAAGCAGTTGGTCCAGAGATTGTGACATTCACTTCTTATGCTGTTTTACTTGAATTCATCATTACAACTCTGGTTTTCTTGGTAAACATGATTTTGCACTGTTGTCTTACATGAGAAACAATTTACTGAGTTTTGCCTGGAGGGTACTGTGAGCTTTGCCTGTCTTGATTTATTTACTTGGTGTTGTGTCTAGACAGTAAGCATGGTATTACCAGCTCTATCTCAGAGTTACAACCTAAACAGAATCTTGTCAGGAAATCTCATAGCTTGTAGATTGCCAAGCAGCAGATGCCTTTGGCTTTTACCCACCTACATCTCTAGGGAGAGCCCACACAGGGCTTACATTGGCCTCCTCTCTATTCAGCCTTTTGTACTTCGCCAGCTGCTGACTGTATTTCTTTCCAGCACAACAGGTTGCAAGACACCTGTGTTAAAGAGTCATAAGCTGCACTGAATCCAACAGACCTAAGGCAGACCTTGCACCACCTTGGTGTCTGCAGTTGCCCACACTCCTAGACTTCTGGTTCCTATGACTTTGCCAACTATGCAACTTATAACCAGCTCTGACTCTGGGAGCTTTGCTGTTCCTACACTGAGGATCCTGGGTCCCGACTGACCCCTCAAGACTATGGAAAGAAATCATCTACTCTGGGATACTCACGTACTTCTTCATAGAAACCTAAGTCAATTCTGATCTCACTCAAAAGGAACCTTCTCTACTATATTAAAATTATGATTATTATCATTATCATCATTACTATTATTATTTTACATACTCACTTTACATCCTGCTCACTGTCCATGTTCCAATCATCTCCTCCTGCAATCTTTACCCCCCTCCCCTCCCCCCTTCTCCTAGTGGCTGGGCCCCCACCTGGTTATCTCCCCCACATATCCTGGCACATCAAGTCATCTCCATGAGGCTAGGTGCATCCACTCCCACTAAGGCCAGACAAGGCAACCCAACTAAAAGGAAATATCCCATGAACAGACAACAGCTTTTGGAATAACCCCCACTCCAGTTGACGAACCTTCTTTTAATGATGGCCATGACAGACTCACCCTATCTTGGACTGCTCTCACCCAATATGTCTTTGCCTGAGCCAACAAAGTGTTTGAGCTCAATACTTCAGTATTCTGTCTGCACCCTTACCTGTCTTTATGTATCCCAATGGGGGTGGCTTGGACCACCCAGACAAGTTGTTTTCTCCTGTTTACCAAACACATGCACACACACACACACACACACACACACACACACACACACACACACAAAGTACTTTCAGATCTTCTGTGGTTCCTGCCTCATGGAACTTGCTTGGCTTCATTATCACCCTTTAGACATATATTTCTTTTGCTGGAACTCTAAGAGCTAACTCTTCATCAGATAGATCTAACAGACTTCTTTAAACCCTTCCCTGTTCTGAAATCTTTGATCAATAGATACTATCTCTTCTTTCATTAAGGTTATGAAAATGCAATTGATTTTTCCCCTTGGCCCAAACTTATGGTCCATCCGAATGACTGCAGGTTGATTATCCCTAGCAAATATGTACTACACAGGTTATAGTGAAGACATATTTCAAATGAATGAACTTATGATGTATATTTGAATAAAAAAAATCCAACCACACTTTCTGGACAAAGTATCCTTTAAAAGATTACAAAACCTCAAGACAAGATTCTCCAGTCAGTGGTTATACATTCTTCAGAGAGACATAATAAGGCAAAGTATTGTGCCTGGATTTGGCTTACTCTGCATTTCTTTTGGCACTAAATTTACTGATAAGTCATTTGGCATTCTCTTTAGATATCACCATTTTCACCTGACGAGTCTTTAGTTCCTTTATATTTCTTTAATATTTTGTTTAAATTTTTAAAGTTTTGTTTTGATTATTTTATATACTTCTGTCTGAATGTATGTGGACATATGTGTACAGGTGTCTTTGAAGGTCAGAGGGTACCAGCTTCTCTGGAGCTTGAAGGTCACTACAATTGTGGCCATTTGCATGTAGGTACTGGAAAGTGATGATCCTCTCCAAGAGTGGCAAGTGCTCTTAACTGCTGAGTCATATTTCCAGCCCATCTGCTCATACATTTTAAAGAAAATTAATAGCTAAATTTTCATTTCTGTCTATTCTTAATGGTTTATCCAATGAGAACCCTAATTGGGAAAAAGGGTGTCGTATAAAATAAACTGATTTAACAGCTCCATTGTAGGCACTTTCTAGATATCTTGAGTTAATATAGGACCTATATTTCATTGATGAGGGCTTCCTCTGTTCTGGACACAAGTGAGCAGCTTACTTCAAGTCTGGTGACATAGATATTGTTGCTTCTGTTTTATGGCTTTTTTCTTTTTCTGTTCCAAAGCTTGTATCTGTGTAGGTGAAATTGTATAACTACTTCTATCCATTTCATGACAGTCTTAGAGGCCCCACTATATATATATATATATATATATATATATATATATATATATATATATATATACTCCCAGCAGTATCATCCCCAAACCCCAGTGGCCTGTATGACCTGTATGACCTCTCATGATCACAGAGTTATGCAGATGTGCCAATCTCTGAGGTGACTTAACCATGATTCCAGTTTAAGCCCCAAAGAGGCAGCATGGAAGGTTACATTCCACATAAACAAATCTAAAGAATTAGTATCTCCAGTAAAACAACCTTCCTGTGATTGAATCTTTGTTGGTCCACATAGATGGCATTTGACTAATGCTTGGGTGTCAGCCTCAGCCTGCATCTGAGCAGTGTGCACCTGCAGGTCTTCATGCTTAACCTTGTGAGGGTCCTGTGTTGTAGCAGCTCTCAAAGTAGAGAGACACTTGACTTCATAGATTGATGCCACTCTATATAGAATGAATAGAAGAATCAACTGATCCCCTCCCATCATAACCAATTTTATTTTAATTAATTTAGTCCTAAAACTCTCAAAAATAATCCAATTTTTCATTAATGTTTCATTAGGTTCTCTATAAAGATGAAAGAGATTCATATCAAGGGGTATTATATTCAAGCACTTTAGAGAACTATTAGATGAACTATTGAAAGAATTTTTAAAGACTTAAAAAGGGAAACGTTTAATTGCTGTGATGATGAAGTGGATTCCTTGAACAAAGCTCAAAGAATTTTCAACTGGTGGATCAGTTCACTTGGCAGTTTTCTGAGCATCTGATTCATCACTGTGGATGCCATGGTTTCTGGAGTGACTCCTCCTGGGACGGAAGTCCAGGGTCAGGACCTCTCAGATGCTTGGGTATATTATAGTTCTTGCTTATTGTTGTCCATCTTTGCAAATTGATAGGCTTAATTTCTAGAGTAGGCTACCTGTGACAGGTCATGTAGCATGATGGATTGTAACTGATCAAAGACTATTGCTGTTCAGTCTGTAAAAATTCTCTACTTGGCAAATTCATAATCATAAAAAAAAACAGGAACAACTTAGCAGTGTTGGTCTACTGTTACAGAAATAGTTTCCAAATCTACACATTCTACTGTATTATAATCTCTTAATCGATAAATAGGACAAAATAACATGTAAATAACCATGTATTAATATTTCTATGTAAAATTGCATATAGGTGAATGGAATGATTAATGCAAGAAAGAAGTAATAAACCTATAGATACATATACACATATGATAAGTAGCTGATAGATAGTTGATTCATAATTCATAGATAGAGAACAACATAAACAAAACAAGCAAACAAAATTCTCTTAAAATCCTGGTGGTATGCAGGGTTTGGAGGCAAAGGAAATTCTGTTCCGTCATGATTAAAACAAGGGAAGCAAACTGCTTGAAATTAAGTTCTAGGCAGTTGATGCTACAGAGAAGTTGGTCCCCAGACTGCCCATGCAGAGATGATGATGATGATGATGATGATGATGATGACGACGACGACGACGACGACGACGACGACAATGATGACGATGACGATGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGCAGTTGTGGTTGTTGTGGTACCATTTTTCAGTAGTGTGCATTTTCCCTTCAACATTTTAGAGCTGAGGGAGTTCTTGACAAAAATCACTCACTCCCATGAGTGGGAAAACATATCGTGACCTCAGTGGCTTTCTCAGACTCCTCAGAAAATTGGGTGTCATGTACTGTCAGCTTCACCCTAATTAAAGGTATTTTGTTTCAAGTAAATTTGGTGCTGGAAGCCAGTGACCCTTTTCTACCATGAAGAAAAGGGAAAGAATTCTATGCCTATTATCTAGTGCTCTCCTCTCCACCAGTTCAGCTCTAAGCCACAAAACCTGAGGAAACTTACATTGATATAGGAGTAAAACAAACACTGGCCTGGGCAAAAGATGAGTTAGAGAGAAGACATGGTGAGGCTACCACAGTGCTTGGAGTAGGTTGATTTTATTCTTGAGCTGTAGCTGGTGGTGTGCAAGCTTGATGTAGTAAGAACCATGTGGTTCACATAACTAAGAATAATCTGAAAGGGAGACTGAAAGGGAGACTGATGAGGTGTGCTTCCCACTGAGTTGTAAAACACTAAAATGGTGTCACCAATCTGCATTTGAGAGATTCCTTGGAGAGCAGTCCTACATGGTTAGAGGTGGGGTGGTCATTCTGTTGGAGTTATTAATCTATTTTAATCAATAATTCCACTTTTGAATCCTCTTTTTTTTTTAATGTCCCATTTATTTTAG
Seq C2 exon
CTGAATGTGGAGCAAGCGTCAAAGGAAATGAAGGAACATTACTCTCTCCAAATTTCCCATCCAATTATGATAATAACCATGAGTGTATCTATAAAATAGAAACAGAAGCCGGAAAGGGGATCCATCTCAGAGCCCGAACCTTCCAACTCTTCGAAGGAGACACTCTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000030719:ENSRNOT00000057897:9
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=0.018
Domain overlap (PFAM):
C1:
PF0008415=Sushi=WD(100=87.5)
A:
NA
C2:
PF0043115=CUB=PU(50.9=94.7)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]