RnoINT0042596 @ rn6
Intron Retention
Gene
ENSRNOG00000030719 | Csmd1
Description
CUB and Sushi multiple domains 1 [Source:RGD Symbol;Acc:1305103]
Coordinates
chr16:78662841-78666466:+
Coord C1 exon
chr16:78662841-78662979
Coord A exon
chr16:78662980-78666278
Coord C2 exon
chr16:78666279-78666466
Length
3299 bp
Sequences
Splice sites
5' ss Seq
AAGGTACGT
5' ss Score
10.75
3' ss Seq
ACACTTTGCTTCCTTATTAGTTT
3' ss Score
6.25
Exon sequences
Seq C1 exon
CTGCTTGTGGTGGGAATCTGACAGGCCCTGCTGGAGTGATTTTATCCCCAAACTACCCACAGCCATACCCTCCTGGGAAGGAGTGTGACTGGAGAATTAAGGTGAACCCAGACTTTGTCATTGCCTTAATATTCAAAAG
Seq A exon
GTACGTGTGCTGCAGACTACCTCTTTTCAGTAGGCTGTTACTGCTGTGCCCAGCTCACCACGTTTGTTAACTCAGAGTGCCCAACTTATAAGGAGTGAGTCATCAGCTCAGGCACCTTGTCAGAGGCAGGGCAGTAGGAGAAGAGAGATTTTGTCTTGATGGCCAGCATTCTACATGAAAGACATACATGGATTTCTTTCACACAGTAGCCATCTGGCCCACGGTGTGTTTTGTACATGAAAGCTTCAGACCAGTGATTAAAAACATGCTGTGGATGCTGGAGAGAATACCACCTTAACATCCCGTTTGCTGCACACTACAGAGGCTGACTCTTTCCCACAGCATGTTCTGCTTGACGGTCTGCAGGGCAGTGCGGTTTTCGTCATTAAAACTGCTGGGATGAAGGAGAGATAAAAACAGGAGATTCCCCATATCAGTGTCCAAGAAATGGTCATTCACACCTGCTATACAAGATGATAAAACTCAGTACCATAAGGATTTATTAAAGTTAACTCCATTGTAACTATGGATTAACCATGAAAGGTCCTCTGCTTCTGCTGTTTGAACTTTTGGACACCAGATGACAGTTGTTTAGGGGACATTTGGAACCTTCTGAACATGAGGTCTTATTGATAGGCATATAATCATATAGGTGGAACTTGGGTGGGGGAATATATCATAGCCCTGCTTACAGGTAGGCTGTTTCTGGGACACCATGATAGAAGTAAGCCAGAGGCCATAACCTCTGGCCTTCAACCAAGAATGGAGAATAAACAGCTATTCCTTACTCACCATTATAAATTATAGCCACTGGGCTAGGAGAGTGAATATATCATTTCTTCCTTTGGCTGCTTTTGTCAAGCAGTTGTTTACTGTGAGAGGAAATACTTTTTACAGAAATAGATTATCACATTAGTATTTGCTATATGGTAATTGCATTTTAGCAAATACTGAGATCTTATCCAATAACAATACTTCGATTTCTTAAAAAAAAAAAAAAAAAAAAAAAAAAACGTAAATGAATGTGATGTTCCGAAAGCTAAATGTCTGAACAGTGGTGGTTGCTATCCAGGCTCTTAAGCCACCAGAACAAAGGAGACTAGATATTTGATTTCTCTGACAGGAAACAGGCTCCTTGTCTTCAGCTTGTGAGCCAGCTCTCAGCCCCTCATGGGTGCTGGCCTCTCTTACTGTCTCTGATCCAGTATAACTGATGGGTCTGAGATTCCACCTTAGTTGGTAGCTGGGTACTAGCTCCTGAAAGTGCTTCTCTTAATGATCAAAAGGACAAATACTTTCAGGATGCTTGTCCAGCATGCGGAATGAGTGAGCCTTTGCTGGTGGAGACAGCCTTGCAATTGTTCCTTGCAGTTTAGTAGACCTTCCTTAAAACCTGGATGTTCATCTGATTCCTGGAGATAAAGAGTGAAGTGACCATTGCATCCAAGCAGAGGCTCATTACTCAGTTTCACACTTTCCCCTGTGGCAATGACCAATGGTCAAAGACACAAAGGGACATTTCATTTGATAATCAATAAGGACATTTATCACAGGAAGTTTCCCTGCTGTGTTGTACAAACCTCTCTGAAAGATATACAACACAAAAAAATCCCTACACTCTTGGGTTCTATGAACCATTAGTTTGTCCCCTATCTGTTTAGTTCTACATTTAGGCAGCTTCTCTGAGCTTAAAATCATTGTGTTAAGATGAGCACCATCAAAAATGGTCCATGATAAAAAAAAAAAAAAAAAAAGATGAGCACCATCTGAGTGACCATGCTGTCACTGTCACAAAAGCCATATGGTGGGAGGGAAGTAGCCAGAACATTGTGTGGGGACAAGTATGGTCAAATAGGAAGAATATGAGACACACTGCTGAGGCCTCCATGTGCTGACATCATCCATAGTCTTCAGAGGACTCTCCCAGAAGACTGAATTCTGATGTATTCTTGTGGGGATGATAAGAGTCTGACATTAGAAAATTGGAAGAGAGCATTCTAGGACCACAGGCAAGCTGTTGACTACAGGGAACAAGATGTATCACTGTCCCTGTAGATTGTATGGTGATACAGATTCATGGGGAATTGAAACTCTCTAAACACACTGGGTTAAACCTAAGGAAGTTACTATGATTTGTAGTTATATAACGTTATGGTAAGTAGAAATAAGCCTGATTATTACAAAGGAAACTGGAATTAATTATAAATTAAACACCAGGACACCATGTCAAAACTATTGAATGTCCAAAAGGTGGTTCAGCACAGAATATGTTTCTTTTATTTCCAATGTCTGATTGAATTTCAGTGTTCAATGGGTAATTATGACCGTAATCACCTTTGCTAGACACAGGTGATGGTACAGGAGAAGACTCTAGATTTATCCATGACAATGACCATGACTAAAATTATTCTTCCAGCAAAATCAAACATAACACTTGTGATTATACCAAATCTCTGAACTTTGAACCTCTGCTCCTCCTTCATCATGTCTGACAGCAGCGGACTTGTAAATAAGATTTGAATTGACAAATTTATAAATTTACAAGCAGATTTTTAAAAAAAAATAGTGATGTCACTGTGACAATTAGAGCAGACAATGCAAGTCTTAACATGGACTGGATGTAGAAAAGAAAGGAGAGAGAAACACAGACTGTGGGAAGGAGGGAGAGCGAGAAGGGATAATAGAAAGATTGGTTGGTACATTCAGCGTGGTAACATGATAGGTAATGTCTGTGCTCTACCCATGCAGAAACCATAACCGTTGGCCCCCTCACCTAAAGAAAAAGTAATAATTACAGTTTTTAATGTAAAAATAAACCAATGAGAGGTTTTCAATTTTTAACATTTAGAATATACATCAGTACCAAGTACATATATTTTAAATCTCAAAATGCTCACCTAATAATCAAGATTCAGTGGGAATCTGTCTGTTTTGAGTCAGGCTTCATTCAAGTCATCCTTAACTTTACTAACTTCATGGGAAGAGGACAGGGTGCCACACCCATGATGCTATACCCCTGATGCCACACCCATGGTGCCATTATTTGTTTAGTTTAAACTTTATTCAAAATTGTCTACTACCAAATACATTGGCCATTATGCAAAACACTGATAGAGATTATGACAAGCAATACTTCTAATTTAGCATGTTGATTAGTGTTGTATTTAATTTCATTAACTGTAATCATTTAAATTATTATACAAAATCAAACTAAATGGTAATGTGTTCCCAAAAACGTACTCTAAGACACAAGGTGAGTTTATGTTGGGGACATAGGTAACACTTTGCTTCCTTATTAG
Seq C2 exon
TTTTAGCATGGAGCCAAGTTACGACTTCCTGCATATCTATGAAGGGGAGGACTCCAACAGCCCACTGATCGGAAGCTTCCAGGGTTCTCAAGCCCCAGAGAGGATTGAGAGCAGTGGTAACAGCCTCTTCCTGGCATTCAGGAGTGATGCCTCTGTTGGCCTGTCCGGGTTTGCCATTGAATTTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000030719:ENSRNOT00000057897:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.021 A=NA C2=0.078
Domain overlap (PFAM):
C1:
PF0043115=CUB=PU(41.5=93.6)
A:
NA
C2:
PF0043115=CUB=PD(57.5=95.3)
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]