RnoINT0042641 @ rn6
Intron Retention
Gene
ENSRNOG00000030719 | Csmd1
Description
CUB and Sushi multiple domains 1 [Source:RGD Symbol;Acc:1305103]
Coordinates
chr16:78842296-78850222:+
Coord C1 exon
chr16:78842296-78842428
Coord A exon
chr16:78842429-78847593
Coord C2 exon
chr16:78847594-78850222
Length
5165 bp
Sequences
Splice sites
5' ss Seq
CAGGTACTG
5' ss Score
9.04
3' ss Seq
TTCTCTCTGTTTCTCTTTAGAAC
3' ss Score
11.58
Exon sequences
Seq C1 exon
ATCCTTCCAACTCTGATGCAGATTCTTCAAATCATTACCAGGGCACCAGCAGTGGCTCTGTGGCAGCTGCGATTCTCGTCCCCTTCTTCGCTCTAATTCTATCAGGGTTTGCATTTTACCTCTACAAACACAG
Seq A exon
GTACTGCTGGGCAGAGAGTTGCCTGCACATGATTGTGGCGTGCTGCAGCAGTGTGAACAATGGCATGCTTGAATTCACATGCACATAGGTTTCCTACAGCTGAGAAGCTGGCACAGAGCATGGGTGTGTTTCCTTCTATAAAGGTGTGCACACACCAGGCTTTCTGTTTGATGATTTTTCTTTTGTTCTGTTTTCCCTCATTTGACTTCATCCATTTTGTCATCAGGGTACACCCAAGTAATTAGCTTTAAAGGAATGAATTGAAAGGGACGGTCGAAGGAAAAGCATATACTTGTACTTGTAGCAAGCTATGGGAGAGTTGCATCATTCCAGCAGGAGAGAAAGAAAAGGTTTCCATGCTGTGGCTCTTTCACCTCTATGAATCAAAGATATATTTCTATATCTATATAAATCTATAATATTCATATAAATCTATATAAATAGGCTTATATAGATCTATACAGATATATAGATATCTATGTAAATATAGATATATAGATGTAGATCTATATAAAAATAGATAGATAGATAGATAGATAGATAGATAGATATGACTTTCTCCTTCAGCAAATTAGAAAGTTCTTAATAGTCTGAGTAGCTATCTGCTCCCCATTCTTTAGAAAAATACATTGACATATATTAGCTTGAAAAATCCTTTTTAATGAGATGTCAAAACTTAGATGTTTTGATCAAATTAGAATAAATGGGTTCCTTTCTTTGGGGGTACTATGCATGAACACACTTCTTTTAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAGAAGAAGGAGGAGGAGGAGAGGAGGAGGAGGAGGAGAGGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGAGAAGGAGAAGAGGAGGAGAAGAGGAGAGGAAGGAGAGGAGGAGAAGGAGGAGAAGGAGGAGAAGGAGGAGGAGAAGAAGAAGAAGAAGAAGAAGAAGAGTAGTCGTAGTAGAAGTAGTAGTAGGAGTAGTAGTAGTAGGAGAAGAAGGAGAAGAAGGAGAAGAAGGAGAAGAAGAAGAAGGAGAAGGAGAAGAAGAAGAAGAAGAAAAAAAAAGGAGGAGGAAGAAGAAGAAGAATGAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGCAGCAGCAGCAGCAGCGTAGACAGGCTAGGATGGACCTCTATTAATAGAGCAAATATATAAGATGCACAGGACCGTGGGTCCTAGTCCACTGCATGCCTGCAATCCCAGCATCTGGGAGGTGAAGAACGGTAGACCCGGCATTCAGTGTCATCTTTAACTACATAGAGAGTTTAATTCCAGCCTGGGCTACATGAGACCCTGTCTGAAATGAAGACCAACTGTGAAGGATTCAAACTTTGTGCCTTTTTTCTACATGGATAATATATGTCTGGGAAAACTTGCTATATACCAAGTCATTCCAAAATTCTATTTGAGTTCTTTTAAGTAGTAACACTTTATAAAAAAAATTATGACCCCCCCAGACATGATGTTAACACTTAAGTGGACCATGTGATTGCTTATGTAACGCACAAGTTTCTACTTAGTCGTTATTATACAAACAAAACTGAAGTGAGAATATTTTGTAAAAACTATGCAATAAGCTTCTTTACATGTATACTGCCACACACGTAAGAAACATGAGATCCTCAGGCTATTTGTAGTTTGTAGCTAAGCTTTTCTTGCCTATGGCTACAGGTGTCCTGACTTTACAAACACAGCCAGGAAAGAAATGGCAGGTATTAGCCACTTTCTGCACACCTTGGTCCCAGGTAATAAAGAAAGAAAAGACATGGGGAAACATTCGCAGAAAGCTGGGCTTCTCACCTGTGCTCAGAAGGAAGAGCTCCAACCTTGCCATAATCCAGAGTCTCAGTACATTCATCCTGGTGGGAGGGGTGGGCTTGTCTCGATTGAAGGTTTCTATGAGGGACCAGTCTCAGGTTGCAGTCATCCTGGAGGAGGAAGCTGCTACTTTTAGCGCACACTGTCAACATCACACTTGGACCAAAAGAAGGCTTTGCCTTCCCTCTAAGTATTACCCTTATCTGGAAGGTTTTGCCATCATGGTACGGTAGAGTCCTTGGATCCTCAATATAGCTATGTCTGTGTCAAACAGCACACATTTACAAAAAGGCTTCCTCTGCTCCTTACAGTCCTGTAACTACATTGTTATCAATTATTTGGAAGAAAATAGTACCCTACACAGCAGGTACTGGAGACTTAGTATCTCTGTCTTCTGATGCTGTTACAGCCATCATGTGTCCTCCAGTACCACAGGGCAAGAGGCACTTTTTCTTTTTTGAGGCAGGAATGAAAATCCTTCTTCTTATGGAATTCCTTCCGTGTTAAGAGCAACTGCGTGGATTCATAATCTGTGTAAATTCATATTCACTCAGTTAGTGTCCTACTGCGAGAACAGCTCAGGCCTGTTAGAAAGGCTTTCTTACCTTTCGACCCTGTCAGGTGTGTGGGGAACCTCTGGTTCTCGCTCAGCCCTGAGACCAGCTGGACAGTTCCCTGTGTGTCAGAGAATCAGGCCCCAGGCTTCCTTAGAGAGGCTAACACCTCTGTGGGTCAGAATCAACTGTCCTTGGCAATGACAATATTGTATAAGCATCTACATTCCTGGATGAGTTAAATGAGTTCTGGCTGTATCTGAAGTGTGCGACAGGGTGCCCCCTAAGTTGATTCAGAACATTACAGAGTGTGTCTTTAAGCCCAGGAGCTTCCTAACAAGTCTCAGCTGTCAGGTCAGGCACTTTCATGAAGGAATGTGGGGAGAGGCTTCCACACTAAGATACCAGCTAAACACAAACTATCCATGTACCACTGCCTTCCTTCTCCAGAGAGTAGAGCTGCCTTCATTGTCACGGTGATGGATCCCCCCACTTCAAACGAACCATGCTCAGAGGGCTGCATGGTGAATAGAGAGAAGGCATGTTTTCCTCCCAGGTTTACTGAGGAAACTGGGGCCATTGTGATGAGCACATCCAGAGACTCCGACATCTCTCTACTCCCCAGCCATATAAGAAAGGAGAATACTCTTGAAAGAAAGGATGTAGAAAGCCAGGGTCCCAGCCTTTCACTGGGTACTTTTCTTTTGAGACTTTGCAATGAGCACTAAATATTTTGGGTTCCTGTCCCATATTTCAACTCCAGTAGACTAAGATATTCCTTAATGACATAGCTGGGCATTACTTAGCAGACACCACAAAGTCCCCACGGGTTGGAGTCCCTTTCCCTCATTCATCCACATTAAGAAGAGGTTCTCCATATGCAGAGGGCCACAGCCAAACAGTAGGCAGCACAGAGGTAATCCTGCTGAAGAAGGGGAGGAAGAAAGGTAGGAGCCGGAAGGGTCAAGGATGCCACAGAAAAATCTACAGAATCAATAAATTTGGACTCACAGGGGCCCCCTGAGGCTGAACAGACAATCAAGGAGCCTGCATGGGTCTAACCTAGGCCCTCTGTATATGTTCTAGTTGTGTAGCTTGGTGTTTTTCTGGGACTCCTAACAGAAGGGGTGGGGCCTGTTTCTGACACCTTTTCATGCATTTGGGACCTGTTTCCTCCTATTGGGGTGCCTCATTAAGCCTTAAGATGAGGGGAGAGGCCCAGTCTTATCGCAACTTGATACAGGATGTTTGGTTGTTGTCTCTAGGAGGTCTGCTCTATTTTGAAGGGACACTGGGGAGGAAGGGATAGGGAGAGGGGTGAGAGAAAAGGCTGAGAGGAGGGGAGAGGAGAATCTGCAGACAGGTTGCAGTATGTGAAGAATAAATTTAATTTCAAAAAATGTCAGCTGAAGAAGAAAAGAAAAAGATGATGTGGAGGAGGAGGAGGAGGGGGGGGAGGGGGAGGAGGAGGTGGTGGTTTTCAATCAGAGTCCATGGTCCTAAGGAAACCTGCCTCACTGAGATAGGTCTCTTGTCTGGTGTGTCTTAGGGTATATGGGTATTACATGTACATTTTAAGTTGGTATGTACAGTTATGCATCCAGGTGCACATACATGTGTGTGTGTCTCTGTAGGCCTGGGATCTACAATGGGTCACTTCTTTGTAGCTCTTCACCTCAGCTTTAAAGACACAATAGCTCACATAACCTGGAGCGCATGGCCTTGGCTAGGATTACCACAAGCCAGTGAGCCCCAGGAATCTGCCTGTGTGTCTCCTCAGTGCTGGGACTACAGATGTGTGTCACTGCTTCTGGGATTTTATGTGACGATTTGAACTCAGGTCCCCATGCTTGTGAGCCAAGTACCTTACTGACGAGGTCAACTGCTTATCCTCTTGTTTAAGTCTTCTTATTCTAAAACCTCCCTTTTAAGCATGGGTTGTGACTAGAGGGTTCCCTTTACCCACAGAAACATTTTGATAATACGTCTCATTTCAATAAACACGCTCCTTAAAATATATAGTTCTTTTGTTTTATACATGAGTGTTTGCCTATGTGTACAGTGCCCATGGATGCCAGCAGAGGGCGACAAATCCCTCCAGAGTAAAATTACAGGCAGTGAGCTGCCAGGTAGGAGCTGGGAACAAAACCTGGACCCTCAGAAGCAAGTGCTCTTAACTGCCAAGCTATTCCTACAGCCCCAAACTGGCTTATAGGTGACCCACCAGAGGTATATATATATATAAATTAACCAGCATTTGGTGAATTCTGCTAATGGTGATGAACTTATTAGAAATTGAAATGAGCTTTGAGGCACAGGCTGAGCACTGACTTCACCACAATGAAGCCTGTCTCGGCTTCACCAAATCCTTGCTGCTTACTGTCAATAGTTGGGTTTCTAGATCAAGTATCTCCCTGCCTTTGATATCTTCATAGCTCCCCAAAACCTCCCTTCAATGCATAGAGAGGTATTTTGGAGATGGGAAATAATTTCCAACTTTACATTATGTTTATAACCCCAAACGGCAGGTTTTAAAGAGTTAACCACCGGTAAAGTAGCTGCTACACCCCACCCTCTCCATAACTTTACAGGAATGCTTCCTGCTGAGAAAGCATGGGGACTGGGTAGAGGCTCTGTCATTCCAGTTAGGGATCTGACTATGTTCTCTCTGTTTCTCTTTAG
Seq C2 exon
AACAAGACCAAAAGTTCAATACAATGGCTATGCTGGCCATGAAAACAGTAATGGACAAGCTTCATTTGAAAACCCCATGTATGATACAAACTTAAAACCCACAGAGGCCAAGGCTGTGAGGTTTGACACGACTCTGAACACAGTGTGTACAGTGGTATAGCCCTCAGTGCCCCCTAGGACCGACTCATAGCCATACCTCTGATGGACAAGCAGTAAAATCCTTTGGTGCCATATACCACCCCCTTCTACTCTTACCTTGCTGCAGCAACGTTGGCCATCGTCTGCTGGCATAACGCAGTGGGAATGTCTTCTCCATCATGCCCGAGTCTTCTGAGGATCAAATTGCAAATACACCTTCATCTGGAAAGTGGCTTATAAAAAGCCCGGTTGCTGCATCCACCAGAAATCAAGACCCCGACAACAGCGAGGGCAAGGAAGACTGCAGAGTCTCCCAGACCGGTGGTACTTAATGCCTCTGACTTTTGTGTCTCTGTGTGGCCAGGATGCCTTTGGTGTAGTCTTCTGAGCACACCGATACATCCCTCAGGTGCGGCGACAACATGGTAGCCACTTGATGTGTGTTTTGTGTTTTTCTGTTTTCTTTTCAACCCTATCCACTGGACATGAATTCTTTACAAAAGAAAAGCCTTCCTGGAGAAGACGCCTTCTGGAAAATGCACACACAGACGCTTTGCTTCTGCCCTGCCTGAGACAGGAGCTCTCCGGATCTTCAGGCTCCACTGGGCGTCCATCAGCCACTAGGGATGTTTGCAGATCTCACAGTCAGAGCTGGTCCATCCCAGAGTTTTTTGATGCTCAACATTTTGCACTAGTGTGTCAAGAATGACTAAGTCTGATTTCTAAACAAACTATTTCCACAGGGTTTGTATCCACTATACATTGTACATACGCATTTTCTCATACCGTATTCTCAAGCAAATGATGCCACTGTCAGTTAAGTTTGGGATGCAAAGGAAGGTCTCCCCGGATACAGAACAGATTTTGAAAAGGAGATAGTGCTAGTAATGCTGAAGAAGTTACTCTTTTAATTGCTTCTGTTGGCCACATTTTCATGTCAAATTCATTGCCTACTTCCAGTGGTGGAAATGAAGCCCGTGTATTCCCCTTGGTATCCCCCCACTTCATGTGCATACGACTATTGTCTACACCATACTAATCAATAACAGGGGGCTCCAGCAATGTCTGTTTTCCATGTACAGATGTGAATAGTAATTTATTTTAGGTAGCTCATGAACTCAGTTCACAGTGAAGTCTTCCCTTCCGGATTGTTTCCTTTCTCTGTTTTGTAACATCACCCTCCCAGAATGCATTGAGAGTCTATCTCACAGCCACACCCAAGCTCAGAGGAATCGAAAGGGAAATCAAAGAAGTCCAAATCAGAATCGGAAGGGCAGGCACCGCTCGCACACCCTCATGATGATCTGTTTTATAGATTATTTGCCTTTTCTGCAAAAAAAAAATCATTACAGTGATTTTTGAAACATTAAAATTCCTTACTGATAGACTATCTATTGTGATATATATAAGATAGGTGGTATGGCCAACAGGGATAAAATAAACAGCCTAAAGACAAGGCAGGGCTAGAGAAATGTCTGTAAGAAATTTCAAAGAGAAGATCATGTTTATTTTTATTTATATTTGTTTGATAAAAGTATTTTTGGAAATATAATGCTTATTTTATTATTTGACGTTTCATGCACAGTCCACGTGGTAAAAATCCCCCCTTTGTACATCCCAGATTTGCACTGATACATGGGTCAGGATGTCATGCTGATGTTCTGTTTGCTGTGGTGACTACATTCATGCCTAGCTTTAAGACAGGTGGATCTGTCTATCTACATGATGTTTAAATGCAGGACTTCCCAGAGGACAGTGGGTAACGGAACATGGCTTGCTTGCGGCTTTGGAAGTTCAGCATTCTGAGCGTTCCAGAGGCCCGGCTGGGCTCCCTCCTTCTAGCCCACTGTTCTTGCAAGGGCTGTCTGTTGTGTGCCAGGGCTCCTGACTTCTTCTGCTGACACTCTGTCCACTGGGTTCCATATTCCAGGACTCCATGTCCTAGGAAAGAGTTTTGACATAGGTTCCTCCAGCCAAGCCGACACACATCCACGGGGTTCCTCTGGGCTCCACAGAGGTTCTTCATTGGCTCCCTGGGATAAATTCAGATGATGTCAGCAAGAGTGTGCTTCTATACCACACATTGAGCCAAAACAAAACAGAGAACGTCAGAAGGTCCACGGACCAGAGTGCGCAAGGGAGAACAGGGTTACTATATATATTAGATGTATATAAAAACACACACACAAACATATATATATTGTACATATCTAAGTTTGAGTCACTCAGACTAGGTGCAAAATGCTGACTTTGGAGTCTAAACTAACGTCTCTGTCCCCACATCCCTGGCCTCTTTCCTGGCCAGTTACATTAAGAAGACTTGACTTAGACAGGGCATACATACATGCAAGGAACCACATCATCAGACCAGTGTCGTTTTCCTTTGTGTGCAAACTGACCTACAGCTACCAGACTGCATCATGGTATTTAAAACCAACATACAATATTGAGCGGCACTCTCAGTTGAGAGCCTAGCTCAATCCTTCCTAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000030719:ENSRNOT00000057897:57
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.311 A=NA C2=0.340
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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]