RnoINT0032865 @ rn6
Intron Retention
Gene
ENSRNOG00000020151 | Cdh1
Description
cadherin 1 [Source:RGD Symbol;Acc:69279]
Coordinates
chr19:38834706-38838395:+
Coord C1 exon
chr19:38834706-38834849
Coord A exon
chr19:38834850-38836576
Coord C2 exon
chr19:38836577-38838395
Length
1727 bp
Sequences
Splice sites
5' ss Seq
GAAGTAAGT
5' ss Score
9.82
3' ss Seq
TCTGGTGCTCTTCCCTTTAGAAC
3' ss Score
10.13
Exon sequences
Seq C1 exon
GACTTTGATTTGAGCCAGCTGCACAGGGGCCTTGATGCCAGACCGGAAGTGATTCGAAATGATGTGGCTCCCACCCTCATGAGCATGCCCCAGTATCGTCCCCGTCCAGCCAATCCTGATGAAATCGGGAACTTCATCGATGAA
Seq A exon
GTAAGTAGGCAAAACCGTGAGCCAAGGCAAGTGCATCTCTTAACGCAGAACCAAGGAGAAAACCATTCCAGTGAGGAATGTTGCCTTCCTGGGCCTACGTCCCCGAGACAAAAGCAAAGTCTACTTGCAAAGATTTGGTAGACCTAGAAGGGGTTCCAAAGCAAATTTAGTTTGCCTGGGTTCCCTGCTTTCATTACACCTATTTGGGGGAGTGCCGTAGGAGGCCAGAGGCCGCTCAGCAGGTAGGGAAAGCAACCCCCGAGGACCAGGGTGTGGGTCTGAGGCACCAGCATAAAAGGGCCAGCATGGTGGCCTGTTTATTCCAGTGTTCAGATCAGAGCATCTTGAATCGGCCAGCTCTAGGTTCTGCTGGGATTAAAGTGCATACAAATACACACTATACATAGCACACGCAATGTTTCCTAGTTTACCTAAGGCTTATAAAAATAGCACATCATGTAACATATTCAGATATTATTGTATGTGTCAGAAACCTGTTCAGTTCTAATCAAAAAACCTTAAGATAATAGGAGATGCTATGTTCTAGTCTGTTGTGTACACACACACACACACACACACACACACTCTACCATTCTGCTCCATTAACTTGGTGTCTTAGTTATGTTTCTTTTTTCCTTTTGGTTTTTCTTTTTCTTTTTTTCTTATTTTTTTCAGAGCTGGGGACCAAACCCAGGGCCTTGCGCTTGCTAGGCAAGCGCTCTACCACTGAGCCAAATCCCCAACTTCCTTTTGGTTTTTCAAGACAGGGTTCCTCCATGTAGCCCTGGCTATCCTGGAGCTGTTTCTTTAAACCAGCCTGGCTTCAATCTCCGAGCTCCACCTGCTGCTGCCTCCCAAGTGCTGAGATTAAAGGTGTGGGCTGCCACTTCCCAGTATTAGTTACATTGTTAGGGCTGTGCTGAAACACCATGACCAAGGTAACGGACAGAAGAGTCTAATTTGGGGCCCTAGAAGGTTAGAGTCCTTGATGATCATGGCAGGGGGCCTGGCAGTGGGTAGACATGCACAGCTGGAGCAGAAGCTGTGAGCTTGTGCTGTGATCTACAAACAGGAAGCAGAGAGACAGAGACACACACAGAGGCAGAGAGACCGAGAGAGCTAATTGGAAATGACCGGCCTTTTAAAATCTCAAACCCAGGCCACGCCTTTAATCCTTGCAACTCGGGAGGTTGTAAGTATTGGTAATCTCTGAGTTTGAGGCCAACCTGATCTACAGTGGGAGTTCCAGAATGGCCAAGGGCTACATAGAAAAAAAACCTGTCTTGAATTCAAAGGAAAACAGAAAAAACCCACAAGTCTGGCCTCAGTAACACACTTCCTCCAACAAGTCCACACTTCCTAATCCTTCGAAATTTGTCCAACTGGGGACCAGGAATTCAAACACTGTAACCCTGACTGACCTTGAACTATGGAGTAGATGACTTTGAATTAATTTCTGATCCCCCATCTTCACTTCTTAGAATTAACATCTAACAATCCTAGCTTGTCGTCTCTCCTTTGAGGATTTTCTGGGCTGAATTATTATCTATATTTATTAGTGTGACTGTTCTCATCTCTCTTTAGCTCTGTTCAGCCTGGTATCATGATTTGTGCTAGGGTGTGTCTGTGTACACCTTAAAGGGTTAACTACTCCCTGGTTACCTTTTCATGTTTTGGGTGTTGCTGGCCTCAGATGCATAATCTAAATCTGGTGCTCTTCCCTTTAG
Seq C2 exon
AACCTGAAGGCAGCGGACAGTGACCCCACAGCGCCCCCTTACGACTCTCTGTTGGTGTTTGACTATGAGGGGAGTGGTTCTGAAGCTGCCTCCCTGAGCTCGCTGAACTCCTCTGAGTCAGATCAGGACCAGGACTACGATTATCTGAACGAATGGGGCAACCGGTTCAAGAAGCTGGCCGATATGTATGGTGGCGGCGAAGAAGACTAGAGAGTCGTTCCTGTGTGGCACCATGGGAGATGCAGAATCATGATGTCAGTGGTCTTTCAGCTCCTTCCCTGACTTTGTAGAAGAGAGACTGATCTGAGAAGTATGCAGATTGCATACTGGTCCCACTCTACCTACCAGTCTGTCTGTGTTAGGAGGGTTTTCACTGGTTGTTGGAATCTTTTTCTAAAATGTTTTTGTTTTTACAGTGCTGTGATGTGATGAACTGTACCCTCTTTTTGTTTTTGTTTTGAGCTATGTTCTGCTCCGGACACACAGCCCCCAAGCCCTTCACCCCTCACTAATTTTTTTACATTGTATACTTTCACTCAATTACCATGTTTATGTTCTGTATTCTAATAGCCACTAAGTTCCTGAATTCTGTTGCCTGGCCCAGGTGCTATTCTGTGACACAGTAGTGCCTGGGCCCTTTTATGGTAAGAGACAGGTTTCTTGGTGTGGGTGCAACTGAGCTGGATAGTGTATGTTTCAAACACCTTTCCTGTGTTCTCTCCCCACCTCCAGAGTGTCTTTACTTATTCAGCTGTGTGTTTGGGGCAGAACAAAAAAATAATGGGACCACTATGCAAGCTGCGAAGATTCTAAGGTGCACACCTGATTCTTAGGCAGATGCCATAGTGAGATATGTTGCTTTGGTTCTCTATCCAATGCTGTGACCGGGACCTGCAGCGAGGTTTTCGGACACCGTGGTTTCTTGCGTTTCTTTCAAACCAGCAGTAAAAAATGGTTTTTTCTGAGAGAGACTGGAGTGCCACCACCAAAGATAGAGGAGAGAAGCCAAGCTTGGGGACAGCAAGCATGCCAGTGAACCTGACCACTGTCATGAGTCATGTGGGTGGCCACATGTCCGTGAACCTGGCCAGTTGGCACACTGATGGTGAGGGTACAAGGAGGCTAGACCTCGTCCCACAAAATTTCTGGAAGAATTAGGGTTGTCTCAGCCAATGTTTCCTAGCTGGAATCCTGTCCATGTATGTGTTCCTGAAGCCCAGGAAATACACCCCTCTAGTGCCTGCTTTTGATGGTAGTTATAGAAAAGACCGGCTGATTTGGACCTGAGTTGCCCAATCTTAAGTACAAATAGAAAACTGAGACTATGCTGGGTGTGTTGGTGCACGCCTTTAATCCCGGCACTCGGGAGGCAGAGACAGTCTCAGATCTCTCTGAGTTCAAGGTCAGCCTGGTATAGTAAGTGAATTCCAGGACAGCCAGGGCTACACAGAAACTCTGTCTTGGAAAACCAAAAAAGAAAACTGAGAATATTAGAGATTGTGCATTTTCTCAGAAAGCAGGAAGAAAACACCACTCTGATGGGAAAAGGGAGGCAAGGCCCTTGAGACTTTTCATTGAAATTGCTGTACTCACATAATTTTGGAAGCAAATGATGACTGCAATCAACTGTGAGAACTGTTGGTTTCTCTGTAGTTTAATTGTCTAATGTTGATAGCGTGCCCTTTGTATGTAGTTTGAGTGTATATGTGTGTGGGTGCTGATAATTTTGTATTTTGTGGGGAGTGGAAAAGGCAAGCAATCGGAACTGTTCTCTAAGATGCATTTTTATGAATTTTATTAAAGAGTTTTGTTAAACTGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020151:ENSRNOT00000027346:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.542 A=NA C2=0.681
Domain overlap (PFAM):
C1:
PF0104912=Cadherin_C=FE(31.8=100)
A:
NA
C2:
PF0104912=Cadherin_C=PD(43.9=92.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CATGAGCATGCCCCAGTATCG
R:
AGGGAAGGAGCTGAAAGACCA
Band lengths:
347-2074
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]