GgaINT0078181 @ galGal3
Intron Retention
Gene
ENSGALG00000016341 | CSMD1
Description
NA
Coordinates
chr3:93000657-93004593:+
Coord C1 exon
chr3:93000657-93000789
Coord A exon
chr3:93000790-93004433
Coord C2 exon
chr3:93004434-93004593
Length
3644 bp
Sequences
Splice sites
5' ss Seq
CAGGTATTT
5' ss Score
7.51
3' ss Seq
TTTCTTGCCTTTTATTCCAGAAC
3' ss Score
9.26
Exon sequences
Seq C1 exon
GTCCCTTAAGTGCAGACACAGACCTTTCAAATCACTATTATGGTACAAACAGCAGTTCTGTTGCAGCTGCCATCCTGGTACCTTTCTTTGCTCTAATATTATCAGGGTTTGCATTTTACCTCTACAAACACAG
Seq A exon
GTATTTGTAAATGTTACTTATTTGGGATCTGAATATACTGTTTGTCTTAATTTTGATAACCATAAGTAAGTAGAGAATGCAACACTAAAGCTTTAAATAATATCTTTGTTCTAGAAAGGCAAACATTACTAAGTATTCCACCAAAGGGGGTCAGTGCAGAGAAGTTCTTAAAGGTGAATTAGAAAAATGAGTCACTGTATTGTGAAGCAAAAACCTATAAATTTTGTTTTGTTTGAATATCAGCTTGAAATCTCAGATCATGTTTATTCTTTCATTTTAATGCTCTATTAAATTAAATTTATCATAGATTCCCCCCCCCCCCCCCGCCCAAAAAAAAGAGAGACTACTTACAGTTCATGCTGAACAAGTTAGTAGGTACTACTAATATTGGCATGACTTTAGCATATATGAAACATGTATATATCAGTAGATAATAGAATAAATCTAGTCATTTTTCCTCAAATTAGGTTTAAAAGCAGATGTATGTAGCTAAAGTATATGTTGGCTAGAGCTTTCTGAGACAATTTTTGTTCTTTTTCTATTGACTTACAATATTCTCTGACAGCCTCACATTATTTGCAGTCTGCAAAATGCTGTTTAGCAGAAATACCGATTTAAACAACACATTCATAAACCTCCATTTATTATGATAACAGGAGTATTCTGAGATTTTATGAAATTGCAGAGACAAAGTGAAGTCCACTGTTGGCCTGTGATGGACTTGACAGTCTACCTAGCTCAGATGGTTAGATGACCTATGATGAAAAATTTTGCAAGGAGACATGAACTTGTTAACTCCAGTTAAAATGATACACGTCCAGAAATGAAATAGTATTTGTTGAAAAACAAAAACAAAACCAAACAACAAAAAAAAATTGATCAGGAAAAACTAAGAATTGTGCCTCAGAAGAAAGTTCCTGAAAGGTACCCTTTTCATGCCTGCGTTCTCAACTAGCTCCTCTAAGAAGAGGGAAGCTTATACAGAAGCACAAGGATGATGAACAGGCATTCATTCAGATAGGGTGAAGAAATGGAAAATAAAGGGAAGATTGCTCACACTTTGCTCTTAGAAAGGGGAGGAAAACTCGAAGTGAAATTTAATAAGACTGTACTGAGACCTATATGTATATTTTGCGGTTGTTCTATGAAGTGTTTTATGTTGGATGGGAGTAGAAGATATTTCCTCTTCTATTTGCTAGAAATAGACATATATATTTAAGAGAGCTAAAATTTTGTCTTTAGAAGAGTAGATTCCGTTACATCACAATTTTTAGAGAGGTTATTAGAAGGTGTCTTCAAGAAATTAACAAGTTTGTTACTCATGTAAAACAATTCGAGGTCACCTTTATCTTCTCTGAAAGAAAGGATGTTGCAAAGGAAAGAATAGAATCTATGACAGTTTTAATGATGCAGTAGCAATTATGCCCCTATAATCTATCTATATCAATGAATTTGAAAGTGTTCTTACAGAAAAATTTTACATATATTTCTGTTGTGCCTATGTCAGATTCATAAGAACTAATTAGAATCAGAGCTGTTAGAGCTTTTTTACATAGTTTCAGAACATTTTATCTATCATTTAGGGAGTGCCTCAGAAGAGAAGACAGCATCTTAGTCTCTCTAAACAAAATGAAAATATTAGGAATTATTTATGCTTAGGAAAACTCCTATGTTAAGATTTTTAAGCATGTTTTGTTACTCCTAAAATTAAAATATTGGGGAATAAAAGGTCAATAAATAAAATTAGATTAAAATTAAACATTAATTAAACTTACAATTAAAAATCAATAAATAAAAAGGTCAATAAAATTACAACAACTATTTGTAAGTTGTCAATTTCCATTACCAACATATTTCCAGTGAGAATTTTCCCTATCTGCTACCCAAAACAGAATCATTTTGTAGAAGAGTTTGATTTTCAGAACCCTCTTGAGAGTTTTATCTTGAGATTCTTTGCTAAATTGTTTAACATTAATTAAACACTAAGCATCTATTTTTTGTTCTCCTTCACTGACTTTCTTGCCCTATTTGTTATTGAAATTATGAAATTCTATGCTGAACCTCTTTTAGATTTTTCTTTATCTACTTCTGGACACTGAGAAATTTAGTCTTGAAGTAGCAAAGTACAGTATTTTATTAAATTTACTGTATCATTTTTCTCAACATATTGAGAAGTCTGAATATTTCTACTTCATTTTTCATTTAATTATTGGCTTAATATATTCTAACAGAACTTTGCATAAAAATATGAACATCCTTGAAGTACTGATATATTCTACATAGTGGTAAAATAATATCCAGAATAGAAGAGCGGTTCCTGAAAGATCATTATTTGAGTCCTTTGATATACAAGTGTCAAAATTACTGTAAATATTAGCTAGAATTTGGCCAATCAGATTACAGATGGACACTTCTTTGCTGAGGTGTCTAGTACTGTTTATTGCTGGACATATGTGTGGAGGTAAGCACGTATACTGTGGCAGACAACTGGAATAACCAAAATTAGTCACCCTTATCTGAAGGGTACTACCGTAACAGTGTACAATTTTCTGGACATTTACTGTCTATTATTGCCTCACTGAAGCTATGCTGGATGACTTTGCACTGATTTACATTTAGTAGTGTCAAGGGGACCTGTTACAGCATTTCACTGGTGCAACAGCAACTTCCTGTTCTGGAATGGTAATAAACTGCCAGTAACACGAAATTACTAAGCTGTTTCCACTGCTGAAAAGCACCTAGGTCAGTAAAGGGTATGAGTGTTTATCTAATCTAAAACCCAAGACACAATTGAAAGAATTAATTACGAGTTGCTTGCTTTTATTTTTCTCCATACATCTCGCCATCTACTCTATTCAAGTCTGTTAAATTGACTATTTGTATTGATTTATATCAGTACATTTATACAGATGGTCCAGTTGTCTTCATAAAAATATGGTAAAAACCAGCATGGGTAAAATCCCAAATGTCTGTGAAAGACAATTAAAATGTGCTTGTTTGTGAGAAAATTAAATTTATCAAGTAAAGATGCTATTGCAGTTTTGCCAGCAAAATGAACACTTTAGAAAGACCATTATGTGTATTTGGAAATTGGTAAGGTGTTAATTTAGTAAAATTGGAATAAGTGTTTCCACTTATGGAAAGATTCTTTTATTGTCAGAGTATAGCAATCTAAAAGTGAAAATGTCATCAGAAACCATCATAATTGTTGCTACTGACAGAAACAAAAACAAAAAATTCTAAATGTTATCAATTCTCAAAGGACTTTGTTCTCTTGCTGCACATTGCTTTCTTTCTGCCTGCCAATTTTGGCACTAACAGGCTATGAAGCTGTCATTCTCTTGACAGATTTTATACAGGGAAAATGCATACTTGTATTATGCCTATGTTGTCTCTGTGTTTTTGCGGTATTGGTTTGCCCATTAAGGATTTGTATTCTTCATGTTCTAAGAACAATTTCCCGACAGATCTATCTTACTTTTTAAGTCCTGGTAACATCCTTTATAGATCTCTCTTTATCTGTATTAGACAGAGCTGTGCAGCTTGTATTGATAGGATGAAAACATTAAAGATAAAATCTGCAGTAATAGTAGAGTTTTTATTTTTGTTGTTTACTAATGGCCATTTCTTGCCTTTTATTCCAG
Seq C2 exon
AACAAGACCAAAAGTACAGTACAATGGATATGCTGGACATGAAAACAGCAATGGACAGGCTTCATTTGAAAATCCTATGTATGACAGAAACTTAAAACCCACAGAGGCAAAGGCTGTGAGGTTTGATACAACTCTGAACACAGTTTGTACAGTGGTATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016341:ENSGALT00000036950:64
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.170
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
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]