GgaINT0078138 @ galGal3
Intron Retention
Gene
ENSGALG00000016341 | CSMD1
Description
NA
Coordinates
chr3:92840743-92845274:+
Coord C1 exon
chr3:92840743-92840881
Coord A exon
chr3:92840882-92845086
Coord C2 exon
chr3:92845087-92845274
Length
4205 bp
Sequences
Splice sites
5' ss Seq
AAGGTACTA
5' ss Score
7.52
3' ss Seq
AATTCTCTTTTTCTTTCCAGTTT
3' ss Score
9.18
Exon sequences
Seq C1 exon
CTGCATGTGGAGGTAACCTGACAGGCCCAGCAGGAGTTATTTTATCACCTAACTATCCACAGCCGTATCCTCCTGGGAAAGAATGTGACTGGAGAATAAAAGTAAACCCTGACTTTGTCATTGCCTTGATATTCAAAAG
Seq A exon
GTACTATTTCTAGATTAATGCCTATGTTTAACAGAATTTCAAATTTCACAACTTAAAATGGCATCACTTATCAGTTTTTAAAGCTTCTAATCATATCTTATGACTATGTGTCGAAGCATACATGTAATATGTGCTATAGCATTGCTTCAAAATATCATAAAGGAAAATAACATAGTTATATGTCACTTTTGATATCAAATACATACCTGAACAACAAAAATCGCTGTAACTTCTGAAAAAAGCTTTGAAAACTGTCCTTTTATGGAAATGCTTGATTTACATTTTTGTATTTTACAGTAGAGATTTGCCCTGTACTGGAAACTGTCTATCAGTTCTTAAAGTTTTTTTGTTTGTTTGTTTGTTTTTTTAACAAATGCAGGTTGAATACACTGGTTGGAATGCAGAAATCAGGCAAAACAAACAAACAAACAAAAACAAACAAGCAAACAAAACCAACCCTAAAAATGTAGTAGTATCTTCTTTGTCAAGAGATAAAAGATATTTGGATACCACTATGTCATTGTGATAAAAGAAGTTTTATTTACTCATTATACCATCATCAACCTATATTTGTTGCATATGTTTTTTACACAAATTTAAGTTAAGAAATGTAATCATATTAAAGTTCCAGTTTGTCATTTATATTTGCATCAGGTCTATGTGATCATCTTGGCAAGTGAAAAGTTCTTTTCTACCTTTCGTTTTGTATCCGAAATTTGATTTTTAAGAGAGTAATATTACTTTCTTATTCAATAGGTGTAGATCAATTATGATTCTTTTACAAAAGGAAGTATAAGTGCTCAGGGTTTTGATGTGCAAAATTTGCACCCTTTTATAGGAAAAGAAAAAAAGATCAGTTTTATCTGTTGACTGACTGCAATATGCTTTCTAATAAAATATTGATCTGCAGTAAATGAAAGAATCAAAGCACAAGGAATCTGAAAGTTATCTAATCAATAATTACAAAAATCTGTTCTTTTAGTATTTGTTCAACTAGCATTCAAGAATGAGAATAGTAATGAGAATAGTTAGTCACAAATTATGCTCTTGAAAATATCTCATGATAGGTATGATAAGTAGCATATGTCTGTGGGATGCCTAAATAATAAGCTAAAATAGAATAGAATAGAATTGAATTGCTCATATTGGAAAGACCTTAAGGATCATCGAGTCCAACAACAATCTAACCATAGTATCTGTCAACGGTTTAAGGGCTGGTCTGGCCCAGTTCCGCGACTAGTGGGGCGGAGGGATTTCACAAAATCCGCGCCTCCAGGAAGGGAAACAGGGGACCCCAAAACAATCAAAAACAGCGGCAACGATCTGAGGAGAAACAAACTAATTTACTAAATATAGTATCGGAATGTAAGATAACACACTATAATACAATATAAATCAACAATAATTGAGAGAAAGATTGTCCGAGAGCCAAAGGCCTTACATTAATACTGAAGCCTTGCGTGCAGTCGGGCGCAGCAGTAGCGAGCCAATCCGACAGGGAACACGGCGAGACGAGAAGAGGGACAAGTCAGATGACCTGCGCCCTTATATCTGTTCCCTTGAGCAGGAATGATAACAGTACTCGAAAAGGCTCTTGGGGAACGTAGTTGTTCTTCTCTTCCAGACAGGTACCCGGAACTAAAGCATTTGCTCCTTAGCTCCCAGTACACTGCATGATGTTGTGATGTGGAATAGTGATAACCAAAAATCATAAAAACATGACAGTATCCCAACTCTAACAACCCTCCACTAAATCGTGTCCCTGAGCACCACATCCAAACGGTTTTTAAACACGACTAGGGAATGGTGATTCAACCACCTCCCTGGGGAGCCTATTCCAGCACTTAACAACCCTTTCTGTAAAGAAGTGTTTTCTAATATCCAAACTAAACCTCCCCTGGTGCAACTTGAGGCCATTTCCCCTCGTCCTATCACCTGTCACCAGTAAGAAGAGACCAACCCTGCTCTCGCTGTAAGCACAGTTCAGATACTGGAAGAGAGCAATAAGGTCTCCCATCAGCCTCCTTTTCCTCAGACTAAACAGCCCCAGTTCCTTCAGTCTCTCCTCGTAGGGCATATTCTCCAAGCTTTTCACAAGCCTTGTTGCCTTTCTTTGGACCTGCTCCAGCACCTCCATGTCCTTTCTGTACTGAGGTGCCCAAAACTGAACTCAGTACTCGAAGTGAGGCCTCACCAGTGCTGAGTACAGGAGCAGGGTTACTTCCCTAGTCATGCTCACCACACCACTGCTGATACACACCAGGATGCCATTGGCCTTCTTGGCCACCTGGGGACAGTGCTGGCTCATATTCAGCTGACTGTCCATCAGTACACCAAGGTCCCTTTCCGTCAGGCGACTTTCCAGCCACTCCTCCCCAAGCCTATAGGGTTGCCTGGGGTTGCTGTGACCAAAATGCAGGACCTGACACTTCGCCCTGTTGAAACTCATACAGTTTACCCTGGCCCATCAGTCCAGTCCATCCAAGTCCCTCTGTAGTGCCCTTCTCCCCTCTGGCAGATCAACACTCCCTCCCAGCTTGGTGTTGTCTGCAAACTCACTGAGGGTGCACTCAATCCCCTCATCAAGATCATTAATAAAGATGTTAAATAGAAGCAGCTCCAATACCAAGCCCTGGGGGACACCGCTCGTGACCAGCCACCAACTGGATTTAGTTCCATTGACCACAGCTCTTTGGGCCCAGCCATCCAGCCAGTGTTTCACTCAGCAGAGTGTACCCCCATCCAAACCATGGACAGCCAGCTTCTGCACAAGAATGTTGTGGGGGATGGTGTCAAAGGCTTTACTGAAGTCCAAGTAGACCACATTGACAGCCTTATCTTTATCTACTAAGTGGGTCACCTTGTCATAGAATGAAATCAGGTTTGTCGAACAGGATCTACCATTTGTAAACCCATGCTGACTGGGCCTGGTCCCCTGGTTGACCTTTAATTGGTCCACAATGGCTCCTAATATTATCCATTCCATAACCTTCCCTGGCACCGAGGTGAGGCTGATAGGTCTGTAGCTACCAGGGTCATCTTTCCGTCCCTTTTTGAAGATGGGCATTATATTTGCCAGTCTCCGGTCCACTGAGACATCCTCAGCTAGCCAGGACTGTCAAAGGTCAAAAGTGAGGTGTTATTTAACATCTTTGTAGGTGGTGTGGAAAGTAGTCTGGAGTGCAACCCTTAACAAGTTTGCAGATGACACCAAGCTGAGTGGTGCAGTTGACACCCTAGAGGGAAGGGATGCCATCCAGAGAGAACTGGACAAGCTTGAGAGGTGGGACCATGTCAACTTCATGAAGTTCAACAAGGCCAAGAACATGGTCCTGCACCTGGATCGGGCAATTCCAAGCAGAGATACAGGGTGGGCAGAAAATGTCTTGAGAGCAGCCCTGAGGAGAAGGATTTGGGAGTGTCAGTTGATGAAAGACTCAACATGAGCTTGCAGCCCAGAAGGCCAACCATATGCTGGACTGCATCAAGAGAAATGTGACCAGCAGGTCACAGGAGGTTATTCTGCCCCTCTACTCCGCTCTCATGAGACCCCACCTGGAGTACTGCTTCCAGTTCTGGAGCCCCCAACACAAGAAGGACATGGAGTTATTGGAGCAGGTCCATAGGAGCTTCTGGTTTTTCAAGAATGTTAATTATTCACTATAATTTATCACAATTCTCTGATAAAATTTGGATATGAACAAAGACAAGTTCCAGAACAGAGATCTGTCTATAGGAAAGCATCCTGTTTCTAAGGTCGTGAATTTATCTTTGTGACAAGTGGAATTAATATAATCTAGCTTAGTCAACTAAAAACTTGACTTAAATGGCTTAAGTTGCAGCAAGTTGTCTGGATCATTTCTGTGATCAGTGGGAAGATGCAGCCTTCTGCAGCAGGTGTTTCATCCCATCTTGAGAAAAGTATTTAAGATAGGGAGGAGTGTATGTTTCTTTTTTATTGACTGTGGATAGAACCTGCATAGTAGATCTTTGGCCTTATAGTAGATCTTTTGGAAAGCTCAGTTTGTTCATATCAATGGTAAGGAGAACTCCATCTAAAGACAATAAATTTTCACTATGAATCATCCTTAAAAGGCATTTATTTCTGGAGAAGAAAACATGTTAGGTAGAAGAGGCAGCCATGGTTATAGTCTTGTTTAATTCATGAAAAATAATCTAAGTCTTAATTCTCTTTTTCTTTCCAG
Seq C2 exon
TTTCAATATGGAACCCAGTTATGATTTTCTACATGTTTATGAAGGGGAAGATTCCAACAGTCCTCTAATTGGCAGTTTTCAAGGCTCACAGGCTCCTGAAAGAATAGAAAGCAGCGGTAACAGTCTGTTTCTGGCTTTTCGCAGTGATGCTTCTGTTGGAATGTCAGGATTTGCTATTGACTATAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016341:ENSGALT00000036950:21
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
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
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]