GgaINT0124475 @ galGal3
Intron Retention
Gene
ENSGALG00000007113 | TNC
Description
NA
Coordinates
chr17:3056830-3059373:-
Coord C1 exon
chr17:3059101-3059373
Coord A exon
chr17:3057103-3059100
Coord C2 exon
chr17:3056830-3057102
Length
1998 bp
Sequences
Splice sites
5' ss Seq
CAGGTATCT
5' ss Score
7.33
3' ss Seq
AATGTTGTTTCCCTCCTCAGGAG
3' ss Score
9.85
Exon sequences
Seq C1 exon
AGGAAGAACCTGAGCTTGGAAACTTATCAGTGTCAGAGACTGGCTGGGATGGTTTCCAGCTCACCTGGACAGCAGCCGACGGGGCCTATGAGAACTTTGTCATTCAGGTGCAGCAGTCTGACAATCCAGAAGAAACCTGGAACATTACAGTCCCCGGCGTACAGCACTCTGTGAACGTTACAGGCCTCAAGGCCAACACACCTTATAACGTCACACTTTATGGTGTGATTCGAGGCTACAGAACCAAACCCCTTTATGTTGAAACCACGACAG
Seq A exon
GTATCTTTTCATCCAGCCTAACAGCTCCCTTTCGTTGCAGACAGGGACACGAGCCAGAGCTATTGCAACTGCTTGACAAAGCTTGCTCACTCGGTCTGCTTTGCATGGGTGCACTGAACTCATTAAGGCTTGGCTGAACATCTCTGGCGTGGAAATGTCTCATGATCAGACTTTCCAATAAGAGTCTCAGTGCCCCCATGGAGCCATTTTGCTTTCAGGAATGCTCTTTTTACCCCTCTCAGAATGGCTTGTTTTGTTCCCTTTATTCACTTTTCTGCTAGCTGACGCTAACTGCAAAACCCAACTGGCTGTTGCACATGCTCAGGAAAGTCCAGGTTGCCTTGTGAAATGATAGTTGTAGCCCAGATAAGCAAAGCCCAAGGGCATGTTTGAGTTTTGCCCTTCAGAATCTATTTCTGAAATTACACACCAGCTTCTGCATACATATAACATCAAGGGCATAGTCTGACTCAAGGACAAGGCCCTTCCATATGTTCTCATAAAGAGAAGAACATGAGCAAATTTCTTCCAAGAATATTTTCATATACTGAGCCACATGAAGTTTAAACAATCAGATTGTTCTGAGAAAGATACAGTGCAAGAAGGCCACATCTAACCAAAATACCATGGCATACTGAGCTGAATACTGAGCTGAAAGAAGGAAGGTAATCCTCACATCATCAGAAGCTTGAGTGAGACTAGTCAAGAGCCATAAACATAATTTTCTGGCTGATCTTGTGAAATGCTGCACTTTGGATAAAGGTTTGCTTATCATGAACTTCTACTGTGAGAAGCAAATAGAAATGTCTGTTCTACATGGCTCAGTGAATCTTTCAGGTGTTAGGATCTCCGTAATGAGCAGGATGCAAATTGGCAATAGAGGGGCTCCAGTGACAACTCTTCCTTTGGGTGATTCCTCTGGGCTTCCTTACAGACCTTGCAACCTCCTGCCATTGTGGGACAGCCAGAGCTTGCTCATATTTTACTTTTCCCAAGTACGTATTGCCCAACACAGAAGGGGGTAAAAGTACACGTAAGAACAAAACAAAATGAAAGCATTATACTCAGCAGAGCTTGCCTATTTCAGTAGTGCTTTAAGTGGCTTGGCTTCAGTAGCAATGTGTGTGGCACAGGGCGCTTGCCTTGGGCTGCATCCTGCTGCAGTCTGGGAGCGCCGTGCTTTGAGGGTCTGGTAGCAGATTGCCCATTGAAAATAGACAAATGTGGCAAGGCAAAAGAAGCTGCAGAGGAACAAACAAGAAAACAGACATCACGGGTGTCCTGCCCGAACACGCAGTGTGCTCTCCCTTTATTAACTTAATGAAAACAGCTGAAGATTCCCTGCTGAGGTTTTCCCTTCCATTTCTGGGTCATACTCGGCATCCGGCTTTTCAGAATTTTCCCTTCTGGGGACTTTCAATTGTCAGAATTTTCTGAGCCTTCCTGGAGCATGTCAGGGATGTCTGCAGAGAGGAAGAAACCCCAAGGCAGCTATCACTGCTTTGCATTTTGGCTCCAGCTCCCAAATTACATGCCAGCTTTCATAAACTTAAGCTGAAAGGGAAACTAGAAGAACTCAAACAAAACACAACCTTTTCCTCTGGATACAGCTTTTCCTCTAGTTTCAGCTTCTCCTAAAACTGGAAGCTGACTTCTCCAAATGCCCTGGGGTGCTTGGAAATGTTCTTTTGGGACTTCTTTCGTGCTCAGACCTCAAAGATGCATGGCTGCAAAAGGAAATAGCTAGAGCTTTTAACCTTCCTTTTTTTCCTTTCTTTTTTTTCCTTCTCTTTTTCCTCTTCTTTAGCATTTTGAGTTGCTGTCATTTATTTTCTTCCCTTTTAAGAACTGTTTTGCTTGTAGCAAGCTTTTACTTAAACCCTTTTCTCCAAGGGCAGCTTGGAGTGCTGTCAGCATGAGCAGAGCGAAGCAGATAATTTCTGAGCAGGACGGGGTACAGGGCTGTCCCCTTCTGACCAATGTTGTTTCCCTCCTCAG
Seq C2 exon
GAGCACACCCTGAAGTTGGTGAGCTAACCGTTTCCGACATTACTCCTGAAAGCTTCAACCTTTCTTGGACGACCACCAGCGGGGACTTTGACGCCTTTACTATTGAAATTATTGATTCTAACAGGTTGCTGGAGCCCATGGAGTTCAACATCTCAGGCAATTCAAGAACAGCTCATATCTCAGGGCTTTCCCCCAGCACTGATTTTATTGTCTACCTCTATGGGATCTCTCATGGTTTCCGCACACAGGCAATAAGTGCTGCGGCTACAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000007113:ENSGALT00000011523:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.250 A=NA C2=0.083
Domain overlap (PFAM):
C1:
PF0004116=fn3=WD(100=88.0)
A:
NA
C2:
PF0004116=fn3=WD(100=87.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGGAACATTACAGTCCCCGG
R:
AAATCAGTGCTGGGGGAAAGC
Band lengths:
342-2340
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]