GgaINT0053528 @ galGal3
Intron Retention
Gene
ENSGALG00000012394 | NID2
Description
NA
Coordinates
chr5:60683258-60684167:-
Coord C1 exon
chr5:60683996-60684167
Coord A exon
chr5:60683416-60683995
Coord C2 exon
chr5:60683258-60683415
Length
580 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGA
5' ss Score
6.65
3' ss Seq
CTACATAATTATCTCCCAAGCAA
3' ss Score
1.66
Exon sequences
Seq C1 exon
GGCTCATCAGCCCCGAGGGGCTGGCAGTGGACCACCTCCGCAGAGCCATGTTCTGGACTGACAGCGGCCTGGATAAGATCGAGCGAGCGCAGCTGGACGGCTCGGAGCGACGGGTGCTCTTCGACACCGACCTCGTCAACCCTCGGGCCATCACCGTGGACCCCGTCCGAGG
Seq A exon
GTGAGACCCCACGTCTGGAGGTTTTGCAAGACTCTTTTAGGATGGCATTTGCCCAGTTTGCAACAGGAGTTGTATGTGGGGGAGTGCTTGGGGTGGGACTGGTCATGAGCGGGGCAGCTTACCGCTCCTTGCAGCCCCAAGACCCCATCCTGGCCCTGGCAGCAGCTCTCCTCCACTGCACACCCTGCAGGAAGGACTGGCTCTGTTCCCCCTCTCCCTCCTTTCATTTAATAACTCAGGGTTTGGCTAAACCTGCTGTTTCAGTGTCGGGATTAGTTTTAAAAGCTTTGAAACGCAGCGTTTGAAAACACAAGCTGTGCCCCTAGGGTGCTGTTGCAATACAGAATGTGCTACTCCTAAGGCTCACCCTCGTCTAGAAGCTGCAGTTTGGGTCGTAAACAAGTTTGACATCATGCTGCTATTCTTTTAGTGATTTTCAGCTCAAATAATTCCAGGCAGCAGAAGGGAAAATGCAGGCCTCCCTCCTGATAAGAACCAGTGCTGTAGAGAAAGCCAGTGTTCTCTTCCTGTCCTATCTGTTGCGTGTCCTGTTTCGCTCACTACATAATTATCTCCCAAG
Seq C2 exon
CAACCTTTACTGGACGGATTGGAATCGAGAAGCACCGAAAATCGAAACTTCCACCGTCAGTGGAGCCAACAGGAGGGTGTTGGTGAACACGGACATCGGGCTGCCCAACGGCCTCACGTTCGACCCCTTCTCCAAGCTGCTGTGTTGGGCAGATGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012394:ENSGALT00000020241:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.019
Domain overlap (PFAM):
C1:
PF0005812=Ldl_recept_b=PD(26.2=19.0),PF0005812=Ldl_recept_b=WD(100=70.7),PF0005812=Ldl_recept_b=PU(0.1=0.0)
A:
NA
C2:
PF0005812=Ldl_recept_b=WD(100=79.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGGCAGTGGACCACCTCC
R:
CTGCATCTGCCCAACACAGC
Band lengths:
310-890
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]