GgaINT0124963 @ galGal3
Intron Retention
Gene
ENSGALG00000004512 | SHLB2_CHICK
Description
NA
Coordinates
chr17:5990226-5991505:-
Coord C1 exon
chr17:5991405-5991505
Coord A exon
chr17:5990491-5991404
Coord C2 exon
chr17:5990226-5990490
Length
914 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
GCTCTTCTCTCCTGTGTAAGATT
3' ss Score
4.84
Exon sequences
Seq C1 exon
GTGAATCATCTTCGCTGTCTCCATGAGTTTGTGGAGTCTCAGACCAACTACTACGCTCAGTGCTATCAGTACATGCTGGACCTGCAGAAGCAGCTGGGCAG
Seq A exon
GTGAGACAAGAAACGGCTTTTGCTTCCCTAAGGGTTACTCCCTCGTCTGGTCATCGCCAGTTCAGGCCTCCCTCCTCTTCAACAGAAGCTTAACAGCCCCCTACAAGCTCTGACAGAGCTTCTGAGCTTACAGAATGGTGCTCAATGCTAACACATCTAGAGCAGGCTTTACCGTTAGATTCATCTGAGATTTATACGTTCATCTCAAAACACGATGGCCAAGAGTCTGAATGTTCTTCTAAATTAGTTAAATGACACAGGAGACAAATTCCTGTTGCCAAGCAACAAGCCTGAGTGTGCTGAGCTGCAGCAGTAAGCAGTTCCATGCTGCAGGGAGGGCTCTTCTGTCTGCTACCTGTTATGCTCTGACCCAGGAGGGACCTCTGTCTGATCACTCACTATTCCTGTTTCATTCTTTTCCATGCTTGCAGCTCCAAAGGAGAAATGTAAGTAAAATGTTACACAGGACCGGTTCTAAGAGCTCTGCTCTACACCTCAGCCAAACCGTGGAGTCTTTGCAGGCTCACTACTAAGGCCAGCAAGGGCCAGAGCTGCACTCCCGTAGTGCAGAATGGGAAATCTACAGATAAACGAGACCTGGCTTCATTGCCATCTCTGTAAAGAGCCCCAAAGCCTCCAGCTGCAGTATCTCCCAGTGCTACACTCAGCAAGTTTGCTGCCAGTCCTTTAGCAGGACGCTGGAAGAAAAGCAAGCAGAGAGATTTCCCTGTTCCACAGCCTCAGCAGCTGAGCACTACGTGCACTTCCCTCCTTTAAGGGCACTGTAGGTACGTTCCAGCTGTTAGCGGAACTCTGCAGTATCACCTCTGCACTGTGGCTGCTGAAGGGAAGCGCCGTTTCTCGGTTCCTCCCAGCAGAGCCTCACCCAACCCTGCTCTTCTCTCCTGTGTAAG
Seq C2 exon
ATTTTCAGGCACGTTTGTAGGGAATGCAGAATCCACATCTCCACCCCCAGCTGCTGCCTCTCCTCCAGCTGTCGCTGCCACCACTCTCCCCGCTGTGCCTACCATCCCAGTTGTCCCCACCATTGTTGGGGTGCCGAATACTGTGGCAGAGAGCGTCCTGAACCCAAATGAAGTCAAGCCTCCTGCCAGCGGGACGCGGAAGGCCAGGGTCCTGTATGACTATGAAGCAGCTGACAGCACCGAGCTGGCACTTCTTGCAGATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004512:ENSGALT00000007187:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.352
Domain overlap (PFAM):
C1:
PF0311413=BAR=FE(12.0=100)
A:
NA
C2:
PF0311413=BAR=PD(0.1=0.0),PF146041=SH3_9=PU(35.3=20.2)
Main Inclusion Isoform:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGAATCATCTTCGCTGTCTCCA
R:
GGTGCTGTCAGCTGCTTCATA
Band lengths:
342-1256
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]