GgaINT0059816 @ galGal3
Intron Retention
Gene
ENSGALG00000006998 | Q5ZKF9_CHICK
Description
NA
Coordinates
chr5:17703003-17705151:+
Coord C1 exon
chr5:17703003-17703128
Coord A exon
chr5:17703129-17704914
Coord C2 exon
chr5:17704915-17705151
Length
1786 bp
Sequences
Splice sites
5' ss Seq
GAGGTCAGT
5' ss Score
7.7
3' ss Seq
TTCCTTTTCTCTTTCTCCAGAAC
3' ss Score
11.37
Exon sequences
Seq C1 exon
CTGCACATCCGTGCTCCCGTGACAATGGTGGGTGCTCACACATCTGCATTGCCAAAGGGGATGGGACTCCAAGATGTTCGTGTCCAGAGCACCTTGTGCTCCTGCAGAATCTCTTAACGTGTGGAG
Seq A exon
GTCAGTTCTGTTTAACAGCACTGCTAAGTGGTTTACACTGGGGAAAAAAAGAAATTAAGAACCACTGGAATACCAAATTTGGTCTATGACATACTGCTAGGTTTTGAGAACTGTCTATCTGGAGGAAGATCAAAAACAACTGAATGAATGAAGTCAGAATGACCAAAATCAAATGGTTACTGTTGCAGGAATTTGCCCACCAAGGTACTTGACTTCCATGTGGTACAAAATAATACGAAGTTCCTGCAGGAGTCTGTATTTGTATCCAGATCGTGGATTTATACACAGCGTTTTCCTAGACATGATGTTGAATTCTGTCTTAAATGCAACTTTTCTACTAGCTGTTTTCTGCTTCAAGTTTTGCACATGTATGCCTTTACACTGTGTGCAGAACACACTTGTTAGACCATAAGGTAGTTGCATCTTCTACTGAGATTTTCATTATTGTATGATGTGACAGTCTGTGCTATAAACGAATGCATATAACAATGTTGATAACCCATGATGATCTGGCAGTTGAAACTGTATGTATGATTCCCGCAGTACTCCAGCTTTTCAAATAACACTGTAACATAAAACACCGTGCTGTCTCATTAGTGACAGTTCAAAACATCAGTTGCAATTCTTTTTAATTAAGATAACTGTTGTCTTTCCTCATTGTAGACATTTGTTTTACAATTCCCTTTCACAGCCCCAGGAATTTTGATAATTGTTACCTTACTATTGCAGAGGGCATTTAAAATGGGGGAAAAATGCTTCTTTTGGGGAGATATCCTGTGTTAAATTATTTGCCTCTTTTGGTCCTCTGGCCTTTTTTTATGTATTCATTTTGTTGTGGATTTCATTTTTCTGGCTGAGCTCTGACCTCCCGTGGGACTGTCCCTTCCATTATAAACTGTTTTCTTTCCCATGACCACAACACGCTATGTGGTTTTGGAGTAGTGGAGGTTACATCTGCAGTTGGAAAAAATAAAACAGTCTACTTATATTTCTTGTTCTACTTCTGTTGAAATACGTGGCCAATGAGAGATTCTTACGTTCCACTGCTTTGGTGTCTTCCCTTGTAAATCTTAAAATTAAGGGGCCTCTTTCAGTCTCTGCTTCTTGTTTATTTTCATCATGATCCTTCACTAAGCTTGCAACAGCTTTGTAATTTGTCTTCCCTGCAGTAGTAGTAGCTCATAACAAGTATTTCAAAATAGGTTGATAGCTGATTTGGTTGGAGAACATTTTGTTCATGTATTCTCATGAACACACTTGACGAGTTTTTAAATGCAAATTTGTGTCTGCCAAGTGCAACCGTAATGCAACATTAAATGTGGCTGTAGATGCAGAAGTAGTAATCTGTCTGCTGAATTACCTGAACCGTACACTCCTATCCAAATTAATTCCAGAATTATCTTGATGTGTCTGTCTGGCATCCTTACCGTATCTACAGCTGCCAGGTCACTGGTTAGGTTTGTAAACCTCAGTATTGCTACGCCCAGTAATCATAACTCAGAAACTTGGAAATCATAGGAATGTCAAAAATTAAATGTATGTATTTTTACTTTGCATATTTGTTTTTCAAGGTCTTGATTTTACTTGATTATCCTTCTTGAACATTTCTCCTTAATGAAGTGTCCACAGCACTTTAAAAATATTTTGCATTTTTACAGAAGAACTTCAGTCCAGGCATACACATCTTTTTCTCCATCTATGGAATATTTCCATCACGTTTTCACTCCGTTGAAAGGGCTAAATGATGAATGAATATGCACATGCGTTTCCTTTTCTCTTTCTCCAG
Seq C2 exon
AACCTCCAACTTGTTCCCCAGACCAGTTTACCTGTGCAACTGGAGAGATTGACTGTATCCCAATGGCATGGCGGTGTGATGGATTCCCAGAGTGTGATGACCAGAGCGACGAGGACAGTTGCCCAATATGCTCCGCATCTCAGTTCCAGTGTGAGAAAGGACAATGTATTGACGCGCATCTGAGGTGTAATGGAGAAATTGACTGCCAAGATAAATCTGATGAAGTGGATTGTGATA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006998:ENSGALT00000011330:17
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=0.000
Domain overlap (PFAM):
C1:
PF146701=FXa_inhibition=WD(100=86.0)
A:
NA
C2:
PF0005713=Ldl_recept_a=WD(100=48.8),PF0005713=Ldl_recept_a=WD(100=46.2),PF0005713=Ldl_recept_a=PU(0.1=0.0)
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:
GTGCTCCCGTGACAATGGTG
R:
TCCACTTCATCAGATTTATCTTGGCA
Band lengths:
345-2131
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]