GgaINT0102356 @ galGal3
Intron Retention
Gene
ENSGALG00000006438 | F1P1C8_CHICK
Description
NA
Coordinates
chr2:8488246-8490376:-
Coord C1 exon
chr2:8489839-8490376
Coord A exon
chr2:8488407-8489838
Coord C2 exon
chr2:8488246-8488406
Length
1432 bp
Sequences
Splice sites
5' ss Seq
GCTGTGAGT
5' ss Score
7.39
3' ss Seq
CTTCTTTCCCCTCCCCGCAGCTC
3' ss Score
12.67
Exon sequences
Seq C1 exon
ATGGAAAAATCCAAAAATTTCCGTAAAGGCGCGCTGCTGGCTGTCGATCCCCCCAAGGCGGCGGCGCAGAGCGCTCCGCTGGCCCTGGTCACCGGCGGCTCCGGCGGCGGCAGCCCTCCGTCTTCGTCGTCCTCCTCGTCGTCGTCGTCCTCCTCTTCTTCCGAGCTCCCCGCCGACTGCCCGCGCACCGACAGCCCCTCTCCGCCTCGCCTGCTGCCCGCGCACTGCGCGCTGCTGCCCAAAGCCGCCTTCCTGGGCGGGGGGGGACCCGGGGGCGGCCACCCGCAGCACCACGCCCTGGGGCTGCACCCCGCGGGGCCGGGCGGGCCGGGCCTCTACGGGCACCCGGTGTACGGCTACCCGGCGTTGGGCGGGCAGCACCCGGCGCTCTCCTATTCCTATTCGCAAGTGCAGGGAGCGCACCCCGCGCATCCCTCCGCCGACCCCATCAAGCTGAGCGCCGGCACCTTCCAGCTGGACCAGTGGCTGCGGGCGAGCACGGCCGGCATGATCCTGCCCAAAATGCCCGACTTCGGCT
Seq A exon
GTGAGTATGCGCTGCTCCCTCCCCGTCTCCCGAGGCTTCCTTTAAACCCTCCCTAACGGGGCTGCGCGTTCGGACCGCTGGCCGGGCGGATTATTGTTACTACTTTCAGTCAGATGTTATGATAACCAGGGGCTATCCGCCCTCCATCCCGCACTATTCCCTCCGTAGGATCCTCCGTAGGATCCTTCTCCTTTCCGAGCGCGGAGAGAGCAGCGCGCCCCGACCGCTCCGCGCAGCCCCAGAGCGCTGCAGGGGCAGCTCCGGGCATCCCTCCCGTCACCCTTACGCTCATTTCCTCATCTTCTTTTTTTTCTTTGACCGGCAAAACGGATTTAGAACGACGCCCTCCGAGCTCGGAGGGTTGCGCGTTTGCTGGAGGTAACGGAGGGCCGCGGGATAAGAGCAGGTGTGGGAGCGCTGCCGTAGCCCCGCGGTGCCATCGGCGCTCGGCAGCGGTGAGGTCCCCACGTGCGGTTCAGGGACGGGCGCTGCCGGAGGTGTGAGCGCCCCGCGGGGATTGCGCGCAGAGCGGCAGCCGAGGTGTCGTTTTACGAAAATCACGCCAGGAAGAAAAAAAAAAGAAAGCAGTCGCGATTTTTAATGTATACGTATATATTTTTTCATGCTCTGCGCGCGTTCGCGGAGACAGAACGCCGTAGTTTGCTCTCGGGTTGGGGCGCTTTGGACTGCGGCGTTCAGGGAGGGGGGGGAGAACCACAGAGGAGCGCTGTCTGAGCGCTGCCCTCAAATAGGGGCTGGGGGTGGGGGTGGCAGAATCGCACCGCCGTGCGAAAATACCCGCGGGCCTCCGCTGCCCTCCCTGCTTTCCTAAATTGGAGGAGCGAAAGTGGCGAAGCGCGGTACCCCGCCGCCTTCCTTGCATTATTTTTGTGAATGAAACCCTCGATTTGAATCGTTTTGAAAAGGGGGAAAATGGGCGAATATCTGTAATATACAGAATATATATATTTTTTTCCTCGTTCCAAGGCCGTTTCTCGTCTCGGCCCTTATAGGCGCGTTCCCGAATGCGGCCGCTGCCGCATCTCGCGGCTCTGGGTTGGGGTTAAAGCAGCGCATCCCGTCCGTTGGGGTTAGGATTAATTAACGCATCCCTCTAATCGCCGCCGCCGGGTTTTGCTTAACGCGTTAAACGCAACAAATCGTCTCTCCCGGGAGATGCCGCTTCGCCGCGATCCCCGGCAGCGTTTCGTTGTGCGGCCCTCGGGAGGACGAAAAGATTTTTCTGATTTCTTTTTTCTATTTATTTAAACGACTTGATTCCACCCCCTCCACCACCCCTTTTGGGCCCTACAGGGAATCCCAACCACGACCGCTCCTCTGTTCCCCTCTCGCATCTCTCTCCGCTGTCCCGCCGTCGGGGCCGCCCCGCGCTGATGGCTGCGTTTTCCCCCCTTCTTTCCCCTCCCCGCAG
Seq C2 exon
CTCAGGCGCAGTCCAACCTCCTGGGGAAGTGCCGGCGGCCGCGCACCGCCTTCACCAGCCAGCAGCTGCTGGAGCTGGAGCACCAGTTCAAACTCAACAAGTACCTCTCCCGGCCCAAGCGCTTCGAGGTGGCCACGTCGCTGATGCTCACCGAGACGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006438:ENSGALT00000010389:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.678 A=NA C2=0.185
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=PU(73.7=77.8),PF088806=QLQ=WD(100=51.9)
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:
CTGCCCAAAGCCGCCTTC
R:
CACTTCCCCAGGAGGTTGGA
Band lengths:
335-1767
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]