GgaINT0072436 @ galGal3
Intron Retention
Gene
ENSGALG00000011792 | F1NMD1_CHICK
Description
NA
Coordinates
chr4:53218092-53219907:-
Coord C1 exon
chr4:53219869-53219907
Coord A exon
chr4:53218273-53219868
Coord C2 exon
chr4:53218092-53218272
Length
1596 bp
Sequences
Splice sites
5' ss Seq
ACTGTAAGT
5' ss Score
8.59
3' ss Seq
TTTTTTTTTTTTTTTGACAGTCT
3' ss Score
9.2
Exon sequences
Seq C1 exon
AATTGAATAAGGAGAACGGAGATAACCTTTTAAACAACT
Seq A exon
GTAAGTACAAATGTTTTATAGAAATCATCAAGGGACTTAGTGCCATCAGTTCAGTGTTTATAAGATTTTTATGCTTGAGATGCAAGTTGAAAAATAACTTTTTTAAGCTACTAGAACAATAGGTAATTCATGAGCCAGAGAAGGTTTTAGCTCTTTTTGTTTTTCTTTTTGGAGTTTTGCTTGCTCTGCAGTGTTCACAGTTAGGCATTCCAACTTGATGGTGGGCTTTAGTTTTGGCTACGGTAAGTAGATGAGTTGCTGTCAGTGAAATTTTCACAAGGACCGCAGTTGTTGTGAGCTGAAAATCTTTTTGGATGAGTGACTGATACCCAATAAAACTAGCAAGACTGAAAAATCAGAGCATTAAAATGTTGTCCAAGTTGCGTCTTCCAAACATTCCATACATGTAGGCCTAAGGAAAGCCCTAGCTTTCTCTGAAAATGGTTGTGCCAGATCTTTTCTTCTACAAGAGAATCTGTTGCTTGCAAAGCCCTTGTTTAGAACTTTGCTTCATCATATATGCATTCATTCCTGCCTCTGCCCTAAGCTGGTAAGCTGCTGTCTCTACAGGTATAACAGCAAACAGCACTCCCAGTATTTTGCTGGCAAAGTAGCTCTTAGACTACTCATGAATTCATCATTCCTTTCTTCTCTTGGCACTAGCAATAAATCTTTGCAAAAGAAGGGCTGTTGTCTTCTACCCTGCACAGAGTTCATGTCTTCTTGCTGATTATTCATCTTTGGGCCTTGCAGGAGGGTCAGAGGTACTGCATAGCTGTGCCAAACACAGAAGTGGAAGTGAGCTATTTGTCTGTCTGGGCTACCTGTCACCATGTGTAGAAGCTGCCTTATTCCTTCCAAAATGTCTTCCATTCCACCCTCTCTTCCCTGCAAAATTTTGGCAGTAGAGTTGGGAGCTTAAAACTTGCAATCTTCAAGGAAAAGACCAGAGGATGGGAGAGAGGAAAGCTGTCCACTGTGAGAGCAAGGCAGTGAAGTAGCCCTGGAGAGGGACAGATTCTGAGTCTTTCTACCATTTTATGCTCTCCAGTGAGGTCTTATAGTTTCTCTGGAAACATGGAAACAGACTCAGTACCTTCTCAGCTGAACCAGTTACAAAGGGTCTCTGAGAACTAGGGATCTGTGGCACCTCTGCCTAGCATTGTCTTGGGAATTCAGCATGTTTCACACGAGCTTTTCGTGTTTAAGTCATTTCTTGTTTGGATCTGACTTTTTTCAATGGAGTAGAAAAAACTTACTGGAGAAAATAAACAGTCTGGTATACAGCCTTCCATTGCCGTGGAAGTTCACACTGCTTTGTGTGTCTGGCAACTAGTTATGTTTTTACCAATCTTTGTTTACATCATATCTATCCTGAGACCCTTGTGACCACACCACCTGACTGCTCTGCTCTTGAAGGCACTGCTTTAGGTAGAAGCTGTCTCTTGGCAGCTCTGCCCTGTTGTGCCTGTGCCAGCAGCCATATGGGCCTGCCCAACAGGCAGACCCTGGGTTTCCTCTATCAGCTAACAGAGCTGCCTTTGTTGGGTTTTTTTTTGGTTGTTGTTTTTTTTTTTTTTTTTTTTTTTTTGACAG
Seq C2 exon
TCTGTGGAATACGAAAGGAGGCATTCTCCTTCACAGGAGTGGAAAGAATAACTGATGGACAGCGTGCACGGGATGGAGAATGGCCATGGCAGGCTAGTATTCAGCTCGATGGGACACATTACTGCGGTGCGTCGGTGATCAGTAATACGTGGCTAGTGACTGCAGCCCACTGCTTTAAAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011792:ENSGALT00000019237:5
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:
NO
A:
NA
C2:
PF0008921=Trypsin=PU(19.3=72.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGAATAAGGAGAACGGAGATAACCT
R:
CAGTGGGCTGCAGTCACTAG
Band lengths:
208-1804
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]