GgaINT0117947 @ galGal3
Intron Retention
Gene
ENSGALG00000011894 | F1NJG4_CHICK
Description
NA
Coordinates
chr1:51291826-51293800:+
Coord C1 exon
chr1:51291826-51292140
Coord A exon
chr1:51292141-51293628
Coord C2 exon
chr1:51293629-51293800
Length
1488 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
GTTTGTTTTTATCTGGGTAGTTT
3' ss Score
6.54
Exon sequences
Seq C1 exon
AAGCAAGAGAAAGAGGGCAGCTGCCCGGGGAGGGGAGCAGGAGAAAGGAGGCAGAAGCGAAGGACAGAAACAGTGCTGAGTCAAAACAGGAAGACCAAGGAGTAGACAAACTACAAAATGACACTGCTCCTGTGGCTGTCATCTTGGAGCAACATCTCTGTACTGGGAGTTTTTCTTACTGTCTTTACCATACTTGTTGATTTCATGAAGCGCAGAAAGAAGTGGAGCCGTTACCCCCCAGGCCCAATGCCACTGCCGTTTGTTGGGACCATGCCATACGTTAATTACTACAACCCGCATCTCTCCTTCGAGAAG
Seq A exon
GTGAGTAGTGGACCCTGCCAACACGTATAGCAGTCTGAGGGCTGGGGAAGTGTTACAGGAATGGCAGACTGCTCTGTGAGTTATCCAGCATGCCTACAGCCATGTTGCAGTTTCTGTTAAAGACAGCTTGCAGGATTTGCCCCAGCAGTGGTGCCCAAAATGCCTGTAGCAATCCTATTCAAAGTCAGGCATTATCTCTTTTCAAAGGAAAAGCACAGCACAGCTTGCAGCAGATCAGCCATGGGCTTTTCCTTGAGTGTGCAAAATCTAAAGGCCCCTTCTTTAAGACAAAACTTTTTAGCTGTCTGTCCAAAACCTGCCAAATGGAAAAACTAAATATAGCATTTGCACTGTTAACCTGCATAGTGTCCAAAAGATTACCATTTTCAAATCCTATCAAATCAGGGCCATTCTCACTGCACTGATTGCTGGTTACTTGACCACTAATTGATTTTAATGATGTATTTCTAGTGTCACTGAAGTACTAATCCCCTTTCAAATCCCATAGCAAAAAAAAAAAAAAAAAAAAAAGGATGAAGAGGGGAAAGGGGCAGATGGATGGGAAGAGGGAGATAGGAAGAAATGGGGGAAGGGGGAGAGAGAGAGAAAAAAGGAGAGAAGGGAGTAAAGGGGGAAGGAAAGGAGGGAAGAGGGAAAGAGGGGAAGAGAGGGGAAGAAATGCAAGGAGAAAAGCAAGGCACAGCAAGGAAAGAAAAAGACAGTGAAAAACACATAGGGAGAGAGAGGGAAAGAACAAAATGAAGAAAGGAAGGAAAGAATACAAAGACAAAAGACAACAAAGACAAAGAACATACAGCTGATAAACTCATCTATGCAATCACCGTTTTGTCAGTAACATGTCTTTTACAGATCATCAGAGAGGTAGGATGTATGCCAGTTAGCAGTCTTCCTAGGAGAGTACGTTCCCCCTGGGGAGAAAGCTGACCTGGAACTCCAGTGTGGAGCTACCTTTTCCAAGCATGCTTCTGGAAATTGGGCTTTGGGTAGAAAAAGAAATTACATACCACTTTATTATCAGTATTTCTGTCTAGCAGAAATTAAAACTACCTCAAAAATTGCTTAGGTTTTCAAATGAAATTACAAGTATCGGGAAACAATGTGTTCCAGAGTGTGCAGTCTTTGAAAATCTCTATACTGGTTCTTGACCTAGTGTTGTCAGACAAAATCCAAAATAGCCACACAATGCTCTGGACAAGTTTCATCAGAATAGTTGTATATTAAATCTTGCCAGCTGCAGTGCATTGCTTCCTGCTTCACATAGGGGATGACACTGCTCCGAGCTGTTGCACTGCAGAGACAATCAATGGTCAAAGGTCAGCTGGAAGTTCTAATAAAACAGTACAAACCACTGAACAGTCAGGTCCTAAGGAAAGATACAGGGATATGTTTTTGACATTACGTTCCTGTACTATTGCGTGTTTTCAGGGCCATGTTTTTTTGTTTGTTTGTTTGTTTTTATCTGGGTAG
Seq C2 exon
TTTCGCAAGAAGTTTGGAAACATTTTCAGTCTCCAGAACTGCTGGACCAATGTGGTAGTGCTGAATGGGTACAAAACTGTGAAGGAAGCCCTGGTCAACAAATCAGAGGACTTTGCTGACCGGCCATACATGCCAGTATATGAACATCTGGGCTATGGACATAAATCTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011894:ENSGALT00000019412:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0006717=p450=PU(5.7=38.8)
A:
NA
C2:
PF0006717=p450=FE(12.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg19)
No conservation detected
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCGAAGGACAGAAACAGTGCT
R:
GTTGACCAGGGCTTCCTTCAC
Band lengths:
358-1846
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]