GgaINT0094727 @ galGal3
Intron Retention
Gene
ENSGALG00000017398 | F1NHU4_CHICK
Description
NA
Coordinates
chr2:109236585-109238919:+
Coord C1 exon
chr2:109236585-109236874
Coord A exon
chr2:109236875-109238770
Coord C2 exon
chr2:109238771-109238919
Length
1896 bp
Sequences
Splice sites
5' ss Seq
TTTGTAAGT
5' ss Score
7.4
3' ss Seq
CCTGTTTCTTTCCTGTTAAGTGA
3' ss Score
7.25
Exon sequences
Seq C1 exon
TGCTGGTGGTGGTGGAGCTGGTGGTGGTGGTGCTGGTGGTGATGGAAGCCAGACTGGTGGAGGAACCGGACAAGACTATGGTGGGACTGGGTATGAAGGAGGTGGCGGCAGTGACTCCAGCACAGACTCGGGTACTGACACTGGTGGAGGATCTACAAATTACGATAGTTATACTGGAACCAGTGATTACGGCAGAAATGAATATCCTGGTGGATACGCCCTACCTGCTTCTACCACACTTAGTGGTTCTGCCATTGGCCTGATGTTTCTCGGTGGATTAATATTTGTTT
Seq A exon
GTAAGTATAAAATTAAGAAAATGGTTATATCAACCTTTTTAAAAGTGCATGTTTTTATTTTTCAGATGACTTTTTTGGTCAGTTGTTTACTCTTGAACTCCCATGGTTAACTCAACAACAACAAAAAAGTTTTAAATTATAAGAATATATTTATATATTTATGTTCTATATATGCACAGATATTTCATTCAGAAATAACCATTTCCATCTGAAAACTTAGGGTTTTTTTCTAAGGTATTTTTCTGTTCTCAGACAACTAGGCAGGGTCAAAATATTTTGCAGCAGATTCAGAAGGTTCTGGGCAAAAGCTGCTTCTATTACTTTACAACATTTGTAATGTAATTTGTTCCGTAGTTACATTACTAAAACAAATAGATCAAGTCAGGTATGAAAAGATGCAAGGAACAAACTTCCTTTGAACTCTAAGCCTGATTTCACTTGCAGAAAGATAAAACTCATCAGTTTAATTTTTTTAATTTTTTGGCCAGTGTTGCTAAATAATTTGTCTGTTAAAAAATGTCTGCAATAACAGGATCAAAGCAGATCATTCATTCATTCACATGTCCTAGTATTTATGAAGAAGCATGAGTTTAAGAGAGAATAATGAGTAAATGAGTAAATCTAGGTTTTATGCAAAATATGAACCTCAGCAATTACTTCCCAGGCCACCACAATCATTCATAATTGTTCTTCTTTCGTGACATGAACATCAAGCAGTGCAGAAATACTGACTACAACAATTCTGGAGACCTGATTTTTTGAGGAGGGTAGTCATATTGGGCCTTGGTCTCTAATTAGTGGGAATCAACAAACAAAATTTTGAAGTTGTAAAAGGCTATCTTGTTTGTAGTTCCCATGTGGTTAATGTTACAGAACAGACTGCCTTTCTGCCTTCAGAAATCTCGTCAGTGGTCTGGAATAAATACATCCTTACTAATGAGGTGTGAAGTAGCACTTTGTGCACTGTATAGCCCTTTTTCTTTACCAAAGAGAAAACTTTGGTATATTTTGATGTTAAAGTGAGAGTTTTAGATACTTTGGTTAGTTTGCTGTAGGCAAACTCCCTGCTAACTCTGCAGGAATACTAATTTACTAACTTAGTTATTTAGGTTAACAGCTTAAACAGAACCAGAATGAATATCGCAGCCCTTTCCTAAAATGAGCAATGTTTTTTTTTGTTGTTGTTGTTTCTTTTGTTTTGTTTTGTTTTTTTTTTTTATGCTAGTTTTTAAAGTATTCAGCAATGTGCAACACTAAATTCTTTCAAGGAATAAACATAATGTACCGCATTGAGAAACCTGACTCGCTCTGTCTAATCATTGGTTAAAACTGGAATTCGGGGTTTGACTGTGTTATTTTTCAAATGAGTATCAAGTACATGTGATGTGGAAATGCAACAGGAGAGTTAGACAAAAATTACTGTAGCCAGACAGATAGCTCTCCACTGATTCTCTTAAGTTTAGTGTTACTAATGTGTATTTCTTTTCAACTACAATGTCTGAAGAGGAAAACGTACTCATCTACATCAAGTGTGAATATCACTGAATGCTATATATAGCAAGACAGGTTTTGTTTGTTTAATTTTCATACATCTGCATCTTATATTCATTCAGTTGAGGCAGATCAAAGTCTGTTTCCAGGTGTATAGGCATAAAATTGGAGTAACAGCTCTACTCCACCCTAATTTTGCTCTGCTATAACTAAAGGCAAAATTATTCTGAGTATCCAAATACATACATTTTCAAAAGCAGCTAATGATTCTGAAAGCTAGACTTGCAGGCTGCTTAGTTTCAAACATTTTGAAATATACATTTTCAAAAGTTCTTGGTCACTTGTAGTCATTCCTATGAAGAAGAGATGTCTTAAATACCTGTTTCCTGTTTCTTTCCTGTTAAG
Seq C2 exon
TGATTCCAATTTTGATGTCAATGAGTGATTGTTGTGGCTGTGGACCTGGAGCTGCAGCTGGAGTTGGAACTGGATTTGAACCTGTACCTGAATGCACAGAAGGGGCAATTCATCCATGGGGAATAGAAGGTGCACAGCCTGAAGATAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000017398:ENSGALT00000036805:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.530 A=NA C2=0.199
Domain overlap (PFAM):
C1:
PF0002812=Cadherin=PD(1.0=1.0)
A:
NA
C2:
NO
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:
GGTGGGACTGGGTATGAAGGA
R:
GCTGTGCACCTTCTATTCCCC
Band lengths:
349-2245
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]