GgaINT0081155 @ galGal3
Intron Retention
Gene
ENSGALG00000016642 | F1NFP2_CHICK
Description
NA
Coordinates
chr3:109489240-109490851:+
Coord C1 exon
chr3:109489240-109489379
Coord A exon
chr3:109489380-109490603
Coord C2 exon
chr3:109490604-109490851
Length
1224 bp
Sequences
Splice sites
5' ss Seq
AGTGTGAGT
5' ss Score
6.96
3' ss Seq
TTTTTTTGTCTCTTTATAAGGCC
3' ss Score
7.6
Exon sequences
Seq C1 exon
ATCACGAGTGGGAAATATGCCAAGGCTGGAGAGTTCCCATGGCAAGTGAGCATCCAGAGCAATGGGAGACACATCTGTGGAGGCAGCATAATCAGTGCGTTGTGGATCCTGACTGCGGCCCATTGCTTTGCAGATGGAGT
Seq A exon
GTGAGTACTTCTTTGCCCGGAGGAGGGCTGCAAGGTTAGCAAAAGGGCTGGAGGGTAGAGGCTTAGAGGAGAGGGTTAGGACATACAGGTTGTCTGGTTTGGAGTAGAGGAGGCTGCGATGAGACCTTGCTGATCTCTTCAACTTCCTGAGGAGGGGAATTGGGGAGGGAGATGCTGGTCCATAATGTGCTTCAACTTTTTGTTGGTCCTGAAGAAGTCAGACAGTTGAACTAGATGATTGTAGGTCACTTACAATTCAACTATTGTGTTGTACTGTACTGTATTGCTCTATCTTATCCTATCCCATGCTATTCTATCCTATCCTTTCTACTCTATTCTGTTCTCTCTGCTCTACTTGGGGTAAAAAAGAACTGCGCAGGCATGATGGAATGATAGCACTGCTCTTCAGGGTGTAGGATATGTATGTCCTTGGGATCACGTGCAAAATATACGTGATGGAGCCAGAAAGAGAGCCCTGAGAGTTTTTCCTTCTTTGGGGGAAATAAAAGATCACAGGTGGCATTACAACAGGAATTTGCAAAAATCCTGATAACCAGAAGATCTAGAAGGCAATGTGGAAGGATGGTGTGAGCGTCCTTCTGTAAATGGTCATGATGTTGTTCTGCTGACCCCCCAAACTGTTTCTGTACATTAGCACATGCTGTGGTACCTTGTAAAAAGAGGTATACTCCACTCCAATTTATCCTAAGCCCCAAATTGCATTGGTGTCATATAGCAAACACCTTTACCTTATGGGTAGTCTGACATTAATCCAGCAGTTTCTGGATAAATCAACCCATGCAATGCCCAATGGAGCAGAGTCCAGCCCTCCAAACTAAGGCAGGTCCAAGAGCCAGGACTGTTCAGTGACAAATGACCTGTGGAACTACAGTCTGGAGCAATTGACAAGGGACAGTGTGGTCATGGAGCAGCCAGCCCTGGGCACAGCTATCCTAAACACCTAGCTTTTTCCATCTGTTCATTATCTGGGCTATTTAGAACTTGCTTGCGTTCACTTTCTAACTCTTCTTCCGCTTCACCTGAAAATTAACTTTGCGTGGAAGTGAGGGCTTATTTCTGTGATATTTGTAGCTAAGCCACCCCTGCTATTTGCAGAGCACCACCCTACCCTGCCCAGGGAAAGGAGGCACCAACCTTTATAACACAAAGCCTTTCCATTTGCTCATGCATATACTATTTTTTTTTTTTTTGTCTCTTTATAAG
Seq C2 exon
GCCACCAGATATTAAGATTGTAATGGGAGCAGTTGACCTTGACTTCCCACTGGAAGTACGTGAACCAAGCAGCTTGATCCTTCATGAAGGCTTTAACAGAATAACCTTGAAGCATGATATTGCTCTGATCATGCTCAACTATCCCATTGAATTCAGCGATGAGAAAATCCCCATCTGCTTTCCCTACATGGATGACATCAGTTCATGGCAACACTGCTGGGTTGCTGGATGGGGAATGATGGGTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016642:ENSGALT00000026867:1
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:
PF0008921=Trypsin=PU(20.7=97.9)
A:
NA
C2:
PF0008921=Trypsin=FE(37.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTCCCATGGCAAGTGAGCATC
R:
CTGCACCCATCATTCCCCATC
Band lengths:
355-1579
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]