GgaINT0080064 @ galGal3
Intron Retention
Gene
ENSGALG00000016565 | F1N9F1_CHICK
Description
NA
Coordinates
chr3:107876061-107877832:-
Coord C1 exon
chr3:107876746-107877832
Coord A exon
chr3:107876202-107876745
Coord C2 exon
chr3:107876061-107876201
Length
544 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGT
5' ss Score
11.11
3' ss Seq
AGCCCCTCTCCTCCCGGCAGGTG
3' ss Score
11.37
Exon sequences
Seq C1 exon
TGCCGACGGGGAGTTTGCTGTGACACACATGACAAAGGCCCACCTCTTCTCCAATGGGAAAGTGAAGTGGGTGCCACCCGCCATCTACAAGAGCTCGTGCAGCATTGACGTCACCTACTTCCCCTTCGACCAGCAGAACTGCAAGATGAAGTTTGGCTCCTGGACTTATGACAAGGCCAAGATCGACCTGGAGAACATGGAACACCACGTTGACCTGAAGGACTACTGGGAGAGTGGCGAGTGGGCCATCATAAACGCCATTGGCAGGTACAACTCCAAGAAGTACGACTGCTGCACTGAGATCTACCCTGACATCACCTTCTACTTCGTCATCCGCCGCCTCCCGCTCTTCTACACCATCAACCTCATCATCCCCTGCCTGCTCATCTCCTGCCTCACCGTGCTGGTCTTCTACCTGCCCTCCGACTGCGGTGAGAAGATCACACTCTGCATCTCCGTCCTTCTGTCCCTCACCGTCTTCCTGCTGCTCATCACCGAAATCATCCCCTCCACCTCTCTGGTCATCCCACTCATCGGTGAGTATCTCCTCTTCACCATGATCTTTGTCACGCTCTCCATCATCATCACCGTCTTTGTCCTCAACGTGCACCACCGCTCCCCCAGCACCCACACCATGCCCCACTGGGTGCGGAGCTTCTTCCTGGGCTTCATCCCACGTTGGCTCTTCATGAAGCGGCCCCCGCTGCTGCTCCCCACCGAGGGGACGACGGGCCAATATGACCCCCCGGGGACCAGGCTCAGCACCTCCCGCTGCTGGCTGGAGACCGACGTGGATGACAAGTGGGAGGAGGAGGAGGAGGAAGAAGAGGAAGAGGAGGAAGAGGAAGAGGAGGAGAAGGCGTATCCCAGCCGTGTGCCCTCAGGAGGATCCCAGGGCACCCAGTGCCACTACAGCTGTGGACGCCAAGCAGGCAAAGCATCAGGGGGCCCAGCCCCCCAGGTGCCCCTCAAGGGGGAGGAGGTGGGCTCGGATCAGGGGCTGACACTGTCACCCAGCATCCTGAGGGCCCTGGAGGGTGTGCAGTACATCGCGGACCACCTGCGAGCCGAGGATGCTGACTTCTCG
Seq A exon
GTGAGTTGGGGGCAACCGAGGGCTGGGGGTGGGGGGGATTCCCCAGCCCAGTGCTCCTTCCATGGGGGTCAGTGATGGGGATATCCAATTGTATCCATGCATACTGAGGGCCTTAGTTCGGGGGATCTATGGTCATCTGGGAAATAAAGGTAGATGTTGCACTGAGCAACATGGTCTAGAGCAGTCACAGCAGTCACAGGCATGGGTTGGTTGTCGGGCTTGATGATCTCAGTGGTCTTTCCAACCTTAATGATCCTATGATTCTATGAAATATGGGTTCCACCACGTCAGCTCAGTGTTCCTCAGGCTGCAGGGTGCTGGAAGCCCCTCTCCCAGCCACACTGCCCTACATTCAGTCAGCATCCCTCACCCAGCTCAGAGCCTGCACCCCAACCCACAGTTTGGGCACACCTGGGTGGGGTTTGCTATGCCTCTAACAGCCTCCCTGTAGAGATCCATCCCCACACCTTATGCTTGAGATATCTCCTAACCCTTGGAGGCTTCACCCTCCACCCGCAGCTCACAGCCCCTCTCCTCCCGGCAG
Seq C2 exon
GTGAAGGAGGACTGGAAGTACGTGGCCATGGTGATCGACCGTATCTTCCTCTGGATGTTCATCATCGTCTGCTTGCTGGGAACCGTGGGGCTCTTTCTCCCACCCTACCTGGCAGGGATGATTTAGGGATCAAGGGTGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016565:ENSGALT00000026738:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.051 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PD(55.6=41.5),PF0293211=Neur_chan_memb=WD(100=54.9)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(12.4=79.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAAGAGGAGGAGAAGGCGTA
R:
AGGTAGGGTGGGAGAAAGAGC
Band lengths:
354-898
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]