GgaINT0061041 @ galGal3
Intron Retention
Gene
ENSGALG00000015384 | F1NA49_CHICK
Description
NA
Coordinates
chrZ:52500394-52503627:-
Coord C1 exon
chrZ:52502745-52503627
Coord A exon
chrZ:52501428-52502744
Coord C2 exon
chrZ:52500394-52501427
Length
1317 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGT
5' ss Score
10.28
3' ss Seq
GTCTCCTCTCTCCTTCACAGGTT
3' ss Score
12.03
Exon sequences
Seq C1 exon
CGCTGATGGACGTTTTGAAGGGTCCCTGATGACCAAAGCCATAGTGAAATACAATGGAGTGGTGACCTGGATGCCACCAGCCAGCTACAAGAGCTCCTGCACGATGGACGTAACCTTCTTCCCCTTCGACAGGCAGAACTGCTCCATGAAATTTGGGTCATGGACATATGATGGCAGTATGGTGGACTTAATTCTAGTGGATGAAAATGTAGACAGGAAAGACTTCTTTGATAACGGGGAGTGGGAGATCTTAAATGCCAAAGGTATGAAAGGCAACAGGAAGGATGGGCTGTACTCTTACCCATTTGTCACTTACTCCTTTGTGTTGAGACGCCTTCCACTGTTCTACACTCTTTTCTTAATAATCCCTTGCCTGGGATTGTCTTTTCTAACTGTCCTGGTGTTTTACCTGCCCTCAGATGAAGGAGAAAAGCTCTCATTGTCCACTTCAGTTCTAGTGTCCCTCACTGTTTTCCTTTTAGTGATCGAGGAAATAATCCCTTCTTCTTCCAAAGTCATCCCCCTGATTGGTGAGTATCTCCTGTTCATCATGATTTTTGTGACCCTCTCTATCATTGTGACTGTCTTTGTTATCAACGTCCACCACCGCTCCTCAGCAACTTACCACCCCATGGCCCCCTGGGTTAAAAGACTCTTCCTCCAGAAGCTGCCTCGGCTGCTCTGCATGAAGGGACACGTAGACCGTTATTCCTTCTCAGACACTGAGGAAAAGGAAACCACCTTGAAATCAAAACTCCCAGGAAAACAGAAACACAAGCAAGCAAAAGATGGAGAGAAAGTCGTGATTGCCTTTCTGGAAAAGGCAGCTGATTCCATTCGGTACATTTCCAGGCATGTTAAAAAGGAGCACTTCATCAGGCAG
Seq A exon
GTAGGTGAAAGTAGGGCAGAGAGACATCACAGCCTCCTACACAGCTGCAACTTCCAAGTTTTTCCTTTTCTGCATGCCTTTCTGTATGCTTCTTCCTCTTGCATTCCTCTTGCATGTTTCCTGGGAGCTTTCCCTGCTGGGTGTGGGAAAGCATGTTACTTCAAGAACAGTGTTGTGTTGTGGGAGTCCCTGTTCTTCCCAGACGGAAGGGGCCACAGCTGGCTGTCCTGGAGGAATTCCTGTCTTGGGAGTATTTGAATAACCTGGCCTTGGTTAAGATGGGGACAGAAGCAAATCTGGAAAACATGAGTTGCCACATTCTCTGAAAGTGCGTCTTTCACAACTGTTCTAGGCAAGTTTTATGGCAATTGCTAGGGCTGACTCTTGGCCTCCCAGCTATTCTCTGTAGTGTAGGGACCCCGTCTTTGTGGCTTGCACTAAAAAAAGTTTGGTTTAGAGCATCTTCTCCTCCATCTTTCTCCTCTCAGCAATCCACCTGGCTATTAACATGGAAAGTTTTAGAAGTTAATTAAGTAACGTGTCCATAAACAATGTACCTCACATACAGGTAGGGCAGCTAAGCGAGGCAACCAGCAGCACATGGAAAGAGAAGCAGTTCTCTTAGCACTCTCCTAGCAAAAGCCAGGGCTTTGTTTAAATTTTATTGATGACGTCAGCAGAGTGATGAACAGTAAACCAAACATGCAGCATGTGAGCATGTAGTGCCCGTGACTGAAGTCTTCTCTTTGAGGCTTGAGTTACTAAAAAAAAAATTGAGAAAAAGTCCCCTGAATCTGTTTTATAAACAGCGCTTCCATTTATTCAGGGTTGTGCCAGTACACACGATGCAGAGCTTCCCTCCTAAATGCATGCAGCATGAGCCAGCAGAGCACTTAAGCAAACACAAGCCGGTGGGACCACTTGTACTGCAAGTAACATCTGCGTCAAAGTGCTTTGCTAGAGCCAGCTCCTAGCCCTCCAAGGGAAAGGCAGTTATGTTAAAAGAAACCTAAATCATTATAAAGACATCCTCAGGCTTCAGTCTGTAAGCTTTTACCTATGCACTTAGCTAAAAGCTTTTGCACAGCCTGAAAGAAGTCTGATTATCACGTGCTCATACCATGAACATGCTCTGGCGTTTTGATAGACTGGCAGGTATGGCTGCTGAAAGCTGACCCACGTTGGTTTCAGGCTATGGCACACTGCAATCTTCTGGTTTCTAAAAGCAGATTTTTTGGAGTTGAAACACGTGTGGTAGTACAAAGAAAGTACTGGCCTCCTTGCTGTTTCTCTTTGCGTCTCCTCTCTCCTTCACAG
Seq C2 exon
GTTGTCCAAGACTGGAAATTTGTAGCTCAAGTCCTGGATCGGATCTTCCTGTGGTTATTCCTGGTGGTGTCAGTGACGGGTTCAGTTCTCATCTTCACCCCTGCATTACAGATGTGGCTGAACAGCACTTTGTAGAAAATACTCCCACGCTAACATACAACAAGCCCAATGACATGGGACGGTGGTGCCTTTGAGACTGGTCTCTGCTCTGCAGGATGGGAAGCAGTGCAAGAGGGAGAGAAGGTGATGTTAACAACAGGCATTGGCTACTACTTCCTTCATGTGGCTCTGACTGTTACAGCCTTGGTGGAGACTGGAGAAGGGCTCGGTGAATGGCTGAATCCAAAAGTGAATTGGGGATGCATAAATGAGTTACAAGTATTTTACTAGTAGTTTGGTTATAATACAGTATAAGCCAGGATTATTAGTTATACTTGGGGATAGCAGTTCTGGCACAACCATTATTTTTCACGAGTAGATGTGTCAGTTAAAATACTACTTAATGAAAGAAATTAGAGTATAGTAGCAGCATAGCGCTCAGTTCTTAGTGCACAGTAGCAAGTCAGTATTCAGCTTATCTACCAAGTAAAAACCACAAAGTCCTTATAGATAGCTTTCTACATGTGTCAGAACAGGCAATTATATAGCATGTGCATTAGAAAAAAAAGCGTGAAGAATTTTTAGATGGGATACCCAAAACCTGAACTCTGTGGCCATACCTTCAGGACCAGCTCAACCATGGGAGAGCTTAGGGCTCTGCCCACCCACTACCGACCTCTACAGCATGCACGTTTTGTCCCTCCTCTTGGCCATCAGGAAGTTGCAAGGTGTTATATTCTTTTCTGTGTAATATGCATTTTTGCCTCATACAGTGAAAGATAATTAAAGGCTGAACAAGTGAGGGTTTTTCCCCTGCTCCTCCACATTTGGAAACTATGATTCCTTCACCTGCATGTTCACAGGACTGGAAGATCACCTGGACTACATCCCCTGAAAGAACGCAACCATGCTGTTCCAGGTGGCAACAAAGGTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000015384:ENSGALT00000024820:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.022 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PD(55.1=38.3),PF0293211=Neur_chan_memb=WD(100=51.2),PF0293211=Neur_chan_memb=PU(63.7=19.7)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(34.1=68.9)
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:
AAGGAGCACTTCATCAGGCAG
R:
CCCTTCTCCAGTCTCCACCAA
Band lengths:
345-1662
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]