GgaINT1016741 @ galGal4
Intron Retention
Gene
ENSGALG00000006169 | LIMA1
Description
LIM domain and actin binding 1 [Source:HGNC Symbol;Acc:HGNC:24636]
Coordinates
chrLGE22C19W28_E50C23:256292-258337:+
Coord C1 exon
chrLGE22C19W28_E50C23:256292-256440
Coord A exon
chrLGE22C19W28_E50C23:256441-258229
Coord C2 exon
chrLGE22C19W28_E50C23:258230-258337
Length
1789 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAGT
5' ss Score
11.81
3' ss Seq
CTAAGTGCTTTATTCTATAGAAT
3' ss Score
6.61
Exon sequences
Seq C1 exon
ATGCAAGTCCAGCACTCAGCCCAGATAAGGTAGAGACCAAGAAAAGCCTGGAGATGCCTCGCTTAACAGAAACTTCAATAAAGGATAGGTTGGCAAAGTATCAGGCAGCTGTGTCCAAGCAGGGCAGTTCCACAGGCCTTGTGACCACG
Seq A exon
GTAAGTCTGTTTGCCTTGAGTAGAAGTGAATTTTAGCCCCAACCTAAGGCTGGGAAGATGTTACAGAAACCAAGCTTTTTGAAGATGATGCCATCTTGTTTTGAAAAGACCTTTGCGCTCCTAGGGCTCATTTCTAGTGAAGAGTTGCCTCTACTGCAGGGAGAAACAAGTACTTGCATCGTGCTGGAGTGATCTTGAAAGCTTTCCAGGAAGTTAATTGCTGGCACCCTGATTGCAGTCCTTCTGAAACTTAACTGACATTCTTTTTCTTTCTGCTGTCTGCATGCTAAAAACAAACAGAAACCTCACTTCTATAATGTACACTAGCTTTAAGCTAGAGGAAATGGTCTCTACCTAACTGAAATGACTTCTCAGTTTTGTCTGTGGTGGAGATTTGATTCTGCTGTTCTTGGGAGGAAAATCTAGTAACCTTCGTGGTATGAGTGGAAAGGCACTGCAGCCTGTGCAGCAGATGCTGTTATCTGCAAATTGCTGATTTGAGTCCTATTTCTCAGGACTTAAATCTGTATTTGGTTTGCCATATGATTTTTTCCAGTTTGTGGCTCAGAGTAGAGTAGCCAATTCAATAATGTCTGTCCTAATGGCAAGAGATTTACCATAGATTTTCTTTTCTTTTGAGACTGTCGTTTGCAATTCCCCAGTGCTATCAGTTTGAGTGTCAGTGCAGCCTCAAGCTCTTAGGAAGTCCCATTTAGCAGAATTTCTTTTGGTTTTAGCCTGGCATGTCAATAAGGGCAGCAGGTAAGGTGCTGATGAGGTTAGTGTTTGCAGTACTTAGAAAAGAAGCTGTAAGTCAAGTCTTGGTTATTTTCTTTTGCTGCCAAAGGAACTAAGTGTCTTTTGATATGGCAGTATGGTATTTGTACTTCCCTTCTCTGAAAATGTGTCACATCTATGCTGCAAAAGAGAGAAATAATCTCTCCTGGGATCAGCTATTTTGTGGGCATTGTTGTGTAATCAGGTCTGGATTAAAACTGAGGGATGTTTTTGCAGTGGGTTAGAGAAATGGTGAGAAGCAATTCTTTTAATAGCAGCGCAAGTGACACAGGAAAGGTAGGGAGAGAGAGCAGCATATTTAGAGATCTGTGTATTGAAACATCAGCACTTAATTACATACCTGTTAGACTCAATTAGCTTACAGAATCCAGTGAGCTCCTAGTGCTGGCACTTGGCTATCTGTCTTCCATGTTACAAAGAAGATGCTTTGTGAACAGCATGAGTCTTTCCCCAATTATCTTGAATCCTGCGGCAATGAAACACGAGGTTGTGCTGGATTATTATTAAAGTGAAAGATTCTTTTGTGTAAATCTTAAGACAGTTTGTAAAGAACAGAAATCTTGGTAAATAACAGTTGGTTTTTTTCCCCCTTTTTTACTAGCATAGAAACAAGTAGGATTTGCTTTTATGTTGTATTTATCAATTACTCAGCACTTTATATGGTGCTTATCTTGAAAAGTTAACATGTATGGAAAGAGAAGATGTGGAGTGAGCAGGAGAAAAATGGAAGAGTTGATCTTAAAGGAAATCTGCAGTCAGAGAAAAGGGCTGTCTTATCTTCACAGCATAAATTTCTACAGCCCTATCTCTTTTCCTTGTTAAAATCCATAACTTTGCAAATGTGTATTGATTTTTTTTTAAAGCCCTTTCACTTAGTTATTGCTGTATATGCTAGGAAAACAGTTTACAAAACAACAACAAAAAAAGAAAAATAGCAAGTACTTTCCTAGGAGAAAAGAGCCTGTCAACTTCTAAGTGCTTTATTCTATAG
Seq C2 exon
AATGAGATTCAAGCCAGTGAAAGTGAACTCAAGAATTACAAATCTGAGCAGAAGGAGAATATGCCACCAAGTTTTGAGGACTGCATTTCCTATCAGGATGGGGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006169:ENSGALT00000009960:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.960 A=NA C2=0.852
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGCAAGTCCAGCACTCAGC
R:
TCCTGATAGGAAATGCAGTCCTCA
Band lengths:
247-2036
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]