DreINT0088107 @ danRer10
Intron Retention
Gene
ENSDARG00000101209 | lamb1a
Description
laminin, beta 1a [Source:ZFIN;Acc:ZDB-GENE-021226-1]
Coordinates
chr25:31188097-31190120:-
Coord C1 exon
chr25:31189932-31190120
Coord A exon
chr25:31188274-31189931
Coord C2 exon
chr25:31188097-31188273
Length
1658 bp
Sequences
Splice sites
5' ss Seq
AGCGTACGT
5' ss Score
7.8
3' ss Seq
TGTGGATTTGTCTTTTGCAGCCT
3' ss Score
9.19
Exon sequences
Seq C1 exon
AGTGTCACTGCAACCATCACTCTCATTCGTGCCATTTTGACATGGCAGTTTACCGAGCCTCAGGGAACGTGAGCGGCGGCGTGTGCGATGACTGCCAGCACAACACTATGGGCCACAACTGCGAACAGTGCAAACCCTTCTTCCACCAGCATCCAGAGAAGGACATCCGCGACCCCAACATCTGCGAGC
Seq A exon
GTACGTGTGCTCTATCATTTCCTTCGGTTCTTTCTCCTCGACCTGTCTGGTCAAGTTTGTGAGGAGTTTCTGGTCCAGCTGTTGCTTTGTTTCAGATTTGGAGCAGAAACACCTGGGCTTTGAAGTAGTTTGTCAGTGCAGTCTTCAAAACACACATGATTGGGTTTCGCATTCCTCCTCTGTTGTGGTGACGGAGGGTTTAGTTTGAACCCTGTGACTACAAAGGAGAAGTGTGGTCTGGGAATTTTGCATTACACTTATTCAATCTTATGATTCATTCATAAAAAATTATTAAAGTGAACACTTACAGTTGAAGTCAGAATTATTTGCCCCCCCTGTTTATTTTTGTTCCCAATTTCTGTTTAATGAAGATTTTCTCAACACATTACTAAACATAATAATTTTAATAACTCATTTCTAATAACTGATTTATTTTATCTTTGCCATGATCACAGTAAATAATATGAGACTAGATACTTTTTAAGACAGCTTAAAGTGACATTTAAAGGCTTAACTTGGTTAATTAGGTTAACTAGGCAGGTTAGGGTAATTAGGCAAGTTATTGTATAACGATGGTTTGTTCTGTAGACTATCAAATATCAAAAAATAGCTTAAAGGGGCTAATATTGACCTTGAAATGGTGTTTAAAAAAATTACACACACACACACACATATATATATATATATATATATATATATATATATATATATATATATATATATATATACATGCATACATATATATATACATACATATATATACATACATACATATATATACACACACACACATATACACACACACACACACACACACACACACACACACACACACACACACACATATATATACATATACATATATATATATATACATATACATATACATATACATATATATATATATATATACATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATACACACATATATATACACACACACATATATATACATACATACATACATATATACATACATACATATATATACATACATACATACATATATATATACATATATATATACATACATACATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGTGTATATATATATATATATATATATATATATATATATATATATATATATATATATATATAATTATTATTATTATTATTACTTATATTTGTGTATTTAATTATACTGTTAAGCTATTAATGTTCTCTAATAAATCTTTTAGTTTCTCTTTTTAAAGTATTGTGCTTACATGTTATTTAGTCACTGGTGCCATTTTAAAAGTATTGTTTTGGTACTAAGAATACCCAACCCAATTATTAAGAGTAAATCACACATCACATACAGTACTTACATATAGTATGGTCATGGTGTAATGCTCCGGTATTCTAACCTTTCCCCCTTTTTTCTGTGAGCGTATCGGGCCCTAAAGAGTCAGCATGCCTCCATGTGTTAGTTTTCCCAGCTGTTCACAGTTCCTCCCATTGTGTGGATTTGTCTTTTGCAG
Seq C2 exon
CCTGTAACTGTGATCCGGTTGGATCCCTCAATGGTGGCGTTTGCGACCCGATGACAGATGTGTCGCTTGGCCTGATCTCGGGTCAGTGCCGCTGTAAACCCAATGTGGAGGGTGAACGCTGCGACCAGTGCAAACAAGGCCATTACGGGCTGAGCGAAGACCCTCTGGGATGCCAAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000101209:ENSDART00000166930:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0005319=Laminin_EGF=WD(100=95.3)
A:
NA
C2:
PF0005319=Laminin_EGF=WD(100=95.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCATCACTCTCATTCGTGCC
R:
TTGGCATCCCAGAGGGTCTTC
Band lengths:
353-2011
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]