DreINT0088231 @ danRer10
Intron Retention
Gene
ENSDARG00000036279 | lamc1
Description
laminin, gamma 1 [Source:ZFIN;Acc:ZDB-GENE-021226-3]
Coordinates
chr2:35994295-35996721:+
Coord C1 exon
chr2:35994295-35994394
Coord A exon
chr2:35994395-35995482
Coord C2 exon
chr2:35995483-35996721
Length
1088 bp
Sequences
Splice sites
5' ss Seq
TCGGTAAGA
5' ss Score
10.53
3' ss Seq
TAATGTAACAACACCTTCAGGTA
3' ss Score
3.28
Exon sequences
Seq C1 exon
GCATCAGACAATGCCAAAGATGCAGAGGGCAATGCCAGAAAAGCCAAAAGTGCTGTCAGAGAAGTACTCAACACAATCAATGCACTGCTAGGCCAACTCG
Seq A exon
GTAAGATCATTAAGAGCTTTCTGTGTTTACAGACATTAATGAAGCTGTTTAAAATATTTTTAAAACACATATTTGTTATACATTCATACTATACATGTATATTTAGATTCGATTCGACAGGGAAAATCAAGAGAAACACAAAAAAATCACATTTCGCTGAAATTCGTAGTTTTATTACTATTTTATTAGTTTTATTTGTAATTTTCTTATAAACTAAATTTTATTTTTTTAATCCTATTTTAACAGACATGACTCTTTAATAAAACTTTTGTTTAAGTGACAAATATCATTTACTATATTCACTGAGAAATGGATACAAGTATTCATATTCAAAAAGGGGTTTACTCACTATTATATAGTCGGGGTGTAACGAATCACTGTTGATCCATGATCCGTACGGATCACAACCCAAATGTCATTATTAATGTTGTTATTAATTAAAGGTGTTTTCTGTCACTGTTTGTTTAGCCTGCGTTAATGCATTCAGTGTAAAGCTGCACAATTAAACATTAAATAATCCTGATCTCAATTCAACATGAATGATAAAAGCTTATGATTTGCATATGTTTAATAATCCTTCCAAGCACTGCATTCAAATTTATGTTTGATCAAGAGAGATTCAGTTTTTACACGTTTTCAGTTACAAACAATTGACTAACACAGAAGTACTGGCACAACAGTTTACAGTTCTAATTTAAACACTACATTCGTGACTCAAAAAACATAGTGTGATCCGAACCATGAGACTTGTGATCCGTTACACCACTAATGTATAGTATAGAAAAAGAGAGATATACATATAACTAATATATTTGCATGTATAAGTACTGTACATGTATCAGATGATTTATAGTATATTAAGTAATTGAAAATGACAAAAAAAGCTAAATTAAATGATAACTATTTAACCTTTAACTGCGCTAACCCAAAAGCAAAAGGAAAAGTTGTGTAAAGTGATACATATTTAGCTTAATATTTTGATTGCTTTTATTGTCTGGAATAATGTATTTTTTTCCCTTCTTACAATGTGCAAAACTATTATGTAATTACACTTCATAACTTCCACTTTAATGTAACAACACCTTCAG
Seq C2 exon
GTAACATCGATAAGGTGGATCTGAGCAAGCTGAATCAGATCGACAACGCTCTCAAAGATGCCAAGGACAAAATGGCGGGAAGTGAGCTGGACAGGAAGCTGAAGGAGCTGAACGACATCGCCAAGAGTCAGGAGGACATGATCAGCGACTACGACCGTCAGATCCAGGAGATTCGAGCAGACATTGCCAACCTGAACGACATCAAGAACACTCTGCCCGAGGGCTGCTTTAACACGCCGTCTCTAGAGCGGCCATAACCTCCTACAGCAACCTAACCTAACCTCCAATCCACAGCGCTACGTCTGCCTTACACTCCACCAAAACGGCCTTTCCCAGTCTTGCCTTTCGTTTCCTTTTACTAGCTTACTGTTCGTATTTCTACACGTTTCTTGGAAATCATCTTTTACAAACGGAAGACAAAAGCAGCTTTTAATTGTGATATGCAGAAATGCTACGTGAAGAGAAATCCAAGTTATGGCGCTCACCAGCCGTGTGTGTGTTTGTGTGCGTTTGTCTATGTATGTGTGTGTGTGTGTGTGTGTTTGCGTAGTAGCAAGAGGTAAGAGGCCACATGACTGCACCACCTCCAGTTCTTCTTCTCATACTTTTACAACACAATCTGAATGATAGTAAAGCGTTTGTTTGAGGAAGTTTGCTACTTAAGCTAGTGTATATCATCATCATCATCAGTAACGCTATTCGCTCAAAGCTAACAGTGAAGGATTCTTAATTTGCTCTATTTTCGGCCCTCGTTTTTAAAGTGTCACGTACATACAGTATTTCAGTTCATGTATATATGAATAGTTCAACGCGGAGAATGAAAGTCCCTGCATGGAGCGCGACATTTCAGTTTTGCGTTGTTATTTTTCAGACGCTGCTGCTGCTGCTTTATTAAAGGTGTCCTGCGATTCGCATTAACACGAAAAACACGCAAAACTCAACACTATGCAACTTTGTACATTGGCGTAGCAAGACTTTTATCTGATACACTGGTGCTAATAATTATTTCAAATGTTATATTTTTGTGTGAATGTTATTTTTTTTCTTTATTTTTTATTATTATAATATAGAGTTGAGGAACTGTTATTTGTGTAAATATGCTTCAATGATTCAGGAATGGCTGATTTTTTATTTTTATTTTTTAACTCAGCCAGCCACCTCACCGGTTCACAAAATAAAAAATCAGCTAAAATTTCTTGCATAATATATATATATATATATATATATATATATATATAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000036279:ENSDART00000004277:27
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.529 A=NA C2=0.329
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AATGCACTGCTAGGCCAACTC
R:
GGCCGTTTTGGTGGAGTGTAA
Band lengths:
350-1438
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]