DreINT0088096 @ danRer10
Intron Retention
Gene
ENSDARG00000101209 | lamb1a
Description
laminin, beta 1a [Source:ZFIN;Acc:ZDB-GENE-021226-1]
Coordinates
chr25:31216288-31218134:-
Coord C1 exon
chr25:31218107-31218134
Coord A exon
chr25:31216461-31218106
Coord C2 exon
chr25:31216288-31216460
Length
1646 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
TTTTTTTTACTCTGACATAGTTT
3' ss Score
6.75
Exon sequences
Seq C1 exon
ATGCTGTTACAACTCGCAGCCCTTTCAA
Seq A exon
GTAAGTTTCATTTTAGCTGTGTTGAAGAAATGTTTCTTTTGCAATTCATTTAAGCTACTGAAGTAGAACTAGTTTTTTATTTTTTTATTTTTTTTTAGTTTATTTGTTTACAGGGTCAGTGCACATACATTACTGTAAAATGTGCCAGAATTAGCCAAGAATGGCTATTTTTCATCCGTAGACCCTTTACAGAATGTTAAAAAGTCACACCTAAAATAGAAGCACAACATTAAACATTAAATACACTTTCATAAGAAATACAGTTAAAAAAGTAAAGAAAAGAAAAAAAGAAAGGAAAAAAAAAAGAACAGACTGATGGGAGCAGAGGACAAAAAGCCAAAGACAACAGTACAAATGTGTCAATAACACAGTACTAATGCTGACAATGCTGATTTGTCAATAACCAATTTCTAACATGAGACTGAAAAGAACGAAAAGTGCATGATCTTCTAATTGTTGGTGGGATGGAGTTCCATTCCCTAGCAGCTCTCACTGAAAATACAGATTGACTGAATTTGCTTTTTTTGAGAGGAATAATGCAGTCTCCTCTGTCACCTCCTCTAGTAGTTCGGTGAGCAGTCGTTCTAATATTTATAAACTGATTTAATGGTGAAGTCGGGTTATGTAAAGTCTTAAACATTAAACAGATATGTACATATGTAATTAAATTTTCCCAACTAAGCAGGTTGTATTTCTTTAATATTAAACAGTGGTGAATATTGAACTGATTTCTTATCAAGGGTTTGAATTGTATTTGTAGTTGTGTCATAACAGTAAAATGGTATTTAAAATTTTACCATTTTTAATTTAATAAAAATAGTATTTATATTGAATTTTTTTTAATATTAATAGTCATTTATGTTGATATCTTTTTTTTTTTTTGCAAATAAATGTTCTGAATGTCGATATTTTTATTTAAAATATTGAGGACACATTATCAGTAGTTTATTAAATAAAACACACATTAACATTTTATTTTAAAGCATACTCATTAATGGCAAATCCTGAAAAATGAGAAGCTAAATTCATCAAGAATTTAATGTACTTTATGAGTTACTTGTTTAGAAAGAAAGAGAGATATGTTTTGAAGAATCATGGAAACCTGCAACTTCTGACATCCATAGTAGAAAAAGAAATGGAAGTCAATGGCTTCTGGTTTTCAATAGTCTTTAAATTATGCTTTTCTTAGTTCAATAAAAGTACAAACTTGCTATCAATTTATTTTGACGGTGCCTGTAACAGATTTTGTTGAATTTAAGTTGCATCAACAAGCCAACTAATTCTCAATAGATTATAAGTAGGTTGGGGTTAGTGTGAGTTGACGTGTACTTGCAAATAATAAATAGTCTGGAAGTAGCAGTATCACCATATATTAAGCAGACAGTCTACTAATACTCAAATGAGAAGTAAATGGCTTTATTTTGATGGTCCCTAATGCACATTTTGTTAATTAAAAGTTGCATTGAAACTACATTCAATGCAACTTTTAGTCAACAAAATGTGTGATAGGGACCATCAAAATAAAGTCTTACCAAAAACTCAAACAGGTTTGAAGCAACACGAGAGTTAGCAAATAATGACAGAATTTTAATACAGATCTACATAAAAAGGCTTTTTTTTCTTTTTTTTTTTTTACTCTGACATAG
Seq C2 exon
TTTTAGGGGCCTGGGCTCTGGCAGATGTGCCTGAGCTGGGAGATGTTTGCACAGAAGGGAGCTGTTATCCGGCCACAGGAGATCTGCTTATCGGAAGAGCTCAACAACTCTTGGCCACCTCAACATGCGGAGTCCATAAACCTGAGCCCTTTTGTATCGTCAGTCATTTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000101209:ENSDART00000166930:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0005512=Laminin_N=PU(15.3=62.1),PF090866=DUF1924=PU(12.1=12.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGTTACAACTCGCAGCCCTT
R:
CTGCAAATGACTGACGATACAA
Band lengths:
198-1844
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]