GgaINT0098643 @ galGal4
Intron Retention
Gene
ENSGALG00000015056 | LAMA3
Description
laminin, alpha 3 [Source:HGNC Symbol;Acc:HGNC:6483]
Coordinates
chr2:102836986-102839131:+
Coord C1 exon
chr2:102836986-102837146
Coord A exon
chr2:102837147-102839022
Coord C2 exon
chr2:102839023-102839131
Length
1876 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
AATGCTGCTTTCTGTCTCAGTTT
3' ss Score
8.6
Exon sequences
Seq C1 exon
GTCAATTTACAGATGACCATAAATGTTCCTCATGTTGGTCGCTATGTTCTTGTTTTTGAATACACCAATGAAGATGACCAGTTATACACTGCTGAGGTAACAGTAAATAGCCCTGGACCTGTCACAGAAGGTAGAGTGAGAATATACAGTTGCAAATACAG
Seq A exon
GTGAGAATTTCTAAGGTAAATACTAAATGGTTAAGCAACCATTCAGTATATAATTATGCCTTTTATATTTTGGAATCCATTGTACTGCATACGTTGTTCAAATATTAGATTGACTGAAAAGCAAATACTTTATTGTCTGGGTATTGCATATATTTTTAAGTCTGTGCAGTCAGCACACTAAATATTGCTGCTGCTTTAGTGAACTTTTTCTGTACAAAGGGATTTTTTATATACACTTAAATCCTTATAAATTATGAATCTTGGAGTCCAGTAGCAGAGCATCCAGCAGCTCTGTTGGCAACAGATGTCTGCAGTATTTATACTTGTTTAGTTAAAAGCAGTCTGAGGGTTTGGCCTATAAAGAAAAGTAGCAGTCAGTTTTACAAAGGTGTTCCCACTGTTGTAACAAGATTTGTTGAAGCGGATGTATAAATGTTTCTCTGAGTTTCTGAGTGTAGCCATCCTTGACTGTTGGGCTGTAGGCAAGGTTGTAAGCCATATGCTGATTTATCCTCATTGACTGCTGAGATTACTGGAGGTGTTTCAGAATTTTGCCTGTTCTGGGTGAGGTTGTCTTTAACACTTGAGCAATTCAGAATATGACTTAAATATGATCCTGCAGGTGTTTGTGCCCCTGAGAGCGTGAGGAGACTGCTGCCATGCATCAGTTTTTCTTGTGAGCCAAGTGTTGGACAGACTGGAGGCTTAAGGTTATTTAGGATGAAACTGCCCAGTAGGAAAAAATTGTTTTCATCAGCATATATGTGATACAGAGCAGAGCTATGTGAAGCAGTGACCTTGCGAGGTTATTGCTAGGCAAAGCTCTTGTTTTCAGCCTGTTATGTAATACTTTGAGCCCCGAGACGCTTTTTATAAAGCTTCAATTTTATTGCTTTTATATCAAACACCTCTTATGGGCTTATTTAGATCTTGTTAGTTTATCTGATACACAAAGAGATTAGTCACGGGGAAAAAAAAACAACAAAGTAAACCTTAGCTTCTTAAATTTAGCAGTGCAGTAAATCCCTTCTGCTGCCATTCTACATTTAAACTAGTAGTCACATTGCAAGTAAATTGCTGTGTCATCTTTCCTGAGCAGAAAGATGCATGTCCCTTCTGTTAAAAAAAGTGAAACAATTGAACCACAATGGTGAAGTACATGCACATCAGAGAAACTTGAAAAATCATGAGTAAAGTGTGCCAGGGCTTGCTCAAAGGGAACTGTTTCCACTTCTGGAAGGCTGTAGGAGTCATGCTCCCTCAGCAAGGCAGGGCTCCAAGCCTCTAGCAAGATTCTTCTTAGTATTGTCTGTCATTACCGAAGATGTAGAGCTAATTGAAGGTAGTCTAAGAGACAGAGACAAGCAATTTTTCACTTGCATAGAGGAGTATCTCAGTGGACAGATAGTTTCCTAAAATCAAGAATTGCGCAGGTGCCATCGAGTGGATGATAGCTGCTGATCCACACCATCAATGTGTAGTGATAGGAAAGCAGCAGCTGGTATATTCTGGCACCTCGAGGAGCACAGACTAGGTACTGGACGTTAATTACATGCCATGTGAAACAGCTTGGAGAACATCTGCAGACAGCATGTATGTATGTTCACATCTTCCTTAAAGTAGTAGCTCAGCATCAGAGCTGAGGTGTGGAGGTTTGAACACTGTGTAGATCAACCTAAAAAGGGCAAGGAACGTTTTATAGGTGGTGCTTCCTTTGTCACACCAGTAAGGCTGCCTGTTTACCAGTGGCCAGACATAGTTGTTGCTTACAATCCAGCAGAATGACTGGGCACCAGTGGTGGCAGTGAGTTGGGCAATAGAATAAACAGCATGGCCTTGCCAGGAGTCTCATTTTTAATGCTGCTTTCTGTCTCAG
Seq C2 exon
TTTCCTTTGTCGTAGTGTTGTCGTTGATGATAGGAATCGCATTGCAGCTTATGACCTTCTAGCAGATACAAAGGTACATCTTCAGGCATCATCAATTAATTTTCTTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000015056:ENSGALT00000024287:24
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACAGATGACCATAAATGTTCCTCA
R:
AATTAATTGATGATGCCTGAAGATGT
Band lengths:
254-2130
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]