DreINT0088244 @ danRer10
Intron Retention
Gene
ENSDARG00000068288 | lamc2
Description
laminin, gamma 2 [Source:ZFIN;Acc:ZDB-GENE-110222-3]
Coordinates
chr2:36037242-36039151:+
Coord C1 exon
chr2:36037242-36037341
Coord A exon
chr2:36037342-36038535
Coord C2 exon
chr2:36038536-36039151
Length
1194 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGT
5' ss Score
11.11
3' ss Seq
TCATGACTATAATTTTCCAGGAA
3' ss Score
7
Exon sequences
Seq C1 exon
GCTGTCGTGGAGTCCAATGGGGTACTTGAAAACGCAAAGAAAGCCAGGAACGCAGTTAATGATACTCTACAGGACATCGCTGATATTATGAGCTCACTCG
Seq A exon
GTGAGTTTTAGCATTACTTCGCTATATATGCCATGAGAAAGTTTTCTATTTTAGTATTACGCTTTATTTAGTATTAATGAATATTTTGAATAAGCTCCTAGTATTACATTTATTATTTCTATTCATTTACATTTTAGTTATTTGATTGTTAAAGGGATAGTTCACTCAAAACTGAACATTCTGGATCATTTATTCATGTATTACTTGTTTTTTTCTTCTATTGAACACAAAAGAAGATATTTTGACAAAAGCTGAAAACCTCTAACGTCCATTATATTTGTTTCTCCAATGGTACAGGTTTTCAGCTTTCTTCAAAACATCTTTTTTTTTCGTTCAACAGAAAACGGAAACTCAAAAACAGAAAAAATTTGGAACCACTTGAGTATAAATAAACTATCTTAAATAAATTTTTACATCATCATGTCATATTAGAGAACTGACGCTACACTGAAAAAATGCCTTTTGGTACTTGTTTACACTGCTTATTTAAAATGAGTTGAAACAACACAATTCTTAAGGTTTTTTGTGGTTTATGTTCAATCCACTTAAATTTGCAAATAATGATCAAGGTAACTTGATTTGTGTTGGGACAACATGATGGAATGATATAGAACCCAGTCAAAGGATTCTTTCAGCGCCCAAATGTGAAGCTTAAACGAGGAGATAGAGAAACTAAACTGTATTAGTCTATATGTCCCTTTTCTTAGCTTCCTTTTCTTGGGCAAGTATTCCATCAATTATGTGAAAATACTTTAATATTTACAACTATTTTAAATTATTATTAATAATATATTATATATATTTTTGCTAGTACTATGTCGGGACAAGACAAGCTTTTGGCTGTATTAGCCACTGGAGCTACAGGACTTGCCAACATAACGCTTTAATTACTGTAAATCTGCTTAAAGGTCACATGAATTTACAATTTTTATTTTTAGATTACTATCTTAGTTTCTGTTCGTTTTTAGGATATCTATTAGTTAGTGTGCTTTAAAACACTGACAAAATTCAGTGTTTTGGCAACAAAAAATAAAAACAAAAATTTTGGGCAGAAATTTTTTTGGGAGAATTTTTTGTCCCTTTTAATTAGCCTTTTCATTCTTCTATTGTTTGCTTTAAATGGAATATATTTCACGACCAGTGTATTGATGGATCAGGATTTAAATCAAACTCATCATGACTATAATTTTCCAG
Seq C2 exon
GAACTCCTGGTACCATCGATGACAAACGAGTGGCCGACTTGGAGAACGCCATCACTAAAAGCCGCAGACGTGTGGAGGACGAGCTGAGGCCTAAACTTAGGGAACTGGAGGCGAAGGACGCCCAGCAGAGAGCCACCATTACAGGCATGATCAATGACATTGACACCATTCTGGCTGACATCGCCAACCTTGAGGAGATCCATAAAAACATTCCTGAAGGCTGTTTTAACATACCACCTATTGAAAGGCCATAAAGGGTTAAAGCAGGAAAAATGACAATGTTACATAACCTATGAACTTATCAACACCGCTTTTCATCTAAAGAGTGTTTTTCGGCGCTAACGTGTGAGAGAGTTTTTTAGTATTTATTTTTTGTTGAATTTTTAAAAACAAATTATTACTGTGAAGTTTGAAATGAGATGAATTATATTTCTGTTTTGCATTATTACCCAAGATAATTCCGTTTCAGATTAATAGATCAATACCAGAACCACATCTAAAATTCATTTTTATTTACCATTTTCAACGTCTATCAAAAAAAGTTTACAATTGTGAAAGAAATGCACAAACTAACACCCTTCATTATTTTGTGATCCTTTTTGTTTTATTAAATTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000068288:ENSDART00000158276:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.471 A=NA C2=0.607
Domain overlap (PFAM):
C1:
PF041117=APG6=FE(25.0=100),PF082327=Striatin=FE(32.0=100),PF060089=Laminin_I=FE(33.0=100),PF045137=Baculo_PEP_C=FE(26.8=100)
A:
NA
C2:
PF041117=APG6=PD(11.4=17.6),PF082327=Striatin=PD(0.1=0.0),PF060089=Laminin_I=PD(1.0=1.2),PF045137=Baculo_PEP_C=PD(57.7=83.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGAAAACGCAAAGAAAGCCAGG
R:
CCTGCTTTAACCCTTTATGGCCT
Band lengths:
342-1536
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]