RnoINT0083989 @ rn6
Intron Retention
Gene
ENSRNOG00000000599 | Lama4
Description
laminin subunit alpha 4 [Source:RGD Symbol;Acc:1560062]
Coordinates
chr20:44125231-44127126:+
Coord C1 exon
chr20:44125231-44125305
Coord A exon
chr20:44125306-44126974
Coord C2 exon
chr20:44126975-44127126
Length
1669 bp
Sequences
Splice sites
5' ss Seq
CAGGCAAGG
5' ss Score
3.33
3' ss Seq
CTTTCCTGTTTCATCTCCAGGCT
3' ss Score
11.65
Exon sequences
Seq C1 exon
TGTGCAACTGTGGGGGCGGCCCATGTGACAGCGTAACCGGAGAGTGCTTGGAAGAAGGATTTGAACTCCCTACAG
Seq A exon
GCAAGGACTGCCCAACTCTAAGGAAATGACTTACCATGACTAACCCACTTTCTCTAATATGCTACACGTGTTGTGAACCATTTGTAGTTTAAAAGAAAATCAAAAATGTGGAAGAAAAGAACTGATTACCACAAGAAATCCTCTGACCTCCACATGCACACTGTGGCACAAGCGTGCGTACATGTGTGCACACGCGCGCGCGCGCGCACACACACACACACACACACACACACACATTTTAAAACTGTAAAGATGGATGTGATATCACTTTCCCTGAAACCTCTGGTTTAGCCCCTGGTATTTGCCCCAGGATACTGGACCCTGTACAAAGGTCCCTGGTGTTCTCGATCTCATTCAGCAGTGAGACAGCTCTTGCTGACATCACTCCCAGACGTTAGACATCTTACTTCTCTAGTCCTCATGCTCAGCTTCTTGCTCTCAGGACAGAGCCCTGTCTGCATTGGCTGACTGGTGCTTCCCGGCAGCTGTAGAAACGGAAAGACGAGGAAACTTAAACAGTTCTTCCCGACTCACCCAAATTGAGGCCTGACTACATTTATAAACTGACAAGGACTTACCAAGTGAGAGCTGCCTTCTCTTTTGCCTAAATTGCCCTGTCACTCACGAGCAAGGAAGCTTTTTTCTCAGAGTACTTGAATTATAGAGAAATTATCAAACTGCAGTTTACCACATCCTAGAAGATGCCCGAGATGTGATACACGGCAGGGCGAAGTCTGCACTTATCTAAGCTGCCTTCATCCCTTGACCAGCATCACTGAAAGGAGCCAGATGCCTATATAGTCCTAACCATTTCCTTCAGCAGCCGGAAGTGTCGTCTGGGGATTCAGTCTAAGGGCACTTATAGGTAGCACTAAGTTAATAACAAATTAACAAATTAGCATGCATTAAGCCTTTCGTGTCCATCAGCTCTGCAGAAAACAGCAGAGCCCGTGGGAAGAATCTTGGGAACCCCCAAGGTGCAAAGAGGTCAAGACAGGGTTCGAGGCTTGGTGTGTGTTCTTTTTGATTGTGTCCGCGGAGGGCAGCTGGGTCCTGGGTGGGGCTCACAGTGTGAAAGGTGAGGAGTGAGGAGAAATTGGGGCTTGTCTCTTGAGCATGCCCAGGTTTAGTCTCAGCCTGGCACCTATCTCAGAGACCAAGACATGACGTTAGCCAACAATTGTACCCTACAGACCTGCTCTGAGGATTCGTTCATCCAGAGGAGCCAGGCCCTCCCTGGGGGACACATAGGCAGGTTTGGCATTCTCTGAGTGACTGAGAAAAACTGATGAGAAAAGAATGATATTTGGCCACCAGCCTGCTCTACCAGCTGCCACCAAGTAAACACCGGAAGCTGACATGAATGAATGGGGGGGGGGGGCTAGTAGGAAAAGTGGGAAGGGCTTCTTTTCTACCCATCCCACGATAGTCCTTTCTGTCAGCAATTAGTGTTTGTATTAACCTGCTGTCCCAGCCTGTCATTATGTTTTATGTGGGACTCCTGCCCGATGTGTGACTTGGTTTGGTAAACACTGGTTCTACATGGCCATATCAACTCCTTGGGAAACAAAACTAGACATGGTCTTAGCCAATGGCGTCCACATTAAAGTCACGTGCTTCCAGGCTGACTTTTGGCTCTGCAGAAATGACTTTCCTGTTTCATCTCCAG
Seq C2 exon
GCTGTGATAAGTGTGTCTGGGACTTGACCGACGACCTGCGATTAGCAGCGCTCTCCATCGAAGAGAGCAAATCCGGGCTGCTGAGCGTGTCCTCCGGCGCTGCGGCCCATAGACACGTGACCGACATGAACTCTACCATCCACCTCCTCAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000599:ENSRNOT00000000737:6
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=PD(1.8=3.8)
A:
NA
C2:
PF134761=AAA_23=PU(14.4=58.8),PF060089=Laminin_I=PU(12.7=56.9)
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:
CATGTGACAGCGTAACCGGAG
R:
TTTGAGGAGGTGGATGGTAGAGT
Band lengths:
206-1875
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]