DreINT0091314 @ danRer10
Intron Retention
Gene
ENSDARG00000045483 | lrtm2a
Description
leucine-rich repeats and transmembrane domains 2a [Source:ZFIN;Acc:ZDB-GENE-041210-218]
Coordinates
chr4:20542122-20544751:+
Coord C1 exon
chr4:20542122-20542718
Coord A exon
chr4:20542719-20544293
Coord C2 exon
chr4:20544294-20544751
Length
1575 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGA
5' ss Score
7.66
3' ss Seq
TCTGTTGCTTTCTGTTGTAGGCG
3' ss Score
11.16
Exon sequences
Seq C1 exon
GTTTTCTAGGTGTGCTGAGTGTGTGTGCTACGTTGCTGCAGTTATGCGCTGGCTGTCCTTCAGAATGTGTGTGCAACTCACTGGAAGCTAACTGCAGTGGGAGGAGTCTAGTATCTGTGCCCGCACTCACTTCTCTCCCGGAGGGCACACATACCCTCCTTCTGGCCAATAACCGCCTCTCCTCCCTGCCCCTCTCTGCTTTTGCCAACCTGAGCACCCTGGAGACACTCGACCTGTCCAACAACTACCTGGACAACCTTCCTTCCAGACTGTTCCGTGAGCTGAGTAACCTGAGCGAATTGAGTTTGCGTAATAACAGCCTGACGGTTTTGGATCGCGAGTTGTTTCGCGGCCTGACCCATCTGCGGAAGCTGGATCTGTCTCTGAACGGGTTGGCCGCTGTGCCACTGGGCCTTCTAGATGAGCTGCAACAGCTAACCTGGCTCTCCTTGGCTGGGAACAGACTTCACGCCCTGGAGAGAGCCACGTTCGAGCCTCTTGTCAACCTTCAGCACCTGGAGCTGGGCATGAACCCCTGGGAGTGTGACTGCAACCTGAGAGACTTCAAACACTGGATGGAGTGGCTAATATACAGAG
Seq A exon
GTGAGAGCTTCGTGTGTGTGGTGTTTTTACTTGCTGCAGGTGTACAAACATCATTTAAGCAATAAACCACAAGAGGCTATGAATTTCCTGGATTTTACCAAGGTATTCTTTGGAATAGTCCACGGTGAATTGCCTTCTCTTAACTGTCACTGTCCTTCAGCAGGTGGGACATTTTTGGGGACATTTTGTCTAAAACTGAACTTATCTTGACAAACTAGATCATATAAATATATATTATAATTTTCTAGTGTGAACTCATAAAGAGGCAGCAACAACAGTATAATAATAGACAGCAGTGTTCAATAAATAATTAACCTATTAATATTTAAAATCAAATGAACTATTTTCCTCACAAGTTATAGTATTCAACATAGCAACTTACTGTACTGCATTAAAATTGTATGTGCAATCATGTGAAGTGTATGCTTATTGGCATTTTAAAAGGGCTTTGACTGCAGTTCAACCAACGATAATTTAAAAAGTGATCTGTTTTAGAAGAGGTTTATTAAGCCTCTTAACAGATGGAGCTGTAACCTAATGTAAGTGCATAACACTCCAGACATATTATACCCACACTCTACCTATTAATTTTCCATCCATCTTTTGTCTACTATTGGCAATGAAATGTGGCAAAACCCCAGAAATCATTGTGAAAAAGAACTGAGAATCCTCTGCTTTTTATTCTCCATACCTCTCGCTTTCTGTTTTTCTCGGTCTGTCTCAATCCTTCTACTCTGAGTCAGAGAAACTCATTTCGTTCTATTTCAGAGCAGCTTTAAGAGGGAGGGGGATTTGAAACAGACATGAGAGGCTGAGTCACAAAGCTTTTAGTGTGTGTGAGAAAGAGACTCCAGTCTTGGTGGGCTCTGACTCTCTTGTGCTGCTCCAAAACCTAGTGAGCTGCATATGGAGGCAAGATTTTAAGGCATCATAGATGCTCTCTTGACATGTAGGTAGGCTTCTTACTTGTGCTGCCTTCTAAGATACTTTTTCGAATAATTTATAACATTTATTTCCATCTAAACTCACAATCAATTTTATTAATAGGATGGTGCAGTTAATTTTATTCAGTACTGAAAGTCTTAAAATATAAATTACGTTACTTGGAATTTGTGTGTTTTGTACAGTATATGTAGTGGATTACTGCAGCATTAGCAAGGTGCCACTGTCAAACAATATTAAAATCAAGTGTGTTTTTGCTGCTCTGTGTGGAAGACTTTGATTGACGTGGAGTTTCTGCCCACATAGAGCACTCCAAATTATTCACTTAAGAGGTTCCATGACAGTTAGCATGACATTCGAAGGCAGCTGTGAGCAGGAGGCAGCATGGCAGCTCACTGGGTTTTGGAACAGAGCTTCTGTATGCATGTCAGGCTTATTAATTATACACCAGCTACTGCTCTTCCTCTCATACAAACACACACACACAAATTGAAGAGTGCTGCTGACCCTCTACGCTGTGCAGTGCTATTTTGGAGGGCTTGAAGCAGCCATTTAAATTAATTAGAGGTGACTATTGTTTACCTCAGAGAGCTAAACTTTTGATTTGTCTTGTTCTGTTGCTTTCTGTTGTAG
Seq C2 exon
GCGGTTATGTCGATGCTGTTGAGTGTACACTTCCGAAGGACTTAAGGGGCCGTGACATCAGGGGCGTTCCTGTGGAGATGTTCAACTACTGTCTGCAATTGGAGGATGAAAATGGGGGCGGGACTGGGAGCACAAAAGGTGGATCGCCACCATGTTTTCGAGGGACAGCCGCTCCGTCATCTGACAGTGCTGTAGTACGTACAGAGGCAGAGCTACCAGACTGTGTGAAGCAGCGCTATCGGCCGGTCAGTGTTCGCAGGGCGATCGGTACAGTAGTGATCGCTGGTGTGGTTTGTGGAATTGTTTGTATAATGATGGTAGCTGCCGCAGCGTATGGCTGTATTTATGCCTCTCTGATGGCAAAATACCAGCGAGAGCTAAAGAAGAGGCAGCCTTTGATGGGTGACGCAGAGGCCGAAACCGACCCAGAGGAAAAACAGATCTCATCAGTTGCATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000045483:ENSDART00000138820:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.237
Domain overlap (PFAM):
C1:
PF0146213=LRRNT=WD(100=13.6),PF127992=LRR_4=WD(100=22.1),PF138551=LRR_8=WD(100=30.7)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACGTTCGAGCCTCTTGTCAAC
R:
ATAGCGCTGCTTCACACAGTC
Band lengths:
351-1926
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]