RnoINT0024727 @ rn6
Intron Retention
Gene
ENSRNOG00000013209 | Barhl1
Description
BarH-like homeobox 1 [Source:RGD Symbol;Acc:620648]
Coordinates
chr3:7491234-7493828:-
Coord C1 exon
chr3:7493606-7493828
Coord A exon
chr3:7492177-7493605
Coord C2 exon
chr3:7491234-7492176
Length
1429 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
GTCTTGATTTCGGTTCCTAGGAC
3' ss Score
9.01
Exon sequences
Seq C1 exon
TGAAGGAGGAGGGCGACCGCGAAATCTCCAGCTCTCGGGACAGTCCTCCCGTGCGCCTGAAAAAGCCACGCAAAGCACGCACCGCCTTCACCGACCATCAGCTGGCGCAGCTGGAGCGTAGCTTCGAGCGGCAGAAATACCTGAGTGTGCAAGACCGCATGGAGCTGGCCGCCTCTCTGAACCTCACCGACACGCAGGTCAAGACCTGGTACCAGAACCGCAG
Seq A exon
GTGAGGTTTCGCTTTGGGGCGGGCTCCGAGGAGCCTTGGGTCTCTCCCAATCTGAGAAAGTAGGGACTCTGAGGCTGTGAGAAAAGACTCACTCACTGTGCCGGTAAGTCCCACAGTGAGGGACAGAAAGGACACCAGGCTGGAATCCAGGACAGGTGGACCTACACGGAGGGTTTCAAGCCACGCTCCATCCCAGCCCAAGTCCCCAAGGACAGCCCTAGGCTAGGCTTTGAGGCTTCTGCGCTCTTTGGATTGAAGGCCCGAGCCCTTAGGGGAGAGTGGCGGCCCCAGTCCCCAGAAAGCAGAGAGGTCTCTGAGATGGTCGTAGTAGGAGTCGGTGGTGACTGCTTGTATCTCAGAGCTTGTCTTCCTTGGGCCTCCTAGCATTTACAGCCAAGAAGGGGCTCTCTGCCTCACCCCAGCTCCTCTGGGACAGAGAGACTGGGAAATTGGTATTAAGACACTGGTCTTGAACCTGCTTCTTACTCTCCTTCTTGGACATTCACAGGACTTAAATAGATAGGTATAATATACATACACAGACACGTCAATCAGCATAGTGACACACATTTCCCACATACATAGCAGAGGCAGGAATGACGCCTTCCATAAACAAGCCTCAGAACACACAGCCCCATTAATAATAAATACCGATTACTGCTTCAGGCATCAATAATTAAGGCTCGTTGCAGTAATTACACAATTATGATGATGATGAATTATTCAGGGGGGCGGGGACAGGGTTAGTGTGACTGAGCCCACCTCAACTTCACTGGGACCTAGGCAGGCATCCCCAACCTCACTACAGGTGGGTACTGAGCCTTTGGGTTTGATTTCCTGACGTCTGCCTTGCCCTAGGCCTCTCAACTTCTGCGTCAGAGGGGCTCCTGGCTATCTATCCCACACTCTGGGAGGCCTGAGTGTGGGGTAAGCTGGGAGAAAAAGTGTTCATTCCTTCAGAGAAATCTTTGCTTGCAGTCCCAGCATGCTTGCCTCAATTCCGGGCCTCTGGGACTACACGGGGGTGGGAGGGAGTGTACGGGGTGGGGCAGGACAGAGGCGACCAGTAGGCAGCTCCACCACTTTCATTAGGGGCCTTCCTAGGAGAAGCAAATCCAGAGGAAGCCCCAACATGCGAGTTTGTAAGTGTGCTTGGAACAGGGGTTCTGCTTGCCACTTTGCAGACCTTTGTGAAAACTAGTTCATACCTCAAGCTTTTAATCCGTAAAATGGGGACAAAACTTATGGAAAGCCGGTGGAAGAGGGAATGATGCAGGCGCGTTTGATATGGATACTCCATTATTTATTAACAAGTTAGCATGTCCCCCGTTGGCCATCTTGCGGCTCTCGGTGCCAATCGCTAGGAAGGGGCAAGGGCTGTGAGTGTCCTAGTCCTGATCCCTTCGTCTGTCTTGATTTCGGTTCCTAG
Seq C2 exon
GACTAAATGGAAGCGACAGACCGCTGTGGGGCTGGAGCTGCTAGCGGAGGCAGGCAATTATTCGGCGCTCCAGAGAATGTTCCCGTCGCCTTATTTCTACCCGCAGAGTCTCGTTTCCAACCTGGACCCCGGCGCCGCACTCTATCTGTACCGCGGACCCAGTGCGCCACCACCTGCCCTCCAGAGACCTCTGGTGCCCCGCATCCTCATCCACGGACTCCAGGGCGCCAGCGAGCCGCCCCCACCGCTGCCCCCGCTGCCCGGCGTCCTTCCGCGCGCTGCGCAGCCCCGGTGAAGCGCGCGCTTGCCCCAAGCCATGCTCTGGGACCCACAGCTCAGCCTGGGCGCGGGTCCCTCCCTTCGTCCCGGGGCAGGGCTGCCCGGCTCCCCGCCGCAGCCCAGTGTCCCCGTGGGAAAGAAATTCACTGAGGCTACCCCTCCCCTGCGTCCTCTCTTGGCTGCTCCATCCAGGAACCACTCACACCCGCCGGATGTACATATGCGCCCCTGCCCACCTCTCAGCCACCCCCAGGTCCCTGCCGGCTTCCCCAGGTGTCCCCTGTCCCCTCAGCAGCAGGTAGGGGACGCCGGTCTCCCAGACCTGGGCCCACCCTTCTTGCGCCTCTGCGGGACAGGGTGGGAGCGCTGTACGGAGTTTCCCTCCCATTTCTTTTATTCTCCCTGAGCCCCGGGCTAGCAGCGGAGCTGTACATACAGTGTGCAAAGTGTATATGAAGTTATTTATTCGTGACCCATGAGCCCGTGACCGTGTCCGTGAATCAGTGAGTCTGTGGCCTGTGCCCTCCCCATCCCGGGTGGGGCAGGAAGGGGCCGAGAGGGCTTGCCCACGCGTCCTGGCCCCCAGCCCCGCTCGCTCCACCCAGGTCCCAGGACAGCCAGATCTCTTGGGTTCTCTTTTTTTAAATGTGGAAATAAACTTCTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000013209:ENSRNOT00000017725:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.427 A=NA C2=0.255
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(89.5=68.0)
A:
NA
C2:
PF0004624=Homeobox=PD(8.8=5.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AATCTCCAGCTCTCGGGACAG
R:
TCCGCGGTACAGATAGAGTGC
Band lengths:
358-1787
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]