DreINT0153744 @ danRer10
Intron Retention
Gene
ENSDARG00000044433 | sned1
Description
sushi, nidogen and EGF-like domains 1 [Source:ZFIN;Acc:ZDB-GENE-100913-1]
Coordinates
chr6:27472430-27477120:+
Coord C1 exon
chr6:27472430-27472537
Coord A exon
chr6:27472538-27477027
Coord C2 exon
chr6:27477028-27477120
Length
4490 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
TGCTTTTAAATCCCTTACAGAGG
3' ss Score
7.59
Exon sequences
Seq C1 exon
AATCCTGTGTTGGAGAGATTTGTAATAAACATCAAATCTGCGAGTACACTAACTCTGGAAATTACAGCTGCACCTGCATGCCCGGATACTACGGTGACAACTGTGAAG
Seq A exon
GTAAGCAGTCTCAAGTTTTATTGCACAGTAGTTGCTTTCCTCAAGTAACTGGGCAGGAGCATGGCACGGAAAAGAACAAGACAGACATCACAATCCCACAGGAATTTGAAGCACTGCCTGAGGAAGACTATGTAGCTGTGATGGATGAGCATAATTATCCAAACCTACAAAACCTCACCAGGTTTACTGCTCAGCCCTTGCAGCAAGTCGCTTGATGTTGTAAATAATTGCTTTATGGCACTTTTTACTACTTTACCAACAAGAGGAAGGACTCTTGTCTAGACTTTAAAGGGCCTCTGTTTTATGAGACAGTGCTAATGCTTGGAATTCACTTCCCTGCAACACAGCCAATGAAACCTGTTTGAATGCTCTGACATTCAACTACAAATCTCAAAAGTTTTGGGTTATGAAGATGATATGAGATGCAACATCCTCATTTCCTGCTTTATCTCCTGGTTTGAGTCTGATTTGAGCCCAATTTGCAAATTAAGAAGTTCGCTGACAGATCAGGATATGATTTAAGGATAATCAGCAGGTGATTGGCGCTTTGCAATCTTTGTGTAAAATACTTAACGACACATCAGAGAGGTTCGCTGACACATCACTGACACCTCGCAAATATCTAGCATGCCATATATCTGGACTGGTTGGCCTAAACATCACTTGATATCAGTTGTAGTGATGAGCTACAGCCAGTGGGACAGCAAGTCAACCCATGATGATTGATTCATGTTCTCCACAGAGCACTTACATGTACACTGGAGTGTTTGAAAGCCAGATATATGAGTGATCTGCAGATAGATCAACTGATAGACACATGCACTGCAGTGTACGCATTCAGAGCTATAACCAACTATTGCAGAGCGTGTCTGTAATGTAGGTCATTATTTAGAAGCCAGTTGCTCTTTCTCATAGTTCCGCCATGAACATTTACTGTCAAAAGCTGTAAAGTGGAATATCAAAAAATGTGTCTATCATAAGCTAACACCGTTTAAAAATAAATAAATAAATAAATTTATTAAACACTATACAGTCAGGTCCATAAATATTTGGACATTGACACAATTCTGACAGTTTTGGCTCTATACACCAACACAATGGATTTGAAATAAAACAAACAAGATGTGCTTTAACTGCAGGCTGTCAGCTTTAATTTGACAGTATTTACATACAAATCAGGTGAGCGGTGTAAGAATTGCCTCTTTATGTTAAGGGACTAAAAGTAATTGGACAACTGGCTTCTCAGCTGTTCCATGGCCAGATGTGTGTTATTCCTTCGTTATCCCAATTACAGTGAGCAGATAAAAGGTCCAGAGTTCGATTCAAGTGTGCTATTTGAATTTGGAATCTGTTGCTGACAACTCTCGAGATGAGATCCAAAGAGCTGTCACTATCAGTCAAGCAAGCCATCATTAGGTTGAAAAAACAAAACAAACCCATCAGAAATATCAAAAACATTAGGCTTGGCCAAAACAGCTAAAAGCTAAGAGCTCAGCAACACTAAAAGACCCGGAAGTTTCTGTGGTGGAAAACTGAATAATTATTTCCTAGTGAAAAAAAACCTTCAAAGGAGTTGGCCAGATCAAGAACTCTCTCCAGGAGGTAGGTGTACTGTATGTGTGTTCACCAGAGTGAATACAGAGGGTTCACCACAAGATGTAAACCATTGGTGAGCCTCAAAACAGTAAGGCCAGATTAAAGTTCTAAAAAAGCCTTTGCAGTTCTGGAACAACATTCTATGAACAAATATGACCAAGGTCAACTTTTTTCCAGAGTGATGGGAAGAGAAGAGTATGGAGAAGGAAAAGAACCGCTTATGATCCTAAGCAGTGAAGCATGGTGGTGGTAGTGTCATGGCGTAGGCATGCATGGCTACCATTGGAACTGGATTTCTTGTATTTATTGATGTGTTTGCAGTAGGATGCATTCTAAAGTGTTTCGGGCAATATTATCTGCTCATATTCAGCCAAATGCTTCAGAACTCATTGGATGGCACTTCACAGAGCAGATGGACAGTGACCAAAAGCATACTGCAAAAGCAACCAAGGAGTTTTTGAAGCGAAAGAACTGGAACCTTATGCAATGGTCAATCCCCTGACCTGAATTTGATTGAGCATATATTTCAGCTACTGAAGACAAAACTGAAGGGAAAATGACCCAATAACAAGCAGGAACTGAAGACAGTTGCTGTTGGGGCCTGGCAAAGCACCACCAGAAATTAAACCCAGCAGCTGATGGTGTCTATGTGTTCCAGACTTCACGCTGTAATTGACTGCAAAGGATTTGCAACCAAGTATTAAAAAGTGAAAGTTTCATTTATGATTTTTATTCTGTCCCATTATTTTGGTCCCTTCACAAGTGGGAGGCACATATGTAATGCCTACACCGTTCACCTGATTTATATGTAAACAGTCTCAAATTAAAGCTGACAGCTTGCAGTTTAAGCACATCTTGTTTGTTTTGTTGTGTATAGAGCCAAAAATGTTAGCAATGGGTCAATGTTCCAATATTTATGAACCTGACTGTGAACATGAGCCCAAACATGTTTTACTTTAGGTTTTCAGAACAATGAGAGATCATCTAGTGTGACCCCTGTTGTGGATCATTTACATGCAGTGGCAGTGCTAGGGTTGAGACTCATCCTGTAAGGATTTCCTAATGATTTGTTTTATTGAAAATTTTCTAAATTTTCCCACTTTACTTTATTGAAAAATAAACATTAACAACCTAACCAAAGTGCATAATAAACAACTAGCATTAGTTATCAATAGCTATCATGGAGTGCTATTAACAACAAATAAAATACCCTAAATTTTTCACTCTGCAGAGAAGCTCAGTAATAACATGGCAATCTCTATCCGAACTTCAGATTGGAGATAACTGCATCACACAGTAGCAACGGTCACCTGTTACTAGCACGACTGTTAAATGGAGACTGGCTTGTTGACTTCTCATTGTGCTAGAATTTCCAGGGGGCTGCTGGGTGTCGAAGCCGAGGGGTTAACAAACAACGGCAGTCACTTTTTCTTATGAAAAAATAATGTTTGCTGATAAATACTTTTGAACTCATTTGAATCTTAACTGCCGCTATTCAATAACAATAGATGAATTGCCGCAAATGTAGACATAATATGGTTTTGCCAGCCTGATCTCATGAGAAAACATAACTATTTTACTTTTTTTCCCCCTCAGTTTAGTGGCTAATTTGTACGAATTTGTATGAGTATTATTTGTATTTGTATTATGAATTGTCAAGATTTTATGTACTGTAAATAAAAGAAATGAGTAAATATAGACTAGTTGTGTTACCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATATATATATATATATATATATATATATATATATATATATATATACATTTAACAGAATAAAATAAAAAAGACAATTAATTAAAAGTTATTTGTAAATGTCTTTTTTGGTTGTTGGCATTAGACATTTTATTACAAACAGTGACACATAAGAGATTTGATACACCTAGAAAAAAGTAAAATATTCCCACTTTAAGCATTTCAATTATAAAAAATCTGTGTAATTTAGATTTTTAGCACCCCGTCTAGTGTTAAGCCCCACATTAGCATCCCAACAACAAATAATCCTGGAGTCACCACTGTCATTTAAGAATGAACACAACCAACCCTGCCGATACTTAAAACAGTGTAGTGTGAATTTGGCATAAATATCCATATATTTAACTATACATTTTGAGCTACAGCAAATCCATCCTACTATTCCCCCTGGAGCTGAAATAACAATCGACGCTTATATAGACTCTCTTAAATCTCCAAAATACCTTCCTGCCTGGCTCACTTGGAATGTGCAGCGGAAAAAGTAATGCAGTCCTTTCAAAAAGAGAAGGTAGAAGCTCACAGGCAGAACCCAGGAGTGTCTAATAGGGCACAGAGATCAAAGACACCGACCTGAAATCACAGCAAAACCTGAAATCCCCTGAAATTCAGCAAATTAAAAACCTATTAATTTCCCCTAAGGTCATACAGTTTGAATTTAAAAATGTTAACAGATAAATAACACCCTCATGACCCTGGACTAAAAGGAAGTATTCTTTTAAAAGAGATATAGTAACTTGTTTGACCCACAATTATTACAGGAAGAGGAAAATAAAAGTGTTTTGGTACAGAAAAGCTGAATACTGACTTAAGAGTCATTCGGCACACCATGAACTGTGTGGGAAATGTTGTGGGAAAGACTGACCCAAGAAATAGGTTTATAATGGACAACAGTACAATGAACACCACCACAGCACACTAGGCTAAACTAAAGAAACCCACAATTTTCCCACACATGAATTTACACTTTGTGCCAATTTGAATGATGTGAAGAAAGAGCCACATATTTTAGATTGGTTGGTGTTTACTTATTCAGAAAATTTAAAACTATGCTGATCTCCTGCCAAAGGCTTCTCTTCATCTGTCTCCTTCTCTTTGCTTTTAAATCCCTTACAG
Seq C2 exon
AGGAGTGCCCCTGTCAGAATGGAGGTATTTGTGTTGATGTGAATGGCACTTGTGACTGTCCTACAGGCTTCACTGGACTCTACTGTCAGTTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000044433:ENSDART00000065255:10
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:
PF129472=EGF_3=WD(100=78.4),PF0000822=EGF=PU(6.7=5.4)
A:
NA
C2:
PF0000822=EGF=PD(90.0=84.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]