BtaINT0103359 @ bosTau6
Intron Retention
Gene
ENSBTAG00000006686 | NPNT
Description
nephronectin [Source:HGNC Symbol;Acc:HGNC:27405]
Coordinates
chr6:20476620-20478726:-
Coord C1 exon
chr6:20478607-20478726
Coord A exon
chr6:20476755-20478606
Coord C2 exon
chr6:20476620-20476754
Length
1852 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
CAATTGGCTTCTGTTTCTAGACA
3' ss Score
6.51
Exon sequences
Seq C1 exon
GTGCCCTGACGTGCTCCATGGCAAACTGTCAGTATGGCTGTGATGTTGTCAAAGGTCAAATTCGGTGCAAGTGCCCCTCTCCTGGGCTCCAGCTGGCTCCTGACGGGAGGACCTGTGTGG
Seq A exon
GTGAGTTGTAAGTCCAAGCATCTCTGTCAGCAGCCTCTTGAGGGTAAGGAAGAAAATGAAATATGATGGAGAGAAAGGAAAAGGGCAGTTAAATAACATCAGGAAATTAGTTGCCCTTGAGAGGCTGTCACATGTCTCACAGGGGGACCCACTCTCTCTGTGAAGACCTTGTGAGGGGCAGGAGGAAGGTGCAGCCAGAGGAAACCGCATGTGCCAAGGCACTGACGTTGAGAGGGAGCGCAGTGTTCAGGGAACAAGAAAAGCTCAGTATTTCTAGGACATAAGGGCAGTGAGCGTTGAAGCTGAGCAGGTAGACAGGGCTAGACTGCATGTCCTGCACTTAAGGATTTGATTTTTTTCTCCTGTAAATTAGGAAGGCAGTAAAGATAAGAGTGTGGGCTTTGATTTCAAAGCTGGCTCTGCCATAGACTTGATATGTAACCTTAGGTAAGAGACTTCCTTTCTTTGAGCTTGAGTCTTCTCATTTTTAAAATGGGAGTAATGCCATATGGAACCCTTGTGAGGATTGAATGAGATCATGGATGCAAAGAGCTTAGCATCTAGTAAGCTAAGCTTGTAGTACCTTACATGGAGTAAGCACTGAGTGAATGGAGGTGTTTGGGGACTTGAGAGATATTTATTGAGTACTTTCTATATTCCAGACACTGTTAAGTGCTAGGATGTAGAGTAATGGACAAAGCAGACCAGATTTTAATCCTTACAAAACTGATATTTTAATGGGAGGGACAGAAAAGAAAGAAATATCCAGTGAAATTACAAACAATATCAACTGTTAATATGAGGTACTAAGAGAGTGAAAAACAGAAAGGATCTGTTTTAGAAAATAATGGTCAAGATAGCCATAAAGTAAGACCTGGACTGCTGGCCATGTGAAGAATCAGCCAAGCAGGTGAACATGTTCTAGAGCACTGCAGTGAAAGAGAGGCTGACTTCTTTGAGGTTTGGAAAGAAAGAAGACCATACCCTTAAGTACACAGTATGAGGGGTGGTGGCTTAAGATACAGCCGGTGAGGGAGGTGAGGACTGTTTATTACAGGGTCACCAAAGACATGGTGAGGAACGAGGAATGGATTCAGAAAGCAAGTAGAAACAGTTGAGAGTTTTGAGCTTGGTAACAATCCCTTCTTAGGTCTCGAGAGTGAAAGTCGCTCAGTCATGTCTGATTCTTTGCGACCTCATGGACTGTAGCCTGCCAGGCTCCTCTGTCCATGGAATTCTTCAGGCAAGAATACTAGAGTGTGTAGACATTCCCTTCTGCAGGAGATCAAACCCAGGTCTCCCTCATTGCAGGCGGATTCTTTACCATCTGAGCTCCCAGGGAAGCCCTCTTATGTCTTAATAAAATCGTTTGTTGGCAATTGAATGGGAATGCTTTGGAGGGGATAAGATTGGCAGAGGACAGGCCAGTTTGGAGGCTCCTATAATAGTCTATCCTGGGAGAGCTTGGACTATAGTCATGGCAGTAGGTGAAGAGCAGAGTAAATGAGTTCACAGAATTTTCCAGAGAAACAAACAGCTGGGATCAATGATGTAGAGATTAAGGGAAATGGGGTTGTCAAGGATGACTCATGTTTCTAGTTCAGGCTAGCAGGGGGATATAGGTGTAGTGCATCCTGTGATGTGGTGCAAGAGGAGGACAGCTTGGGTTGTAAGGATGAATTGAAATTTGGAGATACAGAATTTATGTTGCCTGCCAGGGCCACCAGCCGGATAACATTTATGATGAGCCACTACGTCAGGCAACCGTTTGCAGATAATTGTTTATTTTAAAATCTACTCCACCTGAACATGCTGTTGCTCTTCCTAAAATGCAATTGGCTTCTGTTTCTAG
Seq C2 exon
ACATTGATGAATGTGCTACTGGAAGAGCCTCCTGCCCCAGACACAGGCAGTGTGTGAACACTTTTGGGAGTTACATCTGCAAATGTCATAAAGGCTTCGACCTCATGTACATAGGAGGCAAATACCAATGTCACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000006686:ENSBTAT00000029948:6
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:
PF0764510=EGF_CA=PD(8.9=9.8),PF146701=FXa_inhibition=PD(92.7=92.7),PF0764510=EGF_CA=PU(0.1=0.0)
A:
NA
C2:
PF0764510=EGF_CA=WD(100=95.7),PF0764510=EGF_CA=PU(0.1=0.0)
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:
TGCCCTGACGTGCTCCAT
R:
CGTGACATTGGTATTTGCCTCC
Band lengths:
254-2106
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]