BtaINT0070465 @ bosTau6
Intron Retention
Gene
ENSBTAG00000001740 | HAPLN3
Description
Bos taurus hyaluronan and proteoglycan link protein 3 (HAPLN3), mRNA. [Source:RefSeq mRNA;Acc:NM_001098981]
Coordinates
chr21:20876543-20880779:-
Coord C1 exon
chr21:20880599-20880779
Coord A exon
chr21:20876912-20880598
Coord C2 exon
chr21:20876543-20876911
Length
3687 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGT
5' ss Score
8.23
3' ss Seq
CACCCCGCCTCTCCCCTCAGGCA
3' ss Score
11.01
Exon sequences
Seq C1 exon
TTTGCCCCGGGCCCCAGCCTTGTCTGGACACCCTGGCGCTGCCCGGTGTGTGACGCCATGGGCCTGCGGCTCCCGATCCTGCTGCTCCTGCTGTGTTGTGTCTCCGGCCTGCCTTTCTACAATGGCTTCTACTACTCCAACCGTCCCAACGGCCGGAACCTGGGCAACAGCTACAGTGAAG
Seq A exon
GTGGGTGGCCTCTTGGCTCTGCTCTTAACTCGGCTCTTGGTTCGGCTAGGTGACGAAGGCCTCTCCTGGACCCTGCAAGTTCCGAGTTGGGTGGGGGCTCAGGGTGTGAAGCCAGCAGCCCTGCTCCCATCTGGGCCAGTGCAGTGGTCCAGCCTTCTCGCTAAGATGAGCAGAAGGGTGGTTCTGTTACTCCATGTCTACTGGCCCCTCAGATATGGAGGGCTTCCTTGCTGGCTCAGTCAGTAAAGAATCTGCCCGCAATGCGGGAGACCCGGGTTTGATCCCTGGGTTGGGAAGATCCCCTGGAGGAGGAAATGGCAACCCACTCCAGCATTCCAGCCTGGAGAATCCCACGGAAAGAGGAGCCTGGTAGGCTACAGCCCATGGGGTTGCAAGAGTCAGACATGACTGAGCAACTAAACCAACAGCCCATGGGTGTGGAGCTGAATGCACTGTAGCACAGTCAATTTTGCTTTTTATACTTTCCCCAAAGTCCTGCCAGTTTTGCAAAATTCCACTTAAATGTGACTTCCCCAGGTCTTCCCAGTGGAAAAGGGGTTTGGAGTTAGGGAGATGTGTTTGACTCTCCATTTTGCCACTTACTAGCTATGCAGCTTTGGGCAGGTGACTTTTTTTTTTTTTAATTTTATTTTATTTTTAAACTTTACAATATTGTATTGGTTTTGCCAAACATCGAAATGAATCTGCCACAGGTATACATGTGTTCCCCATCCTGAACCCTCCTCCCTCCTCCCTCCCCAAGGTGACTTTTTAAAAAACTTTCATTTGCGTTTATTTTTTTTTGCGGCATTTCTTCCCCGGGGCGTAAGTTTCTTTTTAAATATTTATTTATTTATTTGGCTGTGCTGGGTCTTAGTTGTGACACTTTGGGATCTTTAGTTAAGGTATGTGGGATCTAGTTCCCTGACCAGGGATGGAACCCAGGCCCCCTGCATTGGGAGTGTGAAGTCTTAGCCACGGACCACCAGGGAAGTCCCAGGGCCATAAATTATTGTTTTTTTTGCTTTGGGGATATCTTTTTCTTCTGTGCAGCCTTCTCTTCTGGTTTAGGAATAATCTGACCTTTTTCAGTAAGGATCATCTACATGTGTCAGGGGAGCTTAGGTATGGGTTGATCCAACCCTGAGCTCTGTAAGTCCTGTCCCTCATCTTTAGAGGCTTTGTTCACCTGGACGTGCTTGATGACCGGAAAATCTCCATCTAAGCTCTGAAGTCTGGAATCACTCTGCATTTCTGAGCATGTGCAATAAAAACTCAGCACTCTTCTTGGGCCACTGACCCTGCATCCAGTCCCACTGTTTGGCCTGGGAACACCTATCAACACCATTGTAATGACGGAATGGCTCACGATATGTTTAAAGTGACATCTTTCAGATACTTGGTGGCTTTCCCGATATGCGTACCCTTCATGGCCTGGGTGGTTTCATGAGTGTTCTTAAAAGAAAGTGAAAGTCACTTAGTTGTGTCCGACCAACTTTTGTGACCCCATGGACTATACAGTCCATGGAATTCTCCAGGCCAGAATACTGCAGTGGGTAGCCTTTCCCTTCTCCAGGGGTTCTTCCCAACTCAGGGATCGAACCCAGGTCTCCCGCGTGTGGGCGGATTCTTTACCAGCTGAGCCACAAGGGAAGCCCAAGAATACTGGAGTGGGTAGCCTATCCCTTCTCCAGGGGATCTTCCCAACCCAGGAATCGAACTGGGGTCTCCTGCATTGCAGGCAGATTCTTTACCAGCTGAGCCACCAGGGAAGCAGTGTTCTTAAAGTGAACATGAAAATTTGAACCTCTTGATTTTGTGCAGTTTTCTGGGTCAAGTGAATAGCAAACCATTTTTAGAGGTCACTTCAGGCCAGTTACTGGAAAAGCCAGGTGACTTTTTATCAGCAGCTTTATGCACCTACTCTGCATCATTTGTTAGGTCATATGACCCTCATAGAAACTTGGACACAGGCAAGTCGTTAGGTATGGCTGTTTTTCAGCATGAGATTCTCTGCAAGGAGCCTCCCTGTCTATCCCTTGCTTACTCCTGAGGTTACCCCTTCCCCTTCTCTATGTACCTCTAAGGTCTCAAGTCTAGACCTAAGGCCATGAGACCATGAGGCCCCAATAGGAAGACTCAAGTGAGAGATGGGCCAGCCTTAGCCCAAAAATCTGGTTCTTATGGAGCATGTTAGGCTCGGAGTTTATTTGTCCCCCTGAGCCTGACTGCAGTCTCCTCTCTAAGCCCTGGCCTCATCTCACCTGTGTCTCTAGGTGTTTGGGAAGAGTCGTGGTGGATGGCTGGACAGAGTGAAGGGCAGGCTGTGGTCTCTTGGGACCAGTGTGTTAGAGAAGGAGACTCAGATGATCTGAGTCCCCCCACACTCCCATCTGAGGTGCTCTTGCTACCAGCTACACCAATTTGCCTTTTGCTTTTCTTTTTTTTTTAGCTAAACCATGTGGCATCTTAGTTCCCCGACCATGGATCAAACCCACCTCCCCCCACTGCCACCGCAGTGAAAGGCTGGATTCTTTCTTCCCCCCATTAAAAAATTTTAAATATATTTAAAAAGTGAACAGGACAGGGAAGTCTGGTGTGCTGCTTTCATGGGGTCATGAAGAGCTGGACATGACTGAGCGACTCAATAACAACAAAACATTTTTACAGTGTTATATTGCTGCTACTGCTGCTGCTGCTAAGTCACTTCAGTCGTGTCCGACTCTGTGCGACCCCAGAGACGGAAGCCCACCAGGCTCTCCGGTCCCTGGGATTCTCCAGGCAAGAACACTGGAGTGGGTTGCCATTTCCTTCTCCAATGCATGAAAGTGAAAAGTGAAAGTGAAGTCACTCAGTCCCATGGACTGCAGCCCACCAGGCTCCTCCGTCCATGGGATTTTCCAGGCAAGAGTGCTGGAGTGGGGTGCCATTGCCTTCTCCATGGTTTCTGCTATACAACACAAATCAGCCATAATTATACACACCCCTTCTGTCTCTAGCCTCCCTCCCCTCTCTGCATCCCATCCCTCCAGGTTCTCACAGAGCACCAGAGATAGCCTCCCTGTGCTACATAGCAACTTCTCATCTGCCATCCATGGACCATCAGTGAAGTCCACCAGTTCTCATCTTCTGCCCAACAAGCCTAGTGGTTTAAGACAACAGCCGTGTACTTTGCTCATGGTTTCATGGGCCAGCGTTTTGGGCTGGGCTCTGTCTCTTCTGTCTTGGCTGTGCTCCCTTGATTGTGCCTGCGGTGGGCGGGCAGGTCAGCTGGAGGCTGGTGGGTCTAGGATGGCCTCAGCTGGAGGGCTTGTCTCTGCTCTCTGCGTGTTCTCACCCCGCAGGGGCGCCCAGGCCTTGTTCTGATGGTGGTTGGCAAGGTTCCCAGAGAGAGAGGCCTCAGCAGGACCCCCTGGAGCCTTGGCTCTGAACAAACACCTCAGAACACTCACTTCCTCTGCATTCATTTGGTCAAAGCAAGTGGCAGGGCCAGCGAGGATTTCAGGGACTGGGGGTGGTTCATAGGTCACCTCCTGAAGGAAGGAGTTGTGAAGTCACATTGCAGAGTGTGTGGGTACAGGGGCGGTGCAATCTAGGACTGGGGGTGAGGGTGAGGGAGGGGTGGCCCCTGCAGGACTATCGACATGCTGCCAGAGGTCCCCATCTGCACCCCGCCTCTCCCCTCAG
Seq C2 exon
GCATCTTCAATGGAGTGAAGCTAGTGGTAGAGACGCCCGAGGAGACCCTGTTCTCCCACCGAGGGGCCAACGTGACCCTGCCCTGCCGCTACCACTACGAGCCAGCCCTGGCCTCTCCGCGGCCCGTGCGCATCAAATGGTGGAAGCTGTCGGAGAACGGGGTCCCGGAGCAGGACGTGCTGGTGGCCATTGGGCTGAGGCAGCGCACCTTTGGGGATTACCGAGGCCGGGTGCGCCTGCGGCAGGACAGAGCGCGGGAAGTGTCGCTGGAGATCCGGGACCTGCGGCTGGAGGACTACGGGCGCTACCGCTGCGAGGTCATCGATGGGCTGGAGGATGAGAGCGGCCTCGTGGAGCTGGAGCTTCGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000001740:ENSBTAT00000002282:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0768612=V-set=WD(100=91.9),PF0019312=Xlink=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
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]