BtaINT0101763 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021945 | NID2
Description
Bos taurus nidogen 2 (osteonidogen) (NID2), mRNA. [Source:RefSeq mRNA;Acc:NM_001102065]
Coordinates
chr10:44896440-44898434:-
Coord C1 exon
chr10:44898277-44898434
Coord A exon
chr10:44896564-44898276
Coord C2 exon
chr10:44896440-44896563
Length
1713 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATA
5' ss Score
8.55
3' ss Seq
GGACCTTTTTGTTTTAAAAGGAA
3' ss Score
6.2
Exon sequences
Seq C1 exon
CAACCTGTACTGGACAGATTGGAATCGAGAAGCACCTAAGATTGAAATGTCGTCTTTAGATGGAGAAAACAGAAGAATTCTAGTGAATAAAGACATTGGACTACCCAATGGTTTAACCTTTGACCCCTTCTCCAAACTGCTCTGCTGGGCAGATGCAG
Seq A exon
GTAATACTGTTGATGGAGTGCCAATACAGAACACTACAGCGTGCAGTGAGTGTGAGCACTCTGATTTTACAACAAAACCAGATCCCACCCTTCAGAACGTCTGGTTTAAATTTATAACACTACAGCAAATGCTCTACGCCTTTCACAGCAGCCGTCCCCAGCCTTTTTGGCACCAGAGACTGGTTTCGTGGAAGACGGTTTTTCCATGGCCGGGGGAGGACAGGACGTTTTGGGATGATTTGAGCAGGTTATATTTACTGTGCACTTTATTTCTATTATTAATTGTATTAGCCCTGCTTCAGATCATCAGGCATTAGAGCCCAGAAATTTGGGACCCCTGTTTTAAAGGACACTTTGTAACGATTGTTACAGTGAACTTCCTGAGGCCTTATGTGTATAAATGAGGCGGTAAGTTTGGGAGCTAGTTCGATGTCCAACTTATTTTTTTACTGCTTTCCCTCCCCCAACACAAGCACTTGGCACATCTTTTAGGTTAAAAATAAGTATTATACACTGTTGGAATCGACAGGCTTAGATAAATGAACAAAGGTTATTATTTTCTTTTCTCAGTATTACAACATCTATCAGATCAGATCAGTCGCTCAGTCGTGTCTGACTCTTTGCGACCCCATGAATCGCAGCACGCCAGGCCTCCCTGTCTATCACCAACTCCCGGAGTTCACTGTCTATAAATATCTGTTATTCTAACAGTCAGTATGCTGTTATGCTGGGGACATTCTTTGAAAAGCAATGTGGCAGGATGGCTTCCTTTAGTAATAAATTTGGGCTGCCTGTTCCCAGGTTCTCTCTCTCTGTTGTATAATTTCATTACTATTAGTACAACTGAAAAGATAACTTTGTTTCATTAGATACTAAAAAAAAAAAAAAAGCTGTTCTTAAGGAATTTGATTTTAATAAAAGGGACGAAAATGCAGGTGGGTCAATATTACAACCCAGCTGCCCAAAACAACAGTGATATTTTTAATAGGTATTTGAAATTTACTTAAAGGGTTCCATGAGAAAACGGCTTCCCCAGTGGCTCAGCTGGTGAAGAATCTGCCTGCACTGCAGGAGACCTGGGTTGGGAAGATCCCCTGGAGAAGGGAATGGCTACCCACTCCAGTATTCTTGCCTGGAGAACTCCATGGACAGAGGAGCCTGGTGGAATACACAGTCCATGAGGTCACACTTGGAAATTCTTGCCTTGTTTAGCTATTAAAATATTTACATTGAAAAATACAAGTCAGGCTAGTATTTTACTTTTTATTCCTGCATAGAAAATAATATAGTCTAAAAAAAAAGGATTTCAGTTAAAAGGCAGCCTTGGCTATTATCATACATTGCTTACAAAGGGCAGGTATTTATCCAAATATTTTAACAGTTTATGAGCTCACAGGTAGACTTCTTTAACACTGATTTAACTTTTATCTCTACTTCCTCCTCTGGGAGAAACTTAGCCAGGTTTCTGTAAATGCAATCCTGTTTTCCAAAACAGAATTAAGAGTTTAAATTCCAGTAAAAACTAGAATGCTCTTAAACAAACTGAAGACTGGTAATAGAACAGGAAAATTTTACAGTTTTTAATTTGTATTATTGCAATGGTGATAAAACATTCCACCTTTGTTTTCTCTGAGAATAAATTTACTTGCCACTGTTTTTGGTAAAAGAAAAAGAATTTTTTCATCATATAAAAGGACCTTTTTGTTTTAAAAG
Seq C2 exon
GAACTAAAAAACTGGAGTGTATACTACCTGATGGAACTGGACGGCGTGTCATTCAAAACAACCTCAACTACCCCTTCAACATTGTGAGCTACGCAGATCACTTCTACCATACCGACTGGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021945:ENSBTAT00000029257:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.019 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0005812=Ldl_recept_b=WD(100=79.6)
A:
NA
C2:
NO
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:
TGGACAGATTGGAATCGAGAAGC
R:
TCTCCAGTCGGTATGGTAGAAGT
Band lengths:
270-1983
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development