BtaINT0101760 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021945 | NID2
Description
Bos taurus nidogen 2 (osteonidogen) (NID2), mRNA. [Source:RefSeq mRNA;Acc:NM_001102065]
Coordinates
chr10:44899668-44901812:-
Coord C1 exon
chr10:44901643-44901812
Coord A exon
chr10:44899798-44901642
Coord C2 exon
chr10:44899668-44899797
Length
1845 bp
Sequences
Splice sites
5' ss Seq
CATGTAAAG
5' ss Score
1
3' ss Seq
TCTGTGTTTTGGTCACACAGGGC
3' ss Score
7.91
Exon sequences
Seq C1 exon
GTATACCCACCGTGGCTCCACCCACGGTCCGGCCCACACCCCGGCCCGACGTGACCCCTCCACCAGTGGGCACCTTCCTGCTCTATGCCCAGGGCCAGCAGATTGGCCACTTGCCCCTCAATGGTACCAGGCTTCAGAAGGACATGGCCAAGACCCTGCTGTCGCTGCAT
Seq A exon
GTAAAGTGGACTTCTCCCCTGGGGGTGGGACTGTATTGGATTATCAGATCTGGGCAAGGTCTGAGGTGCGGGGGTGCTCCTCGAGGGCTTCTGTTTGGCAGTTGTCTTTGGGAACCTTACGCACAGAAGGGAGGGTGCTGTTGCTGGGAGCCACATTGGACTGATCAAGGCCACTTTCTCCAGTTGGTGTGTGGGGTTTCAGCTATGTGGAAAGTGAATTTCAGAGTTGTCAGGATACTGAGGCAGCGTTGGAGATCCACGGGAAAATGATAGGTTAACCCCAGCCCCCAGCGTTCTCTTTAAGCCATAGACATCTCTGCAGATTCTGGAAGTCAACTAGTGATAGCCTTGTTGCGGACCCCTGCCCTCCTCTTTGGTCCTGTTGATCAGCTGCTTATCTTCTCTGAATCTGTCATAGATGAAAATATGGGGAGCACGTGATCCTGGAGAGGAGGAGACAGGGCTTTCCCCAAGGGATGCTAGCTGCTTCCCGAGCTGACAGCTTCCCTATGGTCAACACACTCCATTTTGGAGCAGGGATTTCTTCACTAAGATGGGAGGAAAGAGAAGGGAGTTCAGCAGAAAGGCACTGACACTTATAATGGGTTCCCCTCCCCACTTTAAAGATTTGAATTGTGTGTTATTCCAGACACTAGCTGCTGATTTTTAGTTTCTCTACAAGATTTAAGTGGGACTTTTTCCTCCAAGAAATCTTGAAATCATTAATGGGCTTATGAATCCCATGATCCCCTGGGTTAATGGAGGCCTGTATAGATGTGCCCCCTTGCTCAAAATAGGTAACTTTCAATTTTCAAGTAAAATTGAAAATTAAAATCCTCCTATATAAAACTGCCCACTTTCCCACAGTAGCCTAATGCTGCTTTTCTTGTCCTGACTCCTCTCCCAGTCAGGCCACCCCCAGGAGGCTTTGTTAGGCAAGCAGGGAGCTTGCGAGACCTCAGGGACAGCCTCGGTGTTGGCTTTGCACATCTGCTGGGCTTCTCAGAGCAGGAGTCTGGGCTGGAAATTCAGTGAAGCAACTTCTGTGCAGAATTTTGGAAAGGAATATCACCGACTCAGCACTTAAAAAAGGATTTTGTCATTTATTTAGCAATAGGGAAGGAGGGGAGAGCTCCCAAGACAGAAGTCAGGTGGCCACCATTCCCCAGTTCCTTCAAGTTGTAATAGACTTTCTTTTACACTAGAGTACAGCCCAAGGACTGCTTTGTAGTAAGACGCAGAGGCGAGGGTTAAGGGTGTCTGCACTTCAAATAGCAGAAAGATCTCACTGACAGGGCAGGGGAGGATTGATTTCATTATATGTTGGCAAATTTTAGAGAGGCTTTTTCAAAAAGTGCTGGATTACATTTGGCAGTCAGTTTTTGTCCAGTGAAACATTACTTACTTTGCTGAGACTAGTATTTGTCCTCTAATCACTGAATGGGCTGATCTTTTCATGAAATCACTCTTGCTTTTACCACCACCAATAATAATGCTTATTGAAGGCTTACAATGTACTCATCACTGGTTGGGATACTTTGTAAGCTTTTATGGTATTAATGTTGATAGCAGCTGTGTGAAGTAGGTTCTGTTAACCTCTGTATGCCTTTGTCACCTTATCTGCAAAATGAAGGTAGTGCCGAAGGAAGTGGCCAAGCCTGGCGCTGGCTCAGGGAAGCCAGCCTCCATCGCCTATACTTCTGCCCACTGTGCCCCGCTGTCCGTAAAACCGTACAGTGCAGCTGGTCAATGCTGCCATGAACAAACGAGTGAGGTGGCTGAGCATGAAGTCGGGGGAAGTGCAAGGAATCCTAATTCTTCCAATTCTGTGTTTTGGTCACACAG
Seq C2 exon
GGCTCCATAGTCGTGGGAATTGACTATGACTGCCGGGAGAGGATGGTGTACTGGACAGATGTTGCTGGACGGACAATTAGCCGCGCCAGTTTGGAACCAGGAGCAGAGCCCGAGATGGTCGTTAACTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021945:ENSBTAT00000029257:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.456 A=NA C2=0.205
Domain overlap (PFAM):
C1:
PF0008613=Thyroglobulin_1=PD(0.1=0.0)
A:
NA
C2:
PF0005812=Ldl_recept_b=PU(71.4=68.2)
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:
TATACCCACCGTGGCTCCAC
R:
CATCTCGGGCTCTGCTCCT
Band lengths:
286-2131
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development