BtaINT0010532 @ bosTau6
Intron Retention
Gene
ENSBTAG00000018137 | A2M
Description
Bos taurus alpha-2-macroglobulin (A2M), mRNA. [Source:RefSeq mRNA;Acc:NM_001109795]
Coordinates
chr5:101341300-101342906:+
Coord C1 exon
chr5:101341300-101341427
Coord A exon
chr5:101341428-101342815
Coord C2 exon
chr5:101342816-101342906
Length
1388 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
TTTCTTCCCTGGATTTTTAGTTA
3' ss Score
6.93
Exon sequences
Seq C1 exon
ACATCTTTGAAATACAATATTCTCCCGAAAAAAGATGAGTTCCCATTTGCTTTGGAGGTGCAGACTCTGCCCCAAACTTGTGATGGACCCAAAGCCCACACCAGCTTCCAGATCTCACTGAGTGTCAG
Seq A exon
GTAAGACCTCTGACTGCATCATGTAGTTCTGGGTATAACAGCCAATCTTCTCACTAGAACTCCGCATTAAGCAGAGCAGCATGACGGTGAATGTCTGTTCTGCATTTATTGAAAAAGCAACCTGTTCCCATGTTGACACAGAATTTCTCAGTGATGAAGTTTACATTGTATATCCCCCACTGCAGGATCTCTTAATGTCTAATCTCCTTATTTACAGCTTATTAACCCCCTCAATAATAATTACATAAAGAACATTACCCCTTGCCTCTAACCTGAATTCCTGATTTTATTCTAATATAATGATTCATCCTGATTTCATTCTATTGTCATGAAATCCGATATTATTCTTGCTTTATCCAGGACAAAGGTGGAGACCTCTTGCAAAGTATGAATAGAAGGGAGTAGTGACTCTCTAGTTAAAATTCCTACTGGTGATAATTAAATCTCAGATTATATATAAAATAATCAATCTGGGGGAAATATATACATATGCAGCCATTTTCAAATAACTACTGGGCTATTTGTATCTGTCCACAAGATATTATGAGCAAACTCTGGCAGATAGGAAGGACAAGGGAGCCTGGCATCCTGTAGTCTATGGGATACAAAGAGTCAGACCCGACTTAGTGACTGAACAACAAGAATATTATAACCTGGTTGGGGATATTATTCAGGAAAAAAGACAAAGTACATGTAACAAATAACTGGATAGATTAGCAATCTCATGCCCATCTATGCTTTTGAACTGTGGTGTTGGAAAAGACTCTTGAGAGTCCCTTGGACTGCAAGGAGATCCAACAGTCCATCCTAAAGGAAATCAGTATTGAATAGTCATTGGAAGGACTGTTGCTGAAGCTGAAACTCCAATACTTTGGCCACCTGATATGAAGAACTGACCCATATGAAAAGACCCTGATGCTGAGAAAGACTGAAGGTGGGAGGAGAAGGGGACGGCAGAGGATGAGATGGTTGGATGGCATCACCAACTCGATGGACATGAGTTTGAGTATGGTGTTGGACGGGAGTTGGTGATGGATAGGAAGGCCTGGCATGGTACAGTCCATGGGGTCGCAAAGAGTCAGACATGACTGAGCGACTGAACTGAACTGCCCAACTATACAGCACTTATAGGGCTTTCTTAAAAGGCAGATGCTCAGAGGTCACACCCATGCAATTCTGATTCATCTGGTCTGGAGTAAGGCCTGGTCTCTGTGGCTTCAACAGTCTCCCCTGAAGATTCTAATGCACAGCCAGTTTTTTTAGCTCCTTGATAAGAAATTTAGGAAGATTTCTGGTACCTTTCAGGACTCTTATGTGCTTAATGGACATAGAAAAAGAATATTTAATGACACAGAAAATCCTAACTCCTTTCTTCCCTGGATTTTTAG
Seq C2 exon
TTATATTGGAAGCCGTCCAGCCTCCAATATGGCAATTGTTGACGTGAAGATGGTATCTGGCTTCATTCCCTTGAAACCAACAGTGAAAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000018137:ENSBTAT00000006167:32
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:
NO
A:
NA
C2:
PF076779=A2M_recep=PU(25.3=71.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAAAGATGAGTTCCCATTTGCTTTGG
R:
CATTTTCACTGTTGGTTTCAAGGGA
Band lengths:
190-1578
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]