BtaINT0010509 @ bosTau6
Intron Retention
Gene
ENSBTAG00000018137 | A2M
Description
Bos taurus alpha-2-macroglobulin (A2M), mRNA. [Source:RefSeq mRNA;Acc:NM_001109795]
Coordinates
chr5:101312151-101313681:+
Coord C1 exon
chr5:101312151-101312312
Coord A exon
chr5:101312313-101313453
Coord C2 exon
chr5:101313454-101313681
Length
1141 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGT
5' ss Score
10.45
3' ss Seq
CTGGTTTTCTAATTCATCAGGTC
3' ss Score
7.46
Exon sequences
Seq C1 exon
GTGCTCCTAGTGGACGGGAAAGGTGTCCCCATGCCAAATAAAGTCATCTTCATCACAGCAAATGAAGCCAACCACAACTCTAACACCACCACTGATGAGCACGGCCTGGCACAGTTCTCCATCACCACCACCAAAATCAAGGGCACCTCCCTCAGTATCAGG
Seq A exon
GTAAGTTTGTAAGGAAGTTACCAATGACATGAAGAAGTCTTAGGAAAAAGGGTTGCAACCGAAAGTGATGGCATTTCCAAGTTGTGTTTAGTCTTAAAGAAGACAGGGAAAAAATGAGAAATTAGAAACTAATTTTAGGTCAATTTTGAAACAGTTTATTAAAAAGGAGGCAGCACAGAGTTGTGGTTAAAGTGGTGGCGGTGGGGGGTGGGGTTTCGACACATGGAGCCTAAGACAGCCTGGGAGAGGCAGGCATCAATTACTTCACTCAAAGAATTGATGCTTTCAAATTGTGGTGCTATAGAAGACTCTTGAGAGTCCCCTGGACAGCAAAGAAATCAAACCAGTCCATCCTAAAGGAAATCAACCCTGAATATTCACTGGAAGGACTGGTGCTGAAGCTGAAGCTCCAATACTTTGGCCACCTGATATGAAGAGCCGACTCATTGGAAAAGACCCTGATGCTGGGAAAGATTGAAGGCAGGAGGAGAAGGGGACGACAGAGGATGAGATGGTTGGATGGCATCACTGACTCGATAGACATGAGTTTGAGCAAACTCTGGGAGATGGTGAAGGACAGGGAGGCCTGGCGTGCTGCAGTCCATGGGGTCACAAAGAGTCAGACATGACTGAGTGACTGAACATAAACAAACATAAACTCAACTCTTGAACAAATGCTAGTTACAGAAAGTGTTCTCAGACGTCTAAGTTTGCAATATTACATTTATTCATAGTATCCATTTGAAACCCATCCTAAATGAGGCATCTCCTCTCCGAAATGCAATTCTTCAGTTTCTGAGAATCAGTTAGTCTCCTCAGTGAGGTTTCATAGCTCCAGTATCTCTGTCTGAATACATAAAGTGGCTACAGAAACGCAAGGGAGCTAATCAGAGTCAAGGATGCCTCCTCATATGCTCTTCAGAAGTATAAATACCAACCCAGGAAGCCTCTGCCATGTAAAGGGTCTGCAATATAGATAAACAAAATAAGGGACACTTCTCTCTCACTTTTTAGTGTGGAGCAAAAGATTTCTAGGTACACTAGTTAAGGTAGGATACTAAACTAAACCAATTCTGTGAGCACACTGCCATTCTCTCTGATATATAATCTATAAGCTAATACTGGTTTTCTAATTCATCAG
Seq C2 exon
GTCAAATACAAGGATCACAGCCCCTGTTACGGCTACCAGTGGCTGTCAGAAGAGCATCAAGACGCTTATCACAGTGCTAATCTTGTGTTCTCCCGAAGCAACAGCTTTGTCTACCTGGAGCCCTTGCCTCGTGAACTGCCCTGTGGCAAAACTCAGACAGTCCAAGCACATTATGTGCTGAAGGGACAGGTCCTAAAGGATCTAAAGGAGCTCGTGTTCTATTACCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000018137:ENSBTAT00000006167:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.259 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0236911=Big_1=FE(56.4=100)
A:
NA
C2:
PF0236911=Big_1=PD(6.4=7.9),PF077039=A2M_N_2=PU(26.2=51.3)
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:
CTCCTAGTGGACGGGAAAGGT
R:
GGACCTGTCCCTTCAGCACAT
Band lengths:
352-1493
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]