BtaINT0086101 @ bosTau6
Intron Retention
Gene
ENSBTAG00000012025 | LMX1A
Description
Bos taurus LIM homeobox transcription factor 1, alpha (LMX1A), mRNA. [Source:RefSeq mRNA;Acc:NM_001191325]
Coordinates
chr3:3863179-3865786:+
Coord C1 exon
chr3:3863179-3863349
Coord A exon
chr3:3863350-3865625
Coord C2 exon
chr3:3865626-3865786
Length
2276 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGA
5' ss Score
9.48
3' ss Seq
GTGTTTCGTCTCCGTTTCAGGTG
3' ss Score
11.68
Exon sequences
Seq C1 exon
CTCAGACAAACGGTGGTGGGAGCGCTGGCATGGAAGGGATCATGAACCCCTACACGGCTCTGCCCACCTCACAGCAGCTCCTGGCCATCGAACAGAGTGTCTACAGCTCAGATCCCTTCCGACAGGGGCTCACCCCACCCCAGATGCCTGGAGACCACATGCACCCCTATG
Seq A exon
GTAAGAGGGACTCAAGCCCCGCAGGGACCTCGCACAGCTTGCTTGCGTGAGTTTTTCATCCCCTCCCAGTTCCCCTCCCTGTGCAGTTCCTAGTTGCTCATTAAAGTTCCAAAGCAGAATAAGTGTCCCACAAAATGCTGCTAGAATCACATAACCTATGGCTCCAGAAGTAAGACCAGTACGCATATCCATGAGTCATGTTTCCATCTGTTCTCCTTTTTAAAACCTTTTTGTTTGAAAAGGAGGTTGTGTTTTCACTGTAGACCTTTTTGTTGGGATTTAACTTCCCAAGTCTTCCGTTTCCTGCCAGATACCACACTTCTGGGAGTAGGAAATGGCAACCTACTCCAGTATTCTTGTCTGGAGAATTGAGGAGCCTGGCAGGCTACAAGTCTCTGAGGGCGCAAAGAGTCAGACCTGACTGAGCAATTAAGCACAAACACCACACTTACCTTGCTATGGCACACTCATGCCGGCTACACACTCGTGCAGTGCATGGGACCCACGTGTGATTCCTGGGTTAAGAAGATCCCCTGGAGAAGGGAATGGCTACCCACTCCAGTATTCTTGCCTGGAGGATTTCATGAACAGAGGAGCTTGGTGAGCTTCAGTCCCTGGCGTCGCAGAGTCGGACAGGACTGAGCAACTAACACCATCAGTTTCACTGCATTTACAAGTTCATGAGCATTGCCAGCAGTGATATAGTCAGAGGCCTTAATTATGCAACTCTTACATGGGAAAGAATACATGGAAAAGCACGGAAAACAAAGGTTCTAATTGGACTCTCCTATTATGGACACAAGTACGTATTCTCATGTAATTCCTAAAACATAAGCTGACTTGTGAAGTAAAGTCCCAGTCCCACTTGCAGCCAAAATGGGGTTGCTTTAAAGGCAGGGTGTGGGGGCAGCTGAGATTCCCCCACTTTCCTGGCTTGCTTCTGAAGCCAGTGGACAACAGCTGGGGCCTGGATGCCCTGATGGAGAGGGCAGGCTCTAGAGTTGAAGGCTGAAGTTCAATCTTAGAGTCAAATATACGCCACTGGGTTTTTTATACAGAGAAGGTATATGGCCTATGTAATGCATTTGCCTGTACTGTGAAATCTGTAATCAGTAACCCTGATAGCTAAAAATAAAGTTTTATTCAATACTCCTTCAAAATGTTAGTATCCGAGATACATGCCTCCGTGCACAGATTTTGTCAACTTCTTTTTTGCCTTCATTATAAAATTATCTATATTGTTGAAATCAGCCTTATCTTTCCCTGGGATGCATTCAGCAAACATTTATTAAGATCCAGCCACTTGCAGGGCCATCATCGACTAACCTCATTCACTCATACCCACGTAGATACATATGGGCATGCTCAGTGACGGCCATCCTCTTTGCTTCCTGAGAAGACACATCTACGCCTGTGTGCACTCCTCTGCTATGCAAAAGCAGGACAAATAGCTCTTGTTTTTTTGCCAATTCATACATTTTCAGAGTCCTAGGGGTCTTGTTACGTAAATTACTCCTGTGATGAATCCTTTAGTACAATGAATAATTAAAGCCACATGACGAGTTTTATAAACAGCAGTTTTCCTCTCTCCCATTTACTTGAAGTGGAGGTGACATGTCCCCACCTCCAGGTTCTGGTCACAGTGGTCCCCCAGCTCTTCCTCAATTTGCCCTGCGAGTTTCATTGTCAAAGGTTATACTAGTTGAGTGCGGACACCTAACCTTCCTTTCCTTTGCAGTACAAATCTGGGGAAACAGCTGGCACTCAGTATGTTTGTGCTGTTTGAAAGGACAAGTATTATCACCAGTGGATTCGTGAGCATCATTCACAGAGTCGATGTTTGTTTTCTTACCCTCCCTCCTGCAAGAACCTTTTCTGTGGCCAGAGTCTTCTAGAAGCCCTGTGCCTGCCTCTGCAGCGTCCGGTGCTGGGTCTCGCCCACCACCAGTGTCTAAACACTCTGATATTTGCTTATGCTGGGCTCGGTTTAGCACTACTTTGTCAGATCGTAGTTTATATTATTTTCAGTTGTTACACGTTAGACATAGCCCTCTAAGGAGGTCTTTGGTGGGCAGGGATTCTGCCCCCTCCTAGTCTTCTATGTAGCTCTCCTGTCGCCCCCAGCGCTCCCCCTTCCCAGCACCCAGTAGACGGCTTTCCATGGTGGGGACGGGGTGGTGTGCTTAGACCGCGCGGGCCAAATTCAGCTGTATGTCCCGGCATCGAGTGAGTCCCTCCTTCCGGACCTTCATGGCAGTGTTTCGTCTCCGTTTCAG
Seq C2 exon
GTGCTGAGCCCCTCTTCCACGAGCTGGACAGTGAGGACACCTCCCTCAGTAACCTGGGTGACTGTTTCCTAGCAACCTCAGAAGCCGGGCCCCTGCAGGCCAGAGTGGGAAACCCCATTGATCATCTGTACTCCATGCAGAATTCTTACTTCACCTCTTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012025:ENSBTAT00000015947:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.629 A=NA C2=0.436
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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]