BtaINT0038338 @ bosTau6
Intron Retention
Gene
ENSBTAG00000018253 | CHRNA1
Description
Bos taurus cholinergic receptor, nicotinic, alpha 1 (muscle) (CHRNA1), mRNA. [Source:RefSeq mRNA;Acc:NM_176664]
Coordinates
chr2:22136992-22139864:+
Coord C1 exon
chr2:22136992-22137231
Coord A exon
chr2:22137232-22137536
Coord C2 exon
chr2:22137537-22139864
Length
305 bp
Sequences
Splice sites
5' ss Seq
AACGTAAGC
5' ss Score
7.35
3' ss Seq
GACACATTCCTCTCTCCCAGGCG
3' ss Score
9.17
Exon sequences
Seq C1 exon
GTTTTTATCGACACTATCCCAAATATCATGTTCTTCTCCACGATGAAAAGGCCATCCAGAGAAAAACAAGACAAAAAGATTTTCACAGAAGACATCGATATTTCTGACATTTCTGGAAAACCAGGGCCTCCACCAATGGGTTTCCACTCTCCCCTGATCAAACACCCCGAGGTGAAAAGTGCCATTGAGGGCATCAAATACATTGCAGAGACCATGAAGTCAGACCAGGAGTCCAACAAC
Seq A exon
GTAAGCTTTGTGGCTTGAGATTCGCACCTTGGGGTTTAAATGGTCACGTGCTTAAGCACAGAGATGGGTTTGGCTTGATGGGAAGGTTGGCATTCAAGGGGCAGCTACTGATGTAAGATGTGCCTGATGACTCCCTAGGCCATCTTAGCAAGTCATCACATTGTGAATAACCTCTTTAAAAGATAAAGATCACAGTGCCAGTGGAGGGAGGATCCACAGTCAAAGGGCCCCTGGATGACGGATAGCACGAACGTTGGGAGTCCGCCATCACCTTCAGGACATTCTGACACATTCCTCTCTCCCAG
Seq C2 exon
GCGGCTGAGGAATGGAAGTACGTTGCGATGGTGATGGACCACATTCTCCTGGCAGTCTTCATGCTCGTCTGCATCATCGGAACCCTGGCTGTGTTTGCAGGTCGGCTCATTGAATTAAATCAGCAAGGATGAGTGGAAAGCTGGGCTGAACCTCCAAACCAGGGAGATCTGTCTAGTTGGATACATGCTCATTTATCAAATATTTAATTTTCTGTATTTATTATTCATGGCAACAGTTTATGTTTACATAAGGTTATGGCCTCCAAGCGTGTTCACATTGCTTCTCCCTTCACTCCTGCTGTGGCTGCCTGGAGAGTGAATCCTTTGCAGTAAGTGAACCTGGATTGCTACAAAAGGCTTTCATTTCCAGCAGCATCTGGAAGAATTTTGCCCATGATAACTGAGGTTTTCTGTTAGTTTTTAAAAAAAATTTTTTTAATTTTAAGCAAAGAGTCTATTCTTTGCTTAATAGTCAGTTTTGTACTACTGAAAAAGCCCCATCTGCCAGTCCCCCAAAGATAAAGCATTTGACTTGGAGAGAAGGAAAGCAATAGAAAGACAACAGGGAAATTCTAGAATGGCCACCAAAATACAAACTGCCTCAAAACCCCAAGTTTTGAGGTTTCTGGAATTTGGAGGTGAGGGAATGTCTTCCCAATCGAACACAGCACCTGAGTTTGATGTTTGGGGTTTGAGGGAAAAGAGTAACTAATCTGAATGGAGTGTGGGGCCAGGCACTGTGGGAATGAGATCACATGTATTTTTTTTTTTAATCCTCATAACTCTGTAAATGTCCCTAGTTTACAAATAAGAAAACTGAACTTGAGGGAGGTTAAGTTCATTATCCAAACTAGCAAGTAGAACTGACATTTGAACCCAGACATTTGAACTGACATTTGAACCCATGTGGATTCACAGTAGCTCTGAGCTGGGCTGGTTCATCGCTCACTTGCTCTTTGGTTCAACCCTAGCTGCATCTGGGCCATCCTGTGACTCTGGTCAGTGTTTTTGAGAGGCTCAGTCCTAGTATTAGCCTTCTTCCTGCCTTCCCAATTAAACCACCCACCTTTCCCCCAGTCTTTATCCCAACCCTGCTTGAGGTTCTAGTTCTATGAATGAAATCACAAATGTGTGCACATATCATCATTTCCACAATTCTGGACACATGAGTAGGAGAGAAAATTTATTTCCTTTCTTCATAGCAACCTACTGGCCACAGGCAGTGCACCCCAGTACTAGAAAATGTACAGCCCTGGGCTCAGTAATGACCATCATCCCCAGAACACATCTGATCCACATCGGTACCAGAGAGAGTGGGGAATGGCAGTACCAGGTGACCAGTTCAATTCAGTCGCTCAGTCATGTCTGACTCTTTGCGACCCCATGAACTGCAGCACGGCCTCCCTGTCCATCACCAACTCCCGGAGTTCACTCAAACTCACGTCCATCAAGTAAGTGATGCCATCCAGCCATCTCATCCTCTGTCATCCCCTTCTTCTCCTGCCCCCAATCCCTCCCAGCATCAGAGTCTTTTCCAATGAGTCAACTCTTCGCATGAGGTGGCCAAAGTACTGGAGTTTCAGCTTTAGCATCATTCCTTCCAAAGAAAACCCAGGACTGATCTCCTTTAGAATGGACTGGTTGGATCTCCTTGCAGTCCAAGGGACTCTCAAGAGTCTTCTCCAACACCACAGTTCTGAACTCAGGGGATTTCAATCTAGGTCTCCTTGGCATTCCCCATGACACACCGGCAGGATTGAGTGCCTCATTTACGAGTAAACTAAAGGGAAAACAGTTTGGCATTTCCTCAAAAATCTAGGCATAGAATTATCATATGATCCACCAACTCCTCTCCTAGGTATACACCCAAAAGAACTGGAAGCAGGGACTTGAACAGATACTTGGATACCAATATTCACTGCAGCATTATTTATAATAGCCAAAAGGTAAAAAACCACCCATGTCCATCAGCATAAGAGCAAATGTATGGAGGAATGAAGTTTTTATAAATACTATAATATGGATCAATCTGGAAAACATTATGCTAAGTAAATAAGCCAGATTTGAAAGGACAAATATTGTATGATTCTGCTTATGGGAGATACCTAGAGTAGTCAAATTCATAGAGACAGAAAACAGAATTGCAATTACCAGGGTTTGGGGAGAGGGGTGAGTTGTTGCTTAGTGGGTAGAGCTTCAATTTGAGACAATGAAAAAGTTCTGAAAGTGGATAGTTGTGGTGGGTGTACAATATCAAGAATGTACTTAATGCCACTGAACTGAATGTTTAAAAATGGTTAAGATGGTAAATTTTATGTGCATTTGACC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000018253:ENSBTAT00000024298:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293211=Neur_chan_memb=PD(31.9=57.5),PF0293211=Neur_chan_memb=PU(56.0=52.5)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(41.3=70.5)
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:
CCCGAGGTGAAAAGTGCCATT
R:
GAACACGCTTGGAGGCCATAA
Band lengths:
349-654
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]