BtaINT0041686 @ bosTau6
Intron Retention
Gene
ENSBTAG00000012849 | COL4A1
Description
Bos taurus collagen, type IV, alpha 1 (COL4A1), mRNA. [Source:RefSeq mRNA;Acc:NM_001166511]
Coordinates
chr12:88879820-88883520:-
Coord C1 exon
chr12:88883343-88883520
Coord A exon
chr12:88879935-88883342
Coord C2 exon
chr12:88879820-88879934
Length
3408 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
TTGGCTCCGGTTCTTCGCAGGTG
3' ss Score
8.64
Exon sequences
Seq C1 exon
GCACGGCGGGCAGCTGTCTGCGGAAGTTCAGTACCATGCCCTTCCTCTTCTGTAACATCAACAATGTCTGCAACTTCGCGTCCCGCAACGACTACTCCTACTGGCTGTCCACCCCGGAGCCCATGCCCATGTCCATGGCTCCCATCACGGGGGAGAACATCCGGCCCTTCATCAGCAG
Seq A exon
GTGAGTCCAGCCCGTCGGAGCAGACACACCACTGAGGGAGAAAGGCCACTCGTCCTCAGGGCGGGGGTTATTTTTGTATTTTTCCATTTTCCTCCCAAACATTCAATTCATTGCCATTTGTTTACTGATTGTGATACCTGAGCTCTGTGATAGAAATCATCCATGCAAAGGATTGGATGTAAAAGTCAGTTATCCTCTTAAAAGTTGTAGTGCAAACCCTGGGTGAGATAGAACACATATCTCGTGTGACTCGCTGGGGTGACCACCTTCCCTGCCACGAGCGAGCAGTGTCTCTGGAATTCCCGCAAACATGGGAGCATCTTCACTGCTTTTTTCTTTCTTAAGATATATATTTTTGGAATCACTCCCTACCCCCATGAAATTTAAAAATAATTTTTTATTTTTGATCGTAGTAAAATACACATAACATAAAATTTACCATCTTAACCATTTTAAAGTGTGCAGTTCAATGGCACTTAATGTAGGAACTTAACTATGGGTGTGAGGGAGTCCTCAAGAAACTGTAACACCTCGGACATAGAGTCCGTCTGTGCTTTATGCGTAAGAAGATTATACTGATGTACTGTGTCCATCACATGTGTATGTCCTAAGAATTTTCTTATTCTCCTCCACTCCACCAGTTTTTGTGCCCTGAAGGTAATACTCTCCCCACTGAGAATGCGTATGTTTGAGTGACTTCCCAAATTAAGTGCTTGCCGCACTAATTAATGTCTGGGGTATGTTTTCAAGTCCCCAAGAATCTGCCTGGTAGGAAATAAAATGGGAAATTGAAATTATTATGACCGAAAAGTACACAGTCGTCTTATCTTTGCTTCTTTCCTTCTAATTAAAAAGTTGCTTCCTTAGCTGCACTCAGAGGTAATAGAACAGAGGCAAATGTATGAATTTGTTTCACTGAGAAGCTAGTCTTCTACAGAGAAGATAACAGAGGATAAAAAGAATGACAAGGCAGGCCAAGTTTGCCTTAGCAGAGTGAGAAGGAGACAGAACACAAGCGTTTCTGTGTTTCTTTTAGGGAAATAGCAGCTTCTGAACAGGAGGAAGGATGTAACGGTGCCGGCTGAGGGGTGTCTGCAGTCGGAAGTTGGGGCTGGGTGCGTGCTGACCGCCTGGTCCCCAGATGGTCACTGCGGGCTTCGAGGGGGCCGGCCAGTTATAGGGTCTGAGGCTCCATCACGTGGAAGGCTGGTCCAGATCCGTCTTCTTAAAAGAACCTACCGTGTGGACCGGAGCAGAAAGGCTGGGAGAGTCCTATTAGAAAAGTCAGGTTTTTTAAGGCCTTACATCCAACCACTTTATTTTGAGCTGTAAGAAAACTCACCTCCTGGACATTAAAATGGGAGCTTCCTGGGAGGCCCCTCTGCAAACACAGATGTCCTTCTGCATATTGGGGTGCCTGTGGGCTGTTCTGTGTCGAGACTTTTCTTGCTCAGACCGTGACAGGCGCATGAGAACGAGAACTAACTGCCTTTGTGTTTCTGTTTAGCTTTCCGTGGACGACAGGTAGATCGTGATTTTCATTTTTGTTTCCTATTTACTGTCTTGGCAAACTTGACATTGACCTTGATTTGGCTGGGACACGGGGGCTCTGGGATGAGTTAGGATGCTCCAGAAACCAGTCCAGGAGTAGACTAGGTCTGGGACCTGCTCTTCCCTGGGGACCCATCACCGCGAGCTGTTCAAATGCCCCTAGTAGGTCTGGGACCTGCTCTTCCCTGGGGACCCATCACCACGAGCTGTTCAAATGCCCCGTTTCAGGGTTTGCGCAGCTCCTTGTTAGCTAACCCACAGACTCTGAGCCGGAAGAGACCTCAGAAGTCACATCCTTTAAGTCACGGCTCTGAAAGCACGTGTATCTACCTCCCCTTTGGTCATCGTGCCACCTGTTCCTCCCGGGCACCCAGCTCCCGTGGTCACTTTGACTTGGTGGTTTCTGACGACCTCTCAAAACTCACAGGTTCTTTCCAAGGCCTTTCCTTTGGGGACGCCCTAAAGCTTAATTTCAGAAAGAATTAACGACACAAAATCCTCCCTTTCCAGCAGAAAGAACAGCAAGCTTTCTGCTGTCACCTGGACACAAGCTTCTAAGCACTTTCTGACTTTCTGCAGACGTGAGGCATCCATAGCTGTGGATGGTTTAATTGCCCTAGAGCACAGACCACTGGTCTGAGAGCCGGAGCTGAGCTCTGATTCTGCCTTATACACCAACTCTGGTCTCAGGCTCTCATGAATAACATGGAGAAGGAGACTCATGAATTTCAAGGGACGACACAGCTCATTAGACCTGCGACTCTGTCCCGGAACACCCATCTGACGGGGTCGAGACCGTGTCTCTGCAGCAGCCTGAACCTGCCAGCCCAGCAGAGGCTATCATGAGTCCCTTTCCTGCACGCTGTCCGCTCCCGGGCCCGGCAGGCAGATGGTGGCAGATTTGAAAGGCCAATTTCAGTAGCTGTTGTTTAATCGAGCCCTTTAATCCATCTGCATTTGTGTGAATAAAATAGAAGTAGCACAACACACACGAGACTCTCACATCCGGGGAAAACCAAGCACTCGTTCCGGCCTGTTCCCACGTCACATCTATTTTCGTGCAAATGTTCCAGCCTAGCTAGGTGTATTATTAACATCATTTGCAGTCATTTATCAGCACTGTTGGCTCTGTGCTCATTCTGTGACTTGAATGTGGTCACTGCTATTGTTTACTTATTTAACAAACCGTGAGTGCACCCTCAGAGGGTGTCTTAGCAGGGTAGGTGCCAGGGAGAACATTCTGGGTCCAGCCCTGGGCAGGTCTCCTCACTGGTCTGTTGGCTCCAGGTCTGGACGGTCCCTGGAAGGAGGCGCACGTGGGCTGCTGGCCCCAGGCTCATTGTTTTTCTTAGTTACTGTAATTCAGCAGATGTTCTTCCACTGAAGATGATTCAGGGCTTAAAGCACCGTGTTCCAGAAGCACTGGCCCTTGAATGGCACCATCTCCTTTTTCTTGAGCATTCCGTGTGTTTGCTGAGGTCCGTGCTCATTGCTGAAACGCCGGAGCATGCTGTGGTTCGCAAAGGAGACACAGACGTCTCCTGCGGCCCCAGCTCCCCCGGGGGAGACGGGCCCTGTTACAACCTGGCTCCGGGTTGCCTTCCCCTTATAACAGAGCAGATGGGGAAATGACAAGTGTTGAGTGTGGCTCAGAGTTTAATATTTGAACACCAAGGCAACTCTATCAAATCAGTGAGAAGCCCTGGGCCTCAGAGTCCAAGCAGGGCACCTGCTCCGTTTGATGAGATGTCACTGGACTGGAAAGACCGAGTGCAGAGCTGGAGAGCGGGTGCCGGGGAGGGGTGGGGGGTGGGCTCCTCGCGCTGAGCTGAGGGTCTTGGCTCCGGTTCTTCGCAG
Seq C2 exon
GTGTGCTGTGTGTGAGGCTCCGGCCATGGTGATGGCCGTGCACAGCCAGACCATCCAGATCCCGCAGTGCCCCACCGGCTGGTCCTCGCTCTGGATCGGCTACTCCTTTGTGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012849:ENSBTAT00000035335:49
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.017 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0141314=C4=FE(53.6=100)
A:
NA
C2:
PF0141314=C4=PD(6.4=17.9),PF0141314=C4=PU(26.3=76.9)
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:
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]
SPECIAL DATASETS
- Pre-implantation embryo development