BtaINT0041300 @ bosTau6
Intron Retention
Gene
ENSBTAG00000013472 | COL1A2
Description
Bos taurus collagen, type I, alpha 2 (COL1A2), mRNA. [Source:RefSeq mRNA;Acc:NM_174520]
Coordinates
chr4:11630973-11634147:+
Coord C1 exon
chr4:11630973-11631020
Coord A exon
chr4:11631021-11634102
Coord C2 exon
chr4:11634103-11634147
Length
3082 bp
Sequences
Splice sites
5' ss Seq
ATGGTATGT
5' ss Score
8.35
3' ss Seq
TGTGTCTGTCCTCTTCACAGGGG
3' ss Score
11.35
Exon sequences
Seq C1 exon
AACTTTGCTGCTCAGTTTGATGCAAAAGGAGGTGGCCCTGGACCAATG
Seq A exon
GTATGTTTATCTCTAATTTTTATCTTAGCCAAAAAATTATTAAATAGGGAATTTACTTTATGTTTAAAGTTCACATAGCCATTTATTTAGCTACTTAGGTTAATAGTACTCAGATCAGATAAAAGCAGTAGCTATTTTTGTATTCAAATCTATAAAAATCTAAGCTTAGATAAAGGGGTTCCATTTTCTCTACAAACATGCTTCCTTATGATAGATCAGATATTTATTTCCAAGAAATAATCTCTGGAAATAGTAACCATAATTTAAGCAAACCAATTTAATTTAGAAGAGTGATCACTCTAATTAACTTTCTTATACCCTTTAATATTGCACAGAATTTTAGGCAACCAATAGAGACACAGAACTATTAAGTTCTATGAACTTGCTAGAAAGGATCAGCAAGTTCTAGTCTAGATCAGCAAGTTCTAGTCTAGCCCGTTCATTTTCTCTGTGTGTGTGTATTAGTCAGTCAGGCGTGTCTGACTCTTTGTGACCGAATGGACTGGGGCCCATCAGGCTCCTCTATCCAAGGAATTCTCCAGATAAGATTACTAGAGTGGGTTGCCATTCCCTTCTCCAGGGTATCTTTGCAATCAAGGATCGAACCCAGCTCTCCCGCACTGCAAGTAGAGTCTTTACCATCTGAGTCACCGAGGAAGCTCATTTTCTATTTAGAGAGTTGAAGGTCTTTCCCAAGGACATACATGTGGTTAATGACAGAATGTCAGGCAAGATGTCTGATAGTCAACATCATAGCTTATGTATCTAGTACTTGAATAAAACATTACATCATTCAACAAGTATTTACCAGTTATCTTCGGTGAGACCCAAACTCTATTATGCCTTTGGGATACAAACAGTGACTGTGACAGATTCTCACCATCTCTCAAGGAATTAATAACATAGGAAATGTTTCTTTTTATCCATTTTTGATAAAAAAATTCTTTTTAAAGTCTGATTAATTATAAATCAGTATAGGAGAGAATATGACTGTGGTGATAAAAGTCTATCTTTTACAAGTAAACCTTCTCACAAGCATTAGTGAGTTTTGTTAGGGAAAAAAAAAACTGATAAGAAAATGCAAAATATATACTCGGATGTATAAAACAGAGGGGGAAATTGCTACAAGTAAAAACATTAAGTTGATTAAACACTGCAGTTTAGTACGTAGCCACACATACTTTAGTGATTTTTTAATTAATTATTTGCAAACAAAAGTATTTATCTGCCCAAAGTTGAGATAGTCCTTAAAATATAAATTTTACCTGGACAATGTATACAACGCTCTGTCTTCAAAAGATGTTCTGCCGTAGCTAATAGTCCGCAATAAACTGATACACCGTAAGGGCAAGACAATATTTTCTGTAAATTAAAACTCTCACTTGAGAAGTAATAGGCCTTTAATTGATGATTTCCAATTTCCTGATTTTGCTGGTAATTTAAAGCATTCATAGCTGAAATGAGGAAGTAGAGATTTTCTCTTGGCTTTGTTTATACTGGATATTTGAAATTAGCCATTTCAGCTAATGCTGGACATTAAAAGCAGTACCCATATCTCAAGAAGAAGCTAAAAAAAAAAAAAAAAAAAAAAAAACTAACTCATTAATTAAAAAAAAAAAAAACACCTACATAAGTCTGGTAAGTTAATATGGATTTCAGATTTCCCTGACTTCGGAACATCTTTCTGGTGGGCAGAAAGCATTATGTTTTACTTTTAAATATCAGTGAAATATAATTTAAGCTTGCACATTGACAGGCATTCACAGATATATGTAATCAACAGATATTTGTTTCACAAACAGACAAGATAGGTAGCAATAAAGCATTAAAATAAATTTCCATGTTGGAAAATCAATAACTATAAAACCCCAAAGGGTTCTTCTCTGAATTAATGAGTAATCATCCTGTACCTAACAGCCTCCACAAAATAAACTACCTTTTATGGAAATGAAATTGTTGCAAATACATGGAAAAATGAATAAATATAATTAAAAATTCATGGTGTCAAGGAAAATTATTTTTTAATATACCCCTGAAAATGTTATTTTGATTGAATAGTGACAGTGTTTCTTTTAACATGGAAGCAATTTCTAAAACCAAAAAAAAAATAATTCTTATAATTAAAATGATGTGTTTTTAAAAAAATCCGTATTGTTTCACTCTGGGCATTAATACAGTGGGGCAGACTTGACTGCAGAGTCCCCATAGACAAGTTACCTGAGGCTTGTTTGTGCAGTATTTTCAGTGTTAGAGGCACGGCCCCTACAGAAGAAATTGCATGGGCCTTGCAAAGGGGGCTCACAGGCGTATGCAGCTCCCAAACCAGAGACGCTTGGTCTGAATCTGTGTGCTACAGAATGAAGAACCAAGGGGAGAACAGTCCGCTGCCATTTGGGCCATATTTTCAATAATGATAACATATAATAGATTCTTCCAGTAGGACATTTCAATAGTATTTTATTTTTCCTTCACCCCTTACTACAACCACTCTTGTTTGACATTTTCACCAGCCACTAATAGCTTTTAATGGAGCCTTAAGATTATAACAAAGATTACAACATAAGATTATTAAACAAAAGATTATAACCTCCCTCTAATCATTAAGAAAGAGTTTCTATCCTTTGCAATTTATGCCCCTTGTGGCAAGAAAAACACCAGTTTCCTAGCTAGGTATGATATGAGGAGATGACATATGATCAAGGAAATCCAGATGGAAATGCTTCACTGGCTGAATGCACGGTAGTTGTATATTCTGTACCATCCAAAGACCGAGTCACTTCATTTCATTAGAAGAATCTCAGTATGCCCAATTACACACGAATTTAAGGAACTGGTGGCCACGCCATCTAACCAAGTTATGGTCTAGATTAGGAGAAGAGGTGAAAGCAAAGGCAGAGAAACAGTGGAAGAAACTTGGGTCAGTAAATGCTTCCTTGGGAGGGACAAAAACTTATGAAATGAAACCAGGACAGTTCTGTTCATTGGTGCATCACAGACTGTGGCACTGCCGAGCTCGTCCTGTCTAATCCACCCCGAAGCCAGGATGACTTGCCAGTGCTAACTGTGTCTGTCCTCTTCACAG
Seq C2 exon
GGGCTGATGGGACCTCGCGGCCCTCCTGGGGCCTCTGGAGCCCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000013472:ENSBTAT00000033863:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(7.5=25.0),PF0139113=Collagen=PU(11.1=43.8)
A:
NA
C2:
PF0139113=Collagen=FE(22.2=100)
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]