BtaINT0040920 @ bosTau6
Intron Retention
Gene
ENSBTAG00000011741 | COL13A1
Description
Bos taurus collagen, type XIII, alpha 1 (COL13A1), mRNA. [Source:RefSeq mRNA;Acc:NM_001105433]
Coordinates
chr28:26394438-26400194:+
Coord C1 exon
chr28:26394438-26394473
Coord A exon
chr28:26394474-26400107
Coord C2 exon
chr28:26400108-26400194
Length
5634 bp
Sequences
Splice sites
5' ss Seq
CGGGTCAGT
5' ss Score
6.55
3' ss Seq
GACTAAACCATTATTTACAGGGG
3' ss Score
3.82
Exon sequences
Seq C1 exon
GGTTTACACGGACCACCCGGGGACAAAGGAAACCGG
Seq A exon
GTCAGTCTGAGTCCTCACACTTTGGCTCTGATCACTAATGTCTTCATGGGGAGGTGGAATGACCAACTGGGGATTCCTGACTCAATGTGGAAATACAGTTTTTCCTGATAAATCATTCTAAATTAAAAGACTTTCTAGTGAGGGGCTTAATTCGTGGCACTCAGGGAGCCTAGGGACCTAATCCTGAAATTGTAGCACGTATTTTTCCACGAGGAAAGGGGAGGCTGAGTCCCAGGGCGGCCATCAGATTAGCATTGCCATTCAGTGACAGGAGTCACAAGCCCAGCTCTCTCTAGGTTGCCCTGATAATGGGCCCCTAAACGAGATTTTTACATCCATCATTGCCGAGTCCTCGTCTTCTGACACCCAGTTTTACCAGGCATCCCAGGTCACTGGTGAGAGAGAAAATAAATCCCAGCTCCAAGAACAAGCAGACAACTGTTGTACACAGGCAAACCTTTTAAAAGGATCCCAGCCGTTGCTTCTCTTGGAAAGAGTCGGCAGGACTATGACATGAGTCACGGCTTTCAGGACCCTGCTCCTCCTTTAGTTTCTGCCATCTTCACCAGGACACAGTCCTGAGTGTCCACGGCATCCACAGCCACCTGACGGCCACATGGCACACTGGTGCCCAGGAGCAGTCATCGCACAACATCTCACCAAGGGCTGGCCTTTGCTTCCTTTCTAGAACGTCTTGTTGGCTGCCTCGTCACGGTGGTTCTCAGTGGGGTGCACGTCCCCTAGAAGGCCAAGAGCATCTTCTAGTGGGAATAATATTCCAGGATCTTAGAGGTAGAAGAAGAGTAGGAAGAACAGGAGAAACATGCTCCAAACTATGATAAGACGTTCTGAGTCCCCACGAGAGTTAGACACAGAGCACGGGACTTGCAGAAGCCTGGTCTTCTGGCTCGTCTTTGAACACTGATAATAGAGCGTTCATGAATAGAACATGCCAGAATCGGTACATTTATATCTGGCATCAGCACCAGTCTCTTCCATTTAAGATGGATTTACTGAACAGTTCCATATTCCTAAAGTTTCCTTTCTGACAGCTGGTCAGAAGCAATCCATTTATCCCATATATTCTATGAACAGGAAAGGAAAGGCAAAGCTACCCTCTCAGACTGTCCATGAAAAGCCCATCGTTGCTTCGCTGTTGCTTGTGGAGGTGAAGCTGGAGATGTTCAAAGCCCCTCACGCCCACTGGCTATGCAAGGGGGCTCCTAAACTTTGCCTCACATCACACCTGGGGCACCCCATCAGAGAGGCTCAGAATAAACCACTGGAATAAACAGACCCACTTCCAGAAATGGGCCAGCCAGTTACGGCGGCCTGGAAAGCCCACCTCCAACACTGGCATCCGAGAGTTCAGGCCACTAAAATAATTGATCATTCCACCTCTCAGTTGGCATACTAACCTCCTTTCTAATTTGTTTCTGGAGTGTTCTGGTTTTCTTTGTTATGTTCAGTTAATACTTGTCAAGCCTCTTTCTTAAGACTTTTCAGTTGGCTTGAGGCACTGGGCCATTTGAAAGCTACAAAACCAATCTTTCCAGTGGTGGTGACTGTGTGGCTCTAGAGGCAGAAGCGAGGCAAGAAAATGCCCTTGTCAGGACTTCCCTGGGAGTCCAGTGGTTAAAACTCTGCCCTTCCAATGCAGGGAGCTCGAGTTGGGGAGCTAAGATTCCACACATCATGCAGTGAAGCCGATAAATAAAAATTTTCAATGCCCTTGTCACAGATGGAGAGATGGTGGGAGGCTGGTGGCTCTGATGCTTAAAGAACCGAGGTCATTGAATGAGCCACTGAGGCCCCATGATTCAGTGGGAAAATATTTCTTCTCCAGATCCTATTCTAAGGTTTTATATACTTCTCCCCTGTCCCACATATAAATTAGCAATATGTCACTTAGTAAAAATCAAGTCCAGAAAACAGGCAAGTTACACGAACCTTCCTTGGAGTGCCTCATAAAAAACCAGTAGACTTCTTCCAAAGGGCAGGTCTCCAAATCAAGGGCCAGATAATTCTTCCGTCCAAGAGATCTGACTCTCAGGAGCCAGAATGTCCTAGAAGAGTACCCCCGACAGCTCGCCTCCTCTTTCAGACCTCTTCACACCACTGGCCTTAATGGGGCTTTTGAGGGGAGAGATGAGCGCTTGGTGATAAAAGCCTCCAAAATGAAGAAAGGTCCAAGCAGAGTCAGCTCTGTGCCATGACCAGTTTTTTCTGGCACCTGGAAACTCAGAAGGCTGACACTTTGGTCTAGGGAAAAGGCCAGAAGTGCTTAGGTGATGCTCAGGTTGGAAGTTTCATTACTGCTTGTGGAGGTGAAGCTGGAGATGTTCAAAGTCCTTCATGCCCACTGGCTATGGAAGGGGGCTCCCAAACTCTGCCTCACGTCACACCTGGGGCACCCCATCAGAGAGGCTCGGATGGGTGCCCCAGGTCTGTTATCCTATCTCCGAGTGACCCAAGACACAGCCTTAAGAACAAGCTACTCCAAGTCCCACTAGAGAATGGTCTTGGGGCCTCCTTCCTGCTCATGGAAGGAGGACGGTCCTCATGGTGGTGGGCAAGGCCCAGAGGCCAAGACTGGCAGTTTTCTTAGGGGACACACATGCCAGGGGAAAGAGTCTGTCCTTGTCACCAGGGGCATTCTCCTTGTCCCTTAACAGCTCTGTGAATTTAGCCCGAGAGCCACTTTTAGGATGAAAAAATTCATCACAGGGTAAAGGGTGGTGTGAATTTGGCAATCGGGGCATCAGGAAAATTGGGTTTCACTGTGGGGCTTCCTGCAAACCAGCCAACTGAAAGGTCTGGGAGCATTCATGCAGCTTCTGTCACTCTCCGAGAGGTGCCGTCTGCAATGTGTGTGTGTGTGCAGGTGTGTGTGTATGGGAGAGTGCATGCGTGTGCATGTATGTACATGGCTTGTGTGCATGCATGTGGGTGCGCATGCATTTTTGCATCTTGCTTCCCCAGGTCCCCTTGCCTCCTTCCTCTCCCCAGTCTGCTCTCTCTTGGCCTGGGCCTGCTTCTTCCTCCCTTTACTCCCTGAATATTTCTCCCTCTAGATAGGTTCACCCATTATAATAATCCCATAGCCTCATCCTTTCCCTTCCAGTCCTCCAGCTTCAGTTTATTTCCTCTAAAAGCAGTGTTGTTCATTTTTTAAGAACGCCCTGCCACTTGATTCTGCCTGCCCCCCTCCCATACCAATTTGACACCCCTCTGCACCAAGGCAGAGGGGTCCTCTTGGGAAAGGGAGCAGCGAGGATGTAGGTGAAGTTACAACTCTGATGACCCAATAAGGCCACTTCCTGTGCCCTTAGAACCTGACAGCCCAGAGTGCAAGTTTCCCATCCTGAAGGGACCTCGGCTAACCCTCTGCCCCCCACAGGCCCATCATCAGGACCTGCAGAGCCCCACTCCCTGGAGCTGTGCTCACACTCTGAACTTAAGGAACTGTGCTCACTTTTGTGCTGGCCTCACCCAGAGTATAAGGGGCACCTACCTGAGAAAGTTTCCCACAGGGCTTCTTCATCCAAATAGCAAGTGGTTTCGCTTGTCCACTGTCTGCAGGTTAACTGTCCCATGATTTCCTCATTGGTGGGCATATCTTAGAGCCAATGCCATGACACCTAAGATGCATAGACACATTTCCTCTTAAACACACTAAGTAGGCATTTGCATTTTAGAAAACTCACTTAGAAGGATGTGTTGGCAATTGCAGGTAACCTCTGAAATCAAGAAATGTGGGTAATTTTCAAAGGCCTGGAGAAACATCTTAAGTATTCTTATCCATTGCCTCCCTCTAAGGAACCCTGTAGCCTTCCACTGCTGGAACACTGTAGACAGGAGGCCCAGCCTCCGACGGCAGCCTTGGCTCCTACAGTGGCTGACAAGAAGTGACAACTGTTACTGCTCTTATTATGAAGCTGCTGTCATGACTGAGCACATACTATAGGCCAGTGCATGCGTGTGTGCTAAGTTGCCTCAGTCGTGTCCAACTCTTTGCAACCCCATGGACTATAGTCTGCCATGCTCCTCTGTCCATGGGATTCTCCAGGCAAGAATACTGGAGTGGGTTGCCATTTCCTCCTCCAGGGGAACTTCCCGACCCAGGGATTGAGCCTGCATCTCTTACGCCTCCTGCATTGGCAGGCAAGTTCTTTATTGCTATGGTGGTTTAGTCACTAAGTCGTGTCCAACTCTTGGATTCTTGCGACCCCATTGACTGTAGCCTGCCAGGCTCCTCTGTCTATGGGATTCTCTAGGCAAGACTACTGGAGTGGGTTGCCATTTCCTCCTCCAGGGGAACATCCTAACACAGGGATCAAACCTGGGTCTCCTGCATTGCAGGCAGATTCTTTACCAACTGAGCTATGAGGGAAGCCCTTTATCCCTATATGCCAGTATTAAGCACTAAATGTGCACAAAGACCTCGCAACAATGTTCTGAGGGAGGTGCTATTATCCACACTTTACAGATGAAGAAACTGAGGCTCAGAGAGGTTAAGTAAGCTCCCAAAGTCTCGCGGCTGAGAAGAGGCAAATCCCGTTCAGCTGCAAGCCTTCTCTCTGACCATTAGGCTACCCACCCCGAGACACAGTGAAAGCCCCCAAGCCTGAGACAACCGGCCTTCAATAGAGGAGAGCTCCAGGGAGACTTCCCAGGGGCATGCTTGGTCCCTCATAAGGAAATCCCACATATAAAACCCCAACTCAAATTCATTACACAGAGTTTCCCACAGCCCTTCTTTAAATGTAGAGTGACCTTGACACATGTAAAATAGGGTTCAGTTTAGAAAGATGATGTTTGCTGAAGCTTTTCAGAAACAAATGAATTCCTTGAGTCAACATATCCGTATACAAGTAGCTGCCCATGACCTCAGACCAGGATGGGCCAGAGAACGGGAGGACCCAGCTGAGAACCTAGACACACAACATACACACATGCACTTGTACACACACACAAGCTCATGTACTACCATGTGTGTCGCACGTGCCTGCATGCCAGGTTCACACACACACACACACACACACACACACACACACACCAGGGCTCTGAACAAAATCACCCTGCCTCCTAAGAGAATGTCAAAGGGATGGACCCAACTGGGACAAAAGCTGTTAGGGCAGACCCTTTTTCTCTAATATGAGTGATCTATGATGATCTTTATTTATTTTTGGCTGTGTGGCACATTGGATCTTAGTTCCCCGACCAGGAATCGAACCCACACCCCTTGCATTGGAAGATGGGAGTCTTAACCACTCGACCTCCAGGGAAGTTCCAGATCCCTTAAAAAAATGAACCCTCAAAGAGAAGGAAATGGGTCCCCCTGTCCATTATATAGATGCATTCCGGGCTCAGAATTAGTATCACCCATCTGCACTTCCTCCCACCTCTGGCTCTCAGCCCTACTGACCCACACACACACCTGCCTTAGCCAAATACTCAGGTTCTTTGTGGGGTGGGGTGGACACTGATCCCTAATCCTGTTGAGGAGACTATCCTAATTGAGAGAATCTATTTTCCCCTCTTTTTTTTTATTCTGTCTCTAACCTTAACACATGAATGATCCTAAAGTTTTGATGTTTTTTTTTTTTTCTTGGACTAAACCATTATTTACAG
Seq C2 exon
GGGGAGAGGGGGAAGAAAGGCTCTAGAGGGCCTAAGGGGGATAAGGGAGACCAAGGAGCGCCTGGATTAGATGCCCCCTGTCCATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000011741:ENSBTAT00000039811:34
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=FE(15.7=100)
A:
NA
C2:
PF0139113=Collagen=FE(40.0=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]