BtaINT0041835 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021310 | COL4A4
Description
collagen, type IV, alpha 4 [Source:HGNC Symbol;Acc:HGNC:2206]
Coordinates
chr2:116009551-116014815:-
Coord C1 exon
chr2:116014741-116014815
Coord A exon
chr2:116009659-116014740
Coord C2 exon
chr2:116009551-116009658
Length
5082 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAG
5' ss Score
8.68
3' ss Seq
TTCGATCCTTCTTTCTTTAGGAC
3' ss Score
10.82
Exon sequences
Seq C1 exon
GAGACAAAGGGGAATCTGCAAGTCAGTTTGGCCTGCCTGGTCCAAAGGGTGAGCCGGGTGGCCCTGGATATCCAG
Seq A exon
GTACAGACCCATCGTTTTTATTCAAACAAAAAAGAGTAAGTGTGTTTTGAAAAATAGAACAATTACTTCATCCTCCTAGCCGGGAATGATTATATCAGTATTTTCTTCCCCCTTTACTCATTAACATACGTATCAGAAGACTATGTATAGGGACTTCCCTGGTGGTCCAGTGGTTAGGAATCTGCCTTTTAAGGGTTCAATCCCAGGTCTGGGAACTAAGATCACAGATGCCATGGGGCGAGTATATCCACGTGCCACAACTAGAGACGCCTGTACAGTACAACAAAGGCCTGACATAGCCAAATAAATAAATAAAACTTAAAAAAAAATAAAGAAACAGAAAACTTGTGTATAACCACTGGTCTAGGAGAATACCAGAGACTCTTCATCTTCTTGCCATCATGGGTCCCATGACCTGGGATGTTAACAACACACTTCCCAGGGTCAAAAATGAAAATTTGGACCCTTTTGCAATCTCTGTAATTAAAAATGATAATTAAGCAAGAACCACTCAGCTGACTACAGTGGCAGGTTTTCATTCCAACCCTTTCTTTTCTACTCAGAAAAGCATAGGTGAATGCCCTGAGGGCTGCTGTTGCTGAGATATAATATTACAGAATACTGCATTTTCTGTGGATCTAGTTTACTAAAAACCAAACCAAAAAAGGAGAAGGCAATGGCACCCCACTCCAGTACTCTTGCCTGGAAAATCCAATGGATGGAGGAGCCTGGTAGGCTGCAGTCCATGGGGTCGCTAGGAGTCGGACACGACTGAGCGACTTCCCTTTCACTTTTCACTTTCACACATTGGAGAAGGAAATGGCAAACCACTCCAGTATTCTTGCCTGGAGAATCCCAGGGACGGGGGAGCCTGGTGGGCTGCCGTCTACGGGGTCCCACAGAGTTGGACACGACTGAAGTGACTTAGCAAACCAAAAAAAAAAAAAAAAAAGGTAAAGCTCCATCATCCACAAGTCTTTGGAAACAGTACTCTGTTTATCAGCAACAGTTGATGGGTAATCCCCTCAGAACAGATGACGGTGTTCCAGTGAGTGCTTGCTCTCCATAGAGGCTATGGTTGCCTACAGTAGATGACCACAGCTGACAAAATACACATAGCCTTTTACTAATTCCGCCTGTTGGAATATACCTGAAGTCAATAATCAGACAGATGTACAAAGGTGTGTACACAGGGATATCCACTACCAGGAAAGAATATTTGTTTCTCCACAGGTAATTGGTTCAATCAGTGATGCCCAGAGCTGTTAAGCTGTAGTGGACAGGTTAGAGACCAGGTTTACATTTAGATGAGCACCTTGTAAATGAAGGGCTTCCCAGGTGGCTCGGTGGTAAAGAATTCGCCTGCCAATGCGGGAGACACAGGAAACACTGGTTCAATCCCTGGGTTGGAAAGATCCCCTGGAAGAGGAAATAGCAGCCCACTCCAGTATTCTTGCCTGGAGAATCCTGTGGACAGAGGAGCCTGGTGGCCTACAGTCCGTGTGGTCACAAAGAGTCGGATGTGACTGAGCATGCACTTGTAAATTAAATATCTCGTATTAATGGTTTCATGCTTTATCTTCAAATTCTCTTTGGTGATGGTCATGTTTCATTCCATATGACAGACTATCTGAGCAGACCTATTATGGGAATTTTTATTTCATTTGTTTACGTATTTATTTATTTTAAAGAATAAATAAAAAATTGTTTTTTTAACTTTAGACATTTTATAGAATTTCAGTCGTCTTTACACGCTATGTGTGTGTGTTAGTTGCTCAATCATGTCTGACCCTTTCTGACCCCATGTACTTATATAGCCCACCAGGCTCCTTTGTCCATGGAGTTTTTCCAGGCAAGAATACTGGACTGGGTAGCCATTCCCTTCTCCAGGGTGTCTTTCTGACCCAAGGATCACACCCACATCTCCTGCATTGCAGATAGATTCTTTACCATCTGAGCCACAAGGGAAGCCATTTACACTCTGTGCTGCTGCTGCTGCTGCTAAGTTGCTTCAGTTGTGTCCGACTCTGTGCGACCCCATAGATGGCAGCCCACCAGGCTCCCCTGTCTCTGGGATTCCCCAGGCAAGAAAACTGAAGTGGGTTGCCATTTCCTTCTCAAATGCATGCATGCATGCTAAGTTGCTTCAGTTGTGTCCAACTCTGTGCGACCCTGTGGACAGCAGCCCACCAGGCTCCTCAGTCCGTCTCCGCAATTCAATAAATTATAGGTACAGGGAAGCCATATTTATAATAACAATGAATTAAATTTTGTTTTTATTCCATAAATTGCTAAAATGGAAATCTAACAAAAGAACAAGCCATTACCCTGGCAAAAACTTCCTTTTCCATTCCCTTCCCTTTGGGTATTTTCCCTCTGGCATGTCAAATAGATTTAGATAATATAATTTTAACTGAGATGTATAGCTTATGTGTGTACATTTGGAGGGGAAAATAGCTTTGAGGTTAGCATTGTAGGGGTTCATAAGAAGTACCAGAATGAGGTCTCAGAAAGGAAAGTCACTGGTTCAACAAAGTCAACCTCCATTACCACTGAACATGTGGTCTTGAGCCAGTTGCTTATCATCTCTGAGCTGTTTGCTCATCTGTAAACTGGCCTTCAGCAGATTACAGGTTGTTCTGAAGATCAAATGAGATTCCTTGAAAGCGATTTGTAAACTGAAAAGTGCTACACAAATGTAATGTGTGATTCATCATTGTCATCGTCAGCAAAACATGAAGAAATATTTCCACACTTACTGCTATTTTTATGTAAAACCTTTAAGAGAGTAAGATTTCATGAGCTGAAAATAGTCCAAAATGGAGACCTTTTATATTACCTAATATTTTAAGTTAAAAATCATAAAGCTGAGTTATTTTATGCATAGGCTCACTTTTTCAAGAAAATTTGCCTTGGTGTTATTTCCCTGGTCTCCTGTGGTTATCACCATTTAAATCATTCCCTTTCCCAAATGCCATAGCTTTTGCTTAAATTTTTAAAGTTACATCATACTTTATGTACCAGCACAGAGTTTACCTAAACATGCAATTTTCATTGACTGGGAAAAAAGCTGGATTGAATTTGAACAAGCCTAACAGGAAGGCATGGACCTGCAGCCTGTCTCAGGGGACTTTATATGATTGTACTGGGTTCTGTTCTACTTCCCCTTCCTTTGTTTCAGAGAGCAAATACAGTAGAGATTAACTCAGAAGTTCTGTTCTTAATACAACTGTGATTGGAGAGGCAAGCCTTTAATAGTTCAGTTTTTTCATTTGCAAAAGGGCTTCCCTGGTGGCTCAGTGGTAAAGAATCTGCTCGCCAGTGCAGGAGACTGGGTTCGATTCCTGGGCAGGGAATATTCCCCTGGAGAAGGAAATGGTAACCCACTCCAGTATTCTTGCCTGGGAAATCCCATGGACAGAGGAACCGTGGCAGGCTACAGTTCATGGGGTCGCAAAAGAGTCGGACGTGACTTAGTGACTAAACAACTTTCATTTGCAAATAGGAAAATGCTGCCCTCAGATGGTAAAGAATCTCCCCACAATGCAGAAGACCTGGGTTTGATACCTGGGTCAGAAAGATCCCCTGGAGAAGGAAATAGCAACCCACTCCAATATTCTTGCCTGGAGAATTCCATGAGAGAAGCCTGGCAGGCTACAGTCGCAGAGAGTTGGACACGACTGAGCGACTAATTCAATGAACACCTTTACTGCAGGGATATTTTCAGGATAAATAAAGCAATACACAGTGAAGCTCATAGATCTAAAATTTGATCAGGAACAAGTATAGACTAACACAGGCTTGTTTCTTGTGTTTTAGAATAGTGACTATGACCTCCGTGGGTTTGTAAATACAATACCATGTAATTTATTTGCAGATTCAACTGATGAATTTTGGCACAGACTATTGGTTTGTCCTATAAATATAAATTGTATTACAGGCATAGATAATGAATAAATACATGGCAAAGTCAACTTCTCTAGTAATCAAATATGACTTAGAGTCTGAAGTATCATTTCATTCTTACTAGATTAGCAAGAAAACAAATCCAAAAACTGAAAAGTCTTCAGTGAGCACATGCTATGCTCTCGGAGTTGTGGGGCTGTGGGTGGGTTACGTGTGGTGATGTGAGTTGATGGAGACTTTATCCAAAACCACTAGGCAACCTCTTTCAAGAACCAAATGCTGAGGGGTCTGTTCTTGAACACTAAAAGCAGCTGAGCCTTTCTCTTTAGCATGTCACGTCCTGAGAAGAGGACCATGGTCGATTTTTTTTTTTTTTAACCTAGTAGATGTATCCACCAGATGTAATATGTGGTTCTGGAAGGGGACCCAGTGAGGACAAAGCAGCTGTGAAGGACATTAAGAGGACAATTGAGGCAACTCAAGCATGGAATGAGTATTGAACATGATTAATTTTCTTGGCTGTGATGATGTTATTTTGGCCACATAGGAAAATGTTCTTATGTTTTCAGACATACCTCCTGAGATATTTAGGGATGAAATTCCATGATGTCTGTGATTTACTTTAAAATACTTCAGCCCTTAAAAATGCATTAAAAACAACCAAAATATCAGACTCTCTTACCTAAAAATTCTACTCCGAGGAATTTTTCTTAAGGAAACAATTTAATAGGAGAAAAAAAACTGATTGAAAATATATAAAGATCATTATGCATAACAGTAAGAGTTAGAAATAACTCAGATGGCCAATAGTAGAGAAAATTAATTAATTTAACTAGGGTTAACTCAATAAGCTATCAGCCCGTTGTTTCAAAACAATAATTAGGAAAATGATATGAAGCTTGGAAGATTACTTATGATACAATGCTAATTAAAAATCAGAATATAAAATTGGAGGCCTTATTTGCACAGTGTTATACATATGAAATACTGTGTTAAGTTGGTGGGATTATAGGTGTTTTGTTTTCCATTTTTCCTATATGTTATCTTTTCAATAGAAAAATTGTATGTATGTAAAAGTAAGAGTAGAAAAGAAAGAGCTGAAACTGGAGGTTTCATAGATTCACTGCTTTGGAGAGCAACTGCCACTACTCAGATGTTCGATCCTTCTTTCTTTAG
Seq C2 exon
GACGTTTGGGAGCATCTGGAGAGCAGGGCTTGCCCGGTGCTCAAGGTCCTGGAGGACCACCCGGAAGGCCAGGACCTCCTGGCTTGTCTGGACCAACAGGATGTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021310:ENSBTAT00000018302:36
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(11.8=30.8),PF0139113=Collagen=FE(35.2=100)
A:
NA
C2:
PF0139113=Collagen=FE(50.7=100),PF0139113=Collagen=PU(32.8=56.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
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]