BtaINT0041810 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021310 | COL4A4
Description
collagen, type IV, alpha 4 [Source:HGNC Symbol;Acc:HGNC:2206]
Coordinates
chr2:116060525-116064159:-
Coord C1 exon
chr2:116064118-116064159
Coord A exon
chr2:116060606-116064117
Coord C2 exon
chr2:116060525-116060605
Length
3512 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGA
5' ss Score
10.1
3' ss Seq
TTGATTTTTTTTTTTTAAAGGGT
3' ss Score
8.57
Exon sequences
Seq C1 exon
GGTAATCCTGGCGTGGGAGTAAAGGGGCAAATGGGAGACCCG
Seq A exon
GTAAGAGTCCCATTTTGCATGGAGGAGCAGGTGTTAAAATGCATGAACTGCCCGTGTCTAGGAGGCTGTTCTGATTATCACTTAACCTGTGTTCATCCTCTCATCACTGCCCACTTTTGTGGCCAAGGATTTGTCTTCACTGACTTATTAAGTTACCCTTACCCTTGGCCATAGAGTGATAGTTCTGACAAAATCTAATAGTAAATTCAAATTAATTTATATGACACACTTCCTCCTAGGCTAAAGAGATGGAATGATTCTGGGAATGCATCCAGAGTAACAATTATGTTTAATTACAGATTTGTTTGACTTAATTTTACAAATTTCATCAGAATCTGAAACTTCACACATAAGTAAAAACATAAACAGCTGCAATCCAAGGCATTTAGCCACACGTTCTTCCACTCCCTCCACCCCTCATACTTATAGTCCTTTCTGCTGAAGTAGGACACTAAATAAGGACAAGCTTCAGCAAAGTGCTTTATGGTGGCTGTTCATCAAGAAGCAATCTGCAGTGTTTAAGAGTTGGTGAGGGGCTCTTTTAAAAAAAATATTTATTTATTTGGCTGTGTTGGGTCTTAGTTGCAGCGCGTGGGACTGTGGTTTTGTCATGTGGGATCTTTCACTGCAGCTTGTGGGCTCAGTAGTTGCAGACTGAGGCTTTCGAGCTCGGTAGTCGCAGATTGCAGGCTTAGTTGCTTCCAGCATGTGGGATGCTAGTTCCCCAACCAGGAATCGAACCTGTATCCCCTGGGTTGTAAAGTAGATTCTTAACCACTGGACCGTCAGGGTAGTCTCTGGTGAGCGGCTCTTTCAACAACTCTGCGTAAAAAGACACTGAGCATCCACCCTGTTCCAGGCTAGGTTTGGTGCTGGGGGTGGGGCTTTAGTGAGACAGACCTGATCCCCCCTCTCATGGGGTCCCAGCATGGTTGGGTAAGTTACTGTACATCCATTTAACAGAAGGACACACTTGCCAAAAATATATTGGAAGACATCATGATGTGGGGAAGAGCAATGCTAAGCAGAAAGTGCAGGTGACAAAGGGCTAAGCTCAACTTTGTAAAACCAGAACAACAACAAAAATTATTGAAATCTACATGTAGAGTAGGATTTCTCAACCTTCACAATACTAATGTATTATCAAGGGGCTGTCCTGTGCAAAGTAGGATGTTTAGCAGCATCCTGGCCTCTACCTACTAGATGTTGGTAAGATCCTTCCGCTTCATTGTGACAACTGAATATGTCAAATGCTCTGCCAAATGTTCGTGAAGGGAAGCACATCCAAACTCTCCCCTCCCTCTCCATGCCCCCCCACTCCCAATCTTGAGAACCACTAACTTAGAGAAATGACTGGGTGAAAAATAGATGAAAACAATGTTTTCCAAACTTGGAATATGTTTGTCAGAACCCCTAAACCTGTGCACCCCATTTTGAGAAATGTCACACAGTGAGGAAGCATTGCCAAGTTAGGGAAGTCAGCACCAACATAGTTGCATGGTTTGCAAACTCAGGCCATTAATCCTATGCTGCTGCTGCTGCTGCTAAGTTGCTTCAGTCGTGTCTGACTCTGTGCGACCCCATAGACGGCAGCCCACCAGGCTCCCCCGTCCCTGGGATTCTCCAGGTAAGAACACTGGAGTGGGTTGCCATTTCCTACTCCAATGCATGAAAGTGAAAAGTGAAAGTGCAGTCGCTCAGTCGTGTCCGACCCTCAGTGACCCCATGGACTGCAGCCTGCCAGGCTCCTCTGTCCAGGGGATTTTCCAGGCAAGAGTACTGGAGTGGGGTAACGTGGAAATATTTGACTATGAGGTGGCTGTTCAAATTATCCACTATACGCTTTTAAAAATTTCTTTTGGATTGTTAAGTAAATAAAGGCATAATTTTGAAATGTTGGTGCAGAGCTCTCACAATGCCCAAGACCATGTTGCCCACTCCATTTTTAGAGCAGACTGTCCTAAATGGTTGTTACTCATGTTTTCATAGGGGATATGATTATGGATCATTTACATTTTGTTCTTTATAATTTATCTTTCTGTACTTTTGACTTAAATGAATATACAGTACTGTCACAACATTATAAAAAAGAACCAGTAGCATGACCAACATTTGGAAGAGGCTCCTTGCTTGCCAGCCCATATGGGTTTTGTAGTTTTATTCCAGTTACAGGAATAAGTATCGTTATCTTACCAATCCATATTATGTATTTATTAAGTAAGCAAATACACAGTGTTTATGCATTTGTTCAATTACTTATTCATGCAACAGACGCCACTAGGATGGCTGCTACACCCTCACTGTGTCAGGCATTAGGGCACATCACGAGAAACAAACTGAACCCACATCCCTAACCTCCTGGTTCTCTATAGTTTCCCAGGTGTGGGTGGGAATTGAATTATTGGTTATATTTTTTCATTTACTTTGCAGAAAGTAATAAGCATTTTATGTGCATTATCTATTCAATAAAAGAATACTTTGAGGCAGGCAGTATTATATTCCCCATTTCACAGAGAAAGAGAGAAAGATTTTGAGGAGTTAAGGATAAGGAGATTTTAAGAAACTTGCCTAAAGGATCCCAGTCTAGTAAGGGCCTATTTCTACACACAGGTGACAACCTGACCTATCACCTGTTTTTAACACAAGAGGGAAGATAATTCCAGGTGCAAAATATTAGAAATATTTAGAAAAGTATGAAATAACTATCTTCTAATTAAGGGTGTGTTTTGGTTGTATTGTGGCAAAACCAATCCAAGGAACATTTTTTTCTTGTAGAGAACATCTCTAATGACCCAAATGAAAACTTTTGATTCATGATTTCCTACAAAGAGATGTAAAATATATTAATGAACTAGATATAACCTAAGTCAAACCAAAGTGGAATAACTCAGTAAGTGATAATATATTATTATGACAGATTATTGCATAGGTGTTGAAAATCAGGTTTTTTTTAAAAGAATTTCTAGTATAATAGGAAAATGTACAAAAAATATTGTTGTAAAATATATTAAATGACTTAACATTTTAATAAAATATAAAAATATAAACTGTATTCTATATTTAAATGACATTATATAGTTTTACTAGTTTTATAATATATTTTAATATGTTTAACACACCATTTAGTCACATATACACGTGTGTGCACATGCATATTATGCACATATATGTATATGTATACATGTGTATATACACGAACATATACAAGCACACGCACACCAAAAGAACTGTACCAAAGTTTTCATAAATATTGTCTCTGGATAGTAGGATTATGGATCACTTTTATTTTTTTAATTCATTTTAAACAATAAGTACGTATTATTTATGAAAAACAATAAACATTTAAAATTCAGTGACATATTTGCCAAGTTTTTTATTTTAAATCCATGATACATGTTACACAGGATTATAAGCATTATATCACAGTTATGAAAAGCTTCTTTGTTTCAAATTTCAGTTCAAAATAAAGTTAAAAATGGCATTCTTATTATCTTGATTTTTTTTTTTTAAAG
Seq C2 exon
GGTGAGGTTGGCCAACAAGGTTCTCCGGGGCCCACTCTGTTGGTGCAGCCACCTGATTCTGGTCTCTATAAAGGAGAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021310:ENSBTAT00000018302:13
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(7.1=28.6),PF0139113=Collagen=PU(10.2=64.3)
A:
NA
C2:
PF0139113=Collagen=FE(29.5=100)
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]