BtaINT0041847 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021310 | COL4A4
Description
collagen, type IV, alpha 4 [Source:HGNC Symbol;Acc:HGNC:2206]
Coordinates
chr2:115971118-115972741:-
Coord C1 exon
chr2:115972455-115972741
Coord A exon
chr2:115971382-115972454
Coord C2 exon
chr2:115971118-115971381
Length
1073 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGC
5' ss Score
8.27
3' ss Seq
CTCTCCTGTTGTCTGGGTAGCAC
3' ss Score
7.06
Exon sequences
Seq C1 exon
GTCTGGCGGGCTCCTGCCTCCCCATCTTTAGCACGCTGCCCTTCGCCTACTGCAACATCCACCAGGTGTGCCACTATGCCCGGAGGAACGACAGGTCCTACTGGCTGGCGAGCACAGCGCCTCTGCCCATGACTCCGCTCTCGGAGGACGAGATCCGCCCGTACATCAGCCGCTGCGCAGTGTGCGAGGCCCCCGCCCAGGCCGTGGCGGTGCACAGCCAAGACCAGTCCATCCCCCCATGTCCGCGGGCCTGGAGGAGCCTCTGGATCGGGTACTCCTTCCTCATG
Seq A exon
GTGAGCCCCAGCGCCTCCGCCATCCCTAAGACCCCCCTCCGCGCCCCTTCCACCTGGACTGGACGGTAATTTGAGAATCCAGGGCTGATGGTCAACAGTTTGGCATGAGGGTCATGAAGGCCACCCGAAACTAAAGCCTGCTGAGGCACAAGGCCACTCTTTTCTGCTTATTGTGGATGAATTTTTGTATTACTTGGGTAGAATTTAGAGGATGGATTTGCATCAGCCCGCAGTGAATGGGGCTTCCCTGGTGGCTCAGACGGTAAAGCGTCTGCCTACAATGCAGGAAACCCCGGTTCGATCCCTGGGTCGGGAAGATCCCCTGGAGAAGGAAATGGCAACCCAGTCCAGTACTCTTGCCTGGAAAATCCCATGGACGGAGGAGCCTGGTAGGCTACAGTCCATGGGGTCGCAAAGAGTCAGACAGGACTGAGCGACTTCACTTCCACCTTTCAGTGAAAGGGGTTTCTTTTTGTGTGTGCGCCCATCTCCTTTCCCATGTACCCTTTCCTTTGTTGTCCTTATGGAGTCGCTGTGTCCTGTCCGACTCTTTGTGACCCCATCGACTGCAGCCCGCCAGGCCCCCCATCTGTCCGTGGGATTCCCCAGGCAAGAATACTGCAGCGGGCTGCCATTCCTTTCTCCAGGGCATTTTGCTGACCCAAGGATGTCCTGCAGTGGCAAGCAGGTTCTTTACCACTGAGCCACCGGGGAAGCCCATCCTTTCTTGCTTGCTCAGTCCTGTCTGACTCTTTGCGACCCCATGGACTGTAGCCTGCCAGGCTACCCTGCTCCATGAGATTTTATACGCAAGAATACTGGAGTGCGTTGCCATTTCCTCCTCCAGGGGATCTTCTCGACCCAGGAATTGAATCCGTGCCTCCCGCGTCTCTGGCATTGCAGGCAGATTCTTTACCACTGAGCCACCTTTCCTTAGCAGATCATAGTCTCGTCTTTCTGGGATGATTTTTAGGGAAAATGTAAAGTCAGGCCCAGACCTGGGTGTGTCACTGGTTGGGTCTGGGGTTGTCTGTGCATGTCTGAGCCCTAATTCTCTCCTGTTGTCTGGGTAG
Seq C2 exon
CACACAGGCGCTGGGGACCAAGGAGGCGGGCAGGCCCTCATGTCCCCAGGCAGCTGCCTAGAGGATTTCAGAGCCGCACCGTTCCTGGAATGCCAAGGCCGGCAGGGAACTTGCCACTTTTTTGCCAACAAGTATAGTTTCTGGCTGACAACAGTGAGACCTGACTTGCAGTTTTCCTCTGCACCATTACCGGACACCTTGAAAGAAAGCCATGCTCAACGCCAGAAAATCAGCAGGTGCCAGGTCTGCGTGAAGCATAGCTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021310:ENSBTAT00000018302:51
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.011
Domain overlap (PFAM):
C1:
PF0141314=C4=PD(59.3=66.7),PF0141314=C4=PU(25.6=31.2)
A:
NA
C2:
PF0141314=C4=PD(72.6=96.6)
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:
CTCCCCATCTTTAGCACGCTG
R:
CGGCTCTGAAATCCTCTAGGC
Band lengths:
346-1419
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]