GgaINT1030793 @ galGal4
Intron Retention
Gene
ENSGALG00000016411 | col14A1
Description
collagen alpha-1(XIV) chain precursor [Source:RefSeq peptide;Acc:NP_990665]
Coordinates
chr2:136487989-136489807:+
Coord C1 exon
chr2:136487989-136488144
Coord A exon
chr2:136488145-136489481
Coord C2 exon
chr2:136489482-136489807
Length
1337 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGT
5' ss Score
10.03
3' ss Seq
CTTGGTGGTGGTGGGTTAAGGTG
3' ss Score
1.61
Exon sequences
Seq C1 exon
GACCTCCAGGCGAGAGCCGAACTGGCAGCCCAGGCCCACCAGGCTCTCCAGGCCCACGAGGCCCTGCTGGCCACACCGGGCCCCCTGGCTCCCAGGGCCCCGCCGGCCCCCCGGGGTACTGTGACCCCTCCTCCTGTGCTGGCTATGGTATGGGAG
Seq A exon
GTGAGTAGGCTGCGCTCGGGGGGAGGTGGGGCAAGGAAACATAGTGCGTCCTTTTAACAGCCAAAGTAAGATGGAGGCTACTGGTGATCCTTGCACTAAAATATGATTAACTCCATAAAAACACGCACGTCCAGTGCTGCTGTATTTAGAGGAATGACCCCACAAACCAAAGGTGCCCGCAGTGTAGTGACCAGAGTCCACCATCTGATTTGGGCCTGTGAATGGCTGAAGTGTATTGGGTTTTGTCTTATATGTGTGCGTGTAACTGTGCGAGCCTGCTCCACCTGAATGTTCTGTGTGTTGAATCCCACCTCCTAATGTTTACGGCAGCAGAGCTGCACATCTGTAGTTTTTAAAACATGTTTCTCCACTTCCTCTTCTGTGTGCCTCTGAATGGCATGAGAGCATGAACATTACTAAACCTGCCCTAGTGTAACCTGGAACAGGGATGCACGTGTCCGTCATTAACAAGTGAAGCAATCTGGAGAAAATGGCTCTTTCTCTATCTTCCATGTATTCTACTTTCCTTGTTTGTAGCACAGAGGCCATGGGAGGAAGTTAACACAGTTATCAAAAGTGATGTTGTCCAGCCTAAAATTGAAATTTATTTTAGCAAGTTACTAGTTACTACAAACGTTATGCATAAGGCTTATTTGTTTGATGTTTACAGTTTAATCTGCCCGTGAAGTGATTTGTATGTTTTACTTATGTGAATGTTTTTGTTGTCGTCTCTTCCTATCCTCTTTCCTCACTTCCCTTCCCTGTTGTTCATTTCCTGTTTTAAGGCCCAATCCCTTACAATGGCTACCAATCCAGAAGGTGAAAGACTCATTCTGGTTCAGTTCTCATTTGGCTGAAGGTCAGATACGGATGCTGAACTGCTCTATGCTTTCCATCAACGATATTGACTACCACTAATGAACTTGCTAGCTGCTGTACATGCACATAGCTTCCTTGCACTGCTAAAAGTTATTGTCTGACCCATTAATCATATATTCCAGCCCATAATTGGAATTAGCTAAAGCAGGCGGATTGTGCAGTGTATAATAAGCACAGTATTACAACTGGACATAAGACAAATTCTGGTGGTGGTTTCCAACTAACTTGGCTGTCTGTTGGTGGGTTTCCAATTGCTCCAGCTTATTAATTTTGTTAAATGTTTTCACTGTTCCTTCATGTGAATAAAAAAATGTGTATTTAAAGATTATATATATACACACACACTCTCTCTATATAAAAGGTATATATATATGTCAGTTTGCTAATGAACGCTTCAATTTTCTGCTCCCCTTCTCCTGTGTTAACCATATGAATACTCTTGGTGGTGGTGGGTTAAG
Seq C2 exon
GTGGATACGGTGAGCCAACTGATCAAGACATCCCAGTAGTGCAGTTGCCACATAACTCCTACCAAATCTATGACCCCGAGGACCTTTATGATGGTGAGCAACAGCCGTACGTAGTTCACGGGTCCTACCCTTTACCATCCCCATACTCCCAGTCCTCCTATCCATCACCTCATCTTGCTCAACCAGAGTTTACTCCAGTTCGAGAAGAGATGGAAGCCGTTGAGCTGAGATCCCCCGGAATTAGTCGCTTCAGAAGGAAGATAGCCAAAAGAAGCATCAAGACTCTGGAACACAAAAGGGAAAATGCAAAAGAGCCCTCTCAATGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016411:ENSGALT00000026472:47
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.923
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(74.1=81.1)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTCCTGTGCTGGCTATGGTA
R:
AGGGCTCTTTTGCATTTTCCCT
Band lengths:
345-1682
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]