GgaINT1010019 @ galGal4
Intron Retention
Gene
ENSGALG00000010521 | COL25A1
Description
collagen, type XXV, alpha 1 [Source:HGNC Symbol;Acc:HGNC:18603]
Coordinates
chr4:37090357-37092841:+
Coord C1 exon
chr4:37090357-37090434
Coord A exon
chr4:37090435-37092709
Coord C2 exon
chr4:37092710-37092841
Length
2275 bp
Sequences
Splice sites
5' ss Seq
TTGGTACAG
5' ss Score
0.92
3' ss Seq
TTCCCCTCCCATGGAAACAGGGT
3' ss Score
6.14
Exon sequences
Seq C1 exon
GGATTCCGTGGAATTAAGGGGGAAAAAGGGGAGCCAGGCCAGCCTGGCCTGGATGGGCTGGATGCCCCTTGCCAATTG
Seq A exon
GTACAGTATTTCTCTTTCCTACCAACCCTGCATGTGGCTCCTTTGTTTGTAGTCAGCCGTTCTCAATGTAAAGTAATGTATTTCTGAGCTGACTTTACATTACTCACATAACGCATGCATGTGCATGAATAAACCAGCTGCTTTGGTGATCGTAACCATAAAGAAAGAGCACACTATCCTCCTGATGCCTCAGACCTAACTCTCAGCAGTTTGCTCCCACATCACATGGCAATTTATAAGTTTGCATCCTTCCTACATTTTCCCTGAGAATTGTTTGTTATTTTCCTCCCAAAATGCCTACTGCCTTACTGACCCTGAACCCAAGTCTTTGTAGAACCCCAGCACAATCACCACTTCTAATCAAGTCTGATGACTTCTGTCTGCACTTGCTCAGTTTTAAAACCCTAGCCCACCCAAGAGCTACTCCGCACCCTGGACTTCCTTTCAAATCCGTGTTGTTGAGGGTGCATGTTTTCAGGATTTGGCCAAAATGAGTTTTATATAAAGAATCAGAAAAAATATTATTTCTGGAAACCAGGTCATAGGTTTCCAGTAAGCAAAGCTGGAGCCTGACCTCTCAGACCTTACACAAGCAGTAACTTTGGTGTCTGGTCTGTTCATCAAATAGTATTTTAACTAGATTTGGAAAGGAAAGTTTACCTGAAGTTTGTAAGAAGATAACGGTCTGCTGCCCAAACCCTCACTGTCTTTGTTATTTAATGTCTCCAATTTAATGGTCTTACCCTTGAAACTTACCTTCCTGCAATACACACAACACTTCCCACTCTATGTTAGCATGAATTCAAGTTCCCACCTATACTAAAATTCTACTCGTTGACCCTCTCCCTTGTACCAATCTGGCAACACTGATTTAATGGCAAAGTAAGTTTAAATTATTTTCCATTTAAAAACTAAACAAACAGACAAGCAGTCCTACATACACATTTTCTAAAGAAGCAGGGAAGAATTTTTTTTAATTGTTCATGGTGAAATTTGATTTGCATGTTCTGATACTGTTTGTTGGTTAAGCACGGTTCTCTAAGATGAATGTTAAATCAAGTAAATTTTCTTTCAACTATACCTCTTCTAATTTAAGGTCAATGAATTTTAATCTTAAATACATAGCCTCTAAGATTAGTCCATGCTCCATTTTGTTTGCTTCCACTTAATGGTAACCATATCTCATATATTTTGTTGGGGATAATCAAGCATGCCTTTGTAATTTAAAATTGTTTCTGTCTCTTTATTATCATTTATATCTGGAGGCTCACTAACAGTTGGTGATGAATGAAAATATATTTCATTTATAGGTCCTTACCATAATAAGCTGCTAAGCAAGCAGCATAATTTCTTGCTTTAGGCAGCAAGCCATTCCCATCAGATTACATGGATGCACATTCAAAAATTCTCATTAATCATTATCTTTGTGTGCAGATCCACGTAGGAAGCATTATAATTCTTTATTCTAAAAAAATGTCAAGACCTGAACTTTTTGCTGTTCGTGTATCGTTTATTAATGTGATATTTGCTCCTAATTCTGTGTATATAACTCTTCGATGGGTAAGCTCTATATAGCTATTTGAGCTGGAATTAGTTCTATGAAAACCTGTGTTATCAAGGTCAAAAATTGGTCTGATCTTGGTGGGTGCATAGAAATGTGTGAAAGTAGGGTGGTGACAGAAAAGAAATGGCATGACATTCACTAGCACCAACGCTAGCGTTCTCCTCTGCTGTATCATTCAGAACTGTTCAGACTTCAAGATTTTGCTGCTACATTCAAAAGCTAAGACTGAAAGTGAACAGAACAGATCATTGCTGAATTTGAGTCTTGCTATCTCATCGCTGAAATAACTTTGTAGTAGGGGCCCAGAAAAAGCAATACCCTCCAGATAAAAGTGATAATGGTTTTTGCTCATTGATCTTGTACATTCAGCTGTAGATTGTTGTGAATGACAGATCATATTTAAAATAATAAGTTGCTCTGACAGCAATAGAAAAGTGATTGAAGTGTTCTTGCAATTAGATAAATGGTAAAAAAATTATTTAGAAAAAAGCATCTTTATGTCAGAGAGGCATGGATGTATTTACAGGGTAAACCACCCCTCTTGTGGCTTTTTCTTTGCCTTGAGAACAGTAGAGATGAAATTAGGAAGCGGTAGCTACCTGTTTGATAAAAATACAAAGCTGCTCCAACTGTTCTAACAGATATAGGCAGAAAAACTGTGCTATCAAACCTAACTGCACTCTTTTTATTTTTCCCCTCCCATGGAAACAG
Seq C2 exon
GGTCCTGATGGATTACCAATGCCTGGCTGTTGGCAAAAGGTAGGATGGGTAGAACTGTTCTCCCCAGGGCAGCATGTCCTTGGCACACAGAAAACCTTGTCACAGTCTGAGCAATACTTCAGAGTCTCTTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000010521:ENSGALT00000017084:35
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.667
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(34.7=100)
A:
NA
C2:
PF0139113=Collagen=PD(10.1=15.9)
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]