GgaINT0070705 @ galGal4
Intron Retention
Gene
ENSGALG00000010521 | COL25A1
Description
collagen, type XXV, alpha 1 [Source:HGNC Symbol;Acc:HGNC:18603]
Coordinates
chr4:37085728-37090434:+
Coord C1 exon
chr4:37085728-37085781
Coord A exon
chr4:37085782-37090356
Coord C2 exon
chr4:37090357-37090434
Length
4575 bp
Sequences
Splice sites
5' ss Seq
AAGGTGACC
5' ss Score
6.78
3' ss Seq
AAGTTAATCTTTACAAACAGGGA
3' ss Score
5.33
Exon sequences
Seq C1 exon
GGTTTCCCTGGTCCTCGAGGAGAAAAGGGTGAAATAGGAGAAAAGGGAGAAAAG
Seq A exon
GTGACCGCAGTGTTATTAACTGTTGCTTGGTTCCTTGGCCCAGTCAGCTCTGCTGTCTTTATTCCATAAATCATCCCATTAAACCTGATCTTTGTTTTCCCTGTGTGCCAAAAGGCAGCTCACAGATGCACACTAAACAAAATCCCGTGTTAGAAAGATCATGAAAATTTATGCACAGAACGAGTGCTACCAATGAGTGCCAAAGCACAGCTTGTTCTTAGGCTCACTTTCTCCATTCATCCTACACTTGTTGAAAGTCCTTGTTAGCCTGAAACTTTTAATGCAGACATCACTGAAGTGAGTAATTTTGGTAGTAATTTCATACAGGAGACTCAGAGCCTCAGCAGTATTTCAGTGTAACTGCTGACCCCAGTGCACTGTGCCTGCACGCGCTGCCTGTCCCATACCAAGTGGCAAAGGAGGGGAACTGTGCTAATCTTTACTATTGGCAGTGGCTTATTTACAGTTAAGAGAAGTACTCAGTGATGCTTGTGGACTGATATTAAATCTTACACTACATTTCTGGTAAACCGAACAGACAGTGTGAGTAACAGAAGAGACCCGATGTCATTTTCACTGTCCAGAGTGGTGTGAAAATTTGTTCGGTAAAATGCAATGTAGGACCAGAAGTGTGTAAAAAAAGTCTCTCTTCAAACAAGTTGAGACTAGCTAATTTCTAGTTAGATAACTTCAAATTGAAATGTAAAAATTATTATCATGACTAAAACACTGTTGAGAGTGATGCTTGGTTTTCATTGACATGCCTTGATAGGCGAGTAGCCCATTACCTCAGTTTTGAGTATAAATCCTAGGCCAGTGTTTTTTGTTTTAGCCTGTCAACAGCTCAACAGTTAAACTATGTCAGTGTTTGCATTATAGTGCCTGCTTAACTTGGCTGTAAAAAAAAAAAAAAATCTAGCTCCCATTACTTCTATAAAATTACAGTCCAGGAGCGCTTAGCACAAAAATATTTGTACAATTGGTTCTATATTTTCAAGCTTTATGAATAGAAGTCTATTATTTATTAAAAATCATTTCTTATGTACTACGTTCTGCTTCAGTAAAGAGGTTTTAGAAAGCTACCAAAAAGAGAATGGTGGTTCAAATTCCACATTCAACTTTTCTACTGCCAAAAAGGAGGAGGATTTAAGAAAAGATGTTATGTGCGTAGGGCAGGAAGGGAGCCCTAATCCCAAAAGTGCAGTTGTCTCTTGATATAAGGGTTGTCAGAAGAGTGCTGAGGTATCACCAGGATGGCTGGGAAGACATCGTCCTATTCCCTGTGCCTCCTGTACTGCCACAGCTCTGCATGTGGGGCTGCAAAGATGATGAGGGGCCTGGACCATCTCCCTTATGAGAAAAGGCTGAGACCTAGGACTTTTCAGCCTGGAGAAGACTGAAAGGGGATCTTATCAATGCTTATTAATATCTAAAGATATCAAGTGGATGGGGCAGGACTCTTTTCAGTGCGGCCCAGCAACAGGATAAGAGGCAACGGGCACAAAGTGGAACGTAAGAAGTTCCATATGGACACAAGGAAGAACTTCCTTATGGTAAGAGTGACAGAGCACAGGCTGACAGGCTGCCCAGACATGTTCTGGAGTCTCCTTTTCTGGAGATATTCAAGACCCATCTAGATGCTTTCCTGTGTGACCTGCTGTAGGAAAACTGCTTTAACACGGGGTTGGTTGGACTCTATGATCTCCAGAAGTCTTTTTCAACCCCAACAATTCTGTGACTGGAGACTGTGCCAGCATGCCAGCCATAGCTGTTTTACAGAAGTGCCACAAACTGGTGTTTCTATAGGCAGTGAGGAAGGACAGGAAAGAAACAAATTTTTTTTTTTATTCATCTGCATGACTTTTCATGCTCCGTATTTCTGATGGAGCTCTATAGGTCTTGGTAAGAACATTATGTACTTGAGGAGAGCACAGTCCGTGGGAAAACTGGTCAAGTCCTCAGGAACTCAGACTACTCTATGCACATATGAGTACTGTGTTGGTTCAAATAGGATCACAGGTTTGCCTTGCAAAGCTTCAAGTATAACTAGTCACCTGCTGACTTATAACACAGCAAGTTAATGAAACAGAGGTCCTAAAGACATAAAGGAGTTAGAAATCAAACTGTACTATCTGTTCTTATAATCATTTTTGAAGTATGTCTATGCTCTGTGCTTACATCTACTCACAGTAAACATATCTGTCTTGCAGTGAGCACAAACAAAGTGAGATTTGACCCTGAAGCTGTTAAGATTCTGTGCTATAATGCCACGCTTCTAGGTTTAACATGAAAACCCAGCCAACTTGTGCTTTTTATATATCACAGCCTTACAATTTGGTATAGAAGGGTAATGTTTGGTTTTTTTTTTTTTCTAAGTATCATCCTGAAACTTTTTGGCACACAGAAAAGATAAACAAGGAACTTTGCCTATCACGTCACAACTGCAATGTGTTTTGTTCACAGAAAAGATATTTTTTCATTTGAATGTGTCAAGTATGCTACGATGCTGAATGAATAATGTGCTTTCCTTTCTATTTAAACAAGTTACAGTGAATTATTTTTTTATTTGTGTAAAAAAAAAAAATGCTTTTTCTGTCTGTGAATGAATTAAGACTTTCCATGCTGGTGTGGTACTAGTTAGATGTCTGTTTACTATGCTTCACCAAAACCCATCTGTCTTTCCAAAGGGGCATTCCTTCCTTCTCCTTCTATCTTCATCCCCCTTAATTCCCCTGTCTTTTTTACCCTTTTCCTCGCAAATTAAATCCTCCCAATAGCCACAACCTCGCTTGCTGGTTCTCCAACGTCATACTAATTTTCCTATGACTATTTTTTCCTGTTCCTTTGTGATATTCCTGATTCACTCATCCTTCCTATCCCATTTTTTACAGTCGCAGCCCAATTTGTTTCTTTCTTTTTTTTTTTCTTTTTTTAACTTGAACCTTTTTTGATTTTGATGAATTTGAGAGCAAGCCTGAAACTCATTTACCATTGTGATCAACTGGTGTGAAATCAATTAGAAAATGAACTCTCCAAACATCTTATACTGCTTGAAGGTGAGGTCATTTATGCAGGTAGCTTTATTGAAGGGATCAACTCATTCCATGAGTAATTAAAGCACTGGAAGTTTTACATTTAAAAAGAAAATTTAGTTCAAAATCAAAGGACTTATACAGTAAAATGAGTAGATGAAATGCTCTCTGCTGTTGAAAGAACATTTAAATAGAAGTTAAATAAAGATTATTTAAATATTAGGCTGTTTAAATAAAGGCACTCTAATGATCCCTTTTAACTAGTTTGTGGTCTCAAGACATTATGAACTCTTTGAAAGTGCCACGGAACCTTTCCATCAAGCAGTTTGGGTGCTTTGATTCCTCTAACAGGGTTTGAAATAAAGGATCCCATTGTATTTAGAGTGACAGGAGCGCACCCTTGATGATGGCAGCGGGTTTCCGTGGATATAACCAACAATGGGATTTGTCCCAAACTCTTACCAGAGTGCGGGAGGTCAATTCAGCAAAGGATGCACCAGGCCGAGTTTACCCTCTATGTGACATCGTAGCCCTTGACAGAATTCTGCCAGAGACTGACCATACCATCCCTTCTGAAGTTTCAGAGAAACTATGACAGTGTCCTCCACTCTTGCAAAGCTACTTTTGACCCATGACAAATCTCTGAAGAAGCTGACGAATCTATGTGCACTTCAGAACCGTCATTTAGAGCAAATAGGAAACCTCTCATTTTGGACTGCGGAGTGGGGGGATTTGCAGATTCACCTCTATCTGAAGAGATCAGTGATTTCAAGCCCTGTTCTAGGATTCAAAGCATTCATGATATTGACAGGAAATGTCAACAACGCAAACTAATACCAACTGATTGCAGTTCTTGCTTGTGATCATATAATTTATTTTTCCACATAATGCACCAACCAAACCAGAACACAGTGGTAAGTGTCCTTTCAGCTCTCCATTGGCTTAAAAAGAAAAACTCAAACTTTTCAACCAATCTATCTTTATTTTTTTTCCAAAAGAATGAAACATGTTTTGTCCAAACCATTGTATCCACAGGGGGAAAAGGGAAAGAAAGGCAAAAAGGGGCCTAAAGGGGAGAAAGGAGAACAGGGTGCTCCTGGATTAGACGCACCTTGCCCATTGGTACGTCTCGCTTGTGTATTGGATGACTGATCATCCTGCTGTAGATTGATGGAATAAGAAATGAGGGGAGAGGAACAAGCACCACCTAGTGTGTCACCTGTTGCACTTGTTAATGCAGCATTATCTCAAAATTCACAAATTAGGGAACAGAGTTGGTTTTTCAACCTCCGAATTTGGTTTAAAGCATCAGAGTTAAGGCCTTCAAGCAAGGTTTGGTTGTTTTTTTTCATTATTTCCTGCTGAATGTTGGAAAAGAATGCAATTCAGTGTGGGCCAGAGTCCCTGACCCCATAGGTTAAAACTGCACCACTGCTGTGAGCTTGCTCCTCTTGCCTTTCTGTTGTTATTTGTTTGCTCCAACTAAGTCAATACCGAAGGCATTTCCTTGACAGTAACGTTGCAAGTTAATCTTTACAAACAG
Seq C2 exon
GGATTCCGTGGAATTAAGGGGGAAAAAGGGGAGCCAGGCCAGCCTGGCCTGGATGGGCTGGATGCCCCTTGCCAATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000010521:ENSGALT00000017084:34
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(3.5=16.7),PF0139113=Collagen=FE(23.6=100)
A:
NA
C2:
PF0139113=Collagen=FE(34.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
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]