RnoINT0039514 @ rn6
Intron Retention
Gene
ENSRNOG00000007657 | Col27a1
Description
collagen type XXVII alpha 1 chain [Source:RGD Symbol;Acc:735115]
Coordinates
chr5:79111658-79114534:+
Coord C1 exon
chr5:79111658-79111702
Coord A exon
chr5:79111703-79114480
Coord C2 exon
chr5:79114481-79114534
Length
2778 bp
Sequences
Splice sites
5' ss Seq
AAGGTGATC
5' ss Score
4.41
3' ss Seq
CTTTGCCACTGTGTACTCAGGGT
3' ss Score
7.96
Exon sequences
Seq C1 exon
GGACTGATGGGCGGCGTGGGGGAGCCCGGACTGAAAGGTGATAAG
Seq A exon
GTGATCTGAACTCTCCCTTACTGCCCCTGGGTTATCTGAGTGCCACTCCGCCTCCCCCATCCCTCGCTGCTTGGCTCCCCTGCCTCCTGCTGTCCTCCCTTCTCAGTCCTCTGCACCTGATTTCTTCTGGTTTCTTCCCGTTTCTTGGTGTGTGGGGTTCAAGTGGGCAGCTGTGGAGGTCTGGTGGTTGAGGCAGATAGGACAAGAGGGGCAAGAGTCTACGGGAAGCCAAGACTGACCTTTGAATCTCAAATGCAGAGCATGACAGCAGGCACACAGGGGTCACAGCCTCAGAGCGTGGAGGGTGGTGACCTCAGAGGACACAAACCCCTGTGTGGGCTTGAGAGTCCAGCCCTAGAGAGTCCAGCACCCAGGCTGAAGCACTATGGGAACCCAGGCCAGCCTCCAAGCACCACCATTTCCTCACTCCCCTGGGAAGGCCACTCCTAGGCCGTGGAACTTCCACTGCCTCAAACCCCTGCCAAATCTTGTTGGAAGGGAGACGTAAGTTCCAAGGCCCAGAGACAGGTATTACCTAGCCTGGATCACACAGCATCAGAATGACCAATCCATACCTGGGGGATATAGGAGTGCTTTGCCTTGTACCGGCGTCTCTTCCTTTCCCATTAGTTTCTATGTGAATCTGAAAGGCCAAAGAGTGGGGCATGTTTAGGGGCAGCACCCTGAGAATCCACAGAGAATGGCCTCCCTGATCAGCTCCTCCTCACCCAGGCTCCTTCACCTGTGTCAGATGGCTGGACCCATGTGTCCTCTGCAGGCATGTGGGTCCCCAGAGAGTTCCACCCCTAAACAGAATGGAAGTCGTAAGGTCAGAGTGGACGACGAGGCTCTGGGAAGTCACTTATTCTAGAACCTACAAGTGACAACTGTGGAAACTGAGACCCAGAGAAGGGAAGATATCGACCAAATCAAAGTCTGTGCTTGATGGTTGGAACTAATCCAAATCCCTGGGCTCTTAAGAAATGGAATTTCCCAGCTCCCCAGCCACCCCCCCAAATATATAGAGCCAGATGTCTCATTCAGTTCCCCTCAGGCAGCCAGCGAGATTAGGCCAACTTCAGCTCCTCCTCTACCTGTTGCTACCTCTCTGTCTTCTCCCATCATGCATAAGCCTATGTTGTGGCCCTTCTAAGCTGTGCCTGGTACTGCCCTTCCACACTTCTCCCTTCTCTGGAAGTGAAGGACTTGTGGGGGTGATAGGGTGTCCTGGCACCTGCCTGCTCTGAGTCTCGAGACAACAGCTCTGTGGAATAGCTAAAGCCCTGGCGGAGGAGAGAGGGCATGGGCAGATGATGTCATGGCAGAGAGAGGGCATGAGCAAATGACATCATGGCAGAGGGCTTTGCAGGGCTGGCTGCCAGTTAGCAGTGCTGGGATACGTGGACATGACCGTAGTGCCATCACGTTCTTGTCACAGCAGCTGGTACCACCAGGGGCACTCCCAACGTTTAGCTCTGAAACACACTGAAGAAGGAGGAAGTCATGTGAGGCTGTTTTGGATGATGTAGACAGAGGAAGCTGTCCTGCCCCTTGGCTGAGTCAGGGTCTCCGGCTGGGGCTCTGGTGGCCGCATACACGCTGCTGCCTCTATTCTCCCAGGACTGCAGAGCTGCCACTCATCCCTGTATTCTTCTCATTTTGACTTTCCATGACCCTACCTGGCCTTAAGCCAGGCATGGCATATCCAGCCTGGCTGTCTGGATCACGTCTTGGTTTCCTCAGTGACTTTTAAGGTCTCCTCTGTATTTTAGTATTTGTAGCCCCTCTTTGCATGTCTCACACACAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAGAGAGAGAGAGAGAAAGAGAGAGAGAGAGAGAGGAAGGAAGGAGAGAGAATACCTCCCCAAACTCTATGACCTTGTACAAGACTTTCCAAACAGAAAAAAAAAAGAAAGAAAAAAATAAAAGAAAAAGAAAAAGAAAGCAATTTAAAAAGAAACTTTCTTCAATTCCAATTTTGTTCTGATGATACAGTTGTGTGCCGTGTCACAGCCTTTGCTGTCACCTTACTCTTCTGAGATTTCCACTTCCTCCTGCTTCTGGGGCTTCATGAGGCCTCAGTGAGCAGAGCTAGTAAACTACTGGGAAGAACTCTCAGATGGTTTCAGCTCTAAAGGGAGCGCCTTTCCATCTGGCCTGAGCACAACTTATTTACCAGAACTGGACCAGGAGGGAGCAGAGGAGGTCTCCCAGTGCCGATCCTGTCACAAAACACTCTCAATCCATCTTAGAAGGGACCCACCCAGAGCTCATCAGGGCTCATTTGATTCACACTGCACACAGTCTTAAGAAGCCAGCCCCTCAGGATCGCTGACTAAGCATTTAATTAGCCGACAGCTGCTTGTACGGAAGGAAGACATGGCAACTCCCAGCAAGCAGTGCCTGGGCTGTCATCCCTGTAGCTTTCACCCTTCCGTACTGACATCAACTGCTGCTGAAGAGGCAGAAGGATGAAGAAATTGTACTACGAGAAAACCAGTGTTCTCTACGCAGCTCTCTGAGCAGCTGTGAAATGGGAGGGATCCCCTCATCCTGGGCCTCCTTGCCCTACCTAGGGGATGGGTCCTTGACCCCTTTAGAGCCGAGGCTGCTGTTGGCCACATGAACAGCCTCCACAAGGCTCCTTGGGGTCCTCTGTCCAGGGTCGGGTGGGGGTGGGGGGAGGAAGCGTCTTGGCTGTATGGCCCTCTCCTTATAATCTCTTTGCCACTGTGTACTCAG
Seq C2 exon
GGTGAACAAGGGGTGCCAGGTGTATCGGGAGATCCTGGCTTCCAAGGAGACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000007657:ENSRNOT00000010333:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.990 A=NA C2=0.944
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(12.6=73.3),PF0139113=Collagen=FE(17.7=100)
A:
NA
C2:
PF0139113=Collagen=FE(21.5=100),PF0139113=Collagen=PU(4.6=16.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
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]