RnoINT0038965 @ rn6
Intron Retention
Gene
ENSRNOG00000000552 | Col13a1
Description
collagen type XIII alpha 1 chain [Source:RGD Symbol;Acc:1595704]
Coordinates
chr20:31504325-31510067:-
Coord C1 exon
chr20:31510041-31510067
Coord A exon
chr20:31504433-31510040
Coord C2 exon
chr20:31504325-31504432
Length
5608 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGC
5' ss Score
9.14
3' ss Seq
CATGTTTTCTCTAACTTCAGGGG
3' ss Score
8.95
Exon sequences
Seq C1 exon
GGTCAGTGTGGAGAATACCCACACCGG
Seq A exon
GTAAGCGATACTTCAAGCCAAGGGTGCTCTATGGTCCATCCTGAAGCCCAGCCACTACCAGAGTTGGAGGGTGGGAGAGTTGGGGGAGGAACCTGAAACCCTGTGTGTAAGGTGCAGTCTCTCTGTCCTACAGCTAACCATGACTTAGTTTCAGTACTGTGACTGGAGGTCCATTTGCAAGGAGCCGGCCTCCCATGGCCTTGTCTGCTGAGCAAGTGTCCAAGAGTCTCTTGAATGTGTGTGTCCCTTTGCCCTCTGTTCACTGGGAGGGGTACATGGATCTGTGTGTGGCCTCTGCCCTGTGTGGTGTGTATGTGTGGGAGGGGGCACTAAACAAATATGAGGGACTTCTGAGTAAGTCTTGGTTTCAGATGCCCCACATCTCCAGGAGGGGAGATTATCTGGCCACTGTATCCTTTGGGGCAGCCTGCATCTTGCCTGTTAAGAACACAGGAAGCCTGTCTCAGCAGGAATGTCATGGTGGGGGTGGGGGTTTCTGGACTAAGACAGCTCCTCCCCGACCCCCTTCTGACCCTGACTTTTTCTGGCTTCATCTAAGCAAAGGGAACCCAAGGTTCATTTGTGCACTTGACAGCAGAGCTCTTGCTGGGGGCAGAGGGGGACAGAGCCCTTCCCTGATTGCTCCCTGAAACCTCAGTGGAACCTGGTGAAAAAGCCCATGGACCACATGTATCATGCTCAGGTCTGGGCAGCAAGTATGAAGAAGAACACCTTAGGTGACCTTCCATCTATAGGGACCTCAGTGTACCAGAAACACAATCGGATGTCCTGGCTGCTACTACAGCTGGGCAAAGTAGAACTTAGGGATGGAGCCCATGGAAAGCCCATCACTCTGCCCCTACCCCAAAACAAACCAAGCTCACAATGTATTTGAGTCTTCAGGGTCTCGGGGAAGGTGTGGCTACTATGGCAAGCCTCTGCCCAGCCTTTCAGAACACAGAAAACCATGCCAGTCCCTGACATCTGGGTCATTGGATCAGAGAGAAGGCTGTGCTAGGTTTGGTGTGTAAGAGGCTCAGGCCAGCAGCCTCCCTGGCAGAGCTGGTTTGTCAGTGGGGAGTGCTTTAGGGCTGCAGGCCCCTGCTGTTTGGACCAGCCAGATCCTGATACAGCAATAGAAGAAGGCCAGCTGTGTTTATTTGAAATGATAGTCTTGCAAGATGGTTTTATTATCCAAAAGAAATACGGCATCCCCCACCCCCACCCACCCAGTACAGAGACAATACCACTGCTAGAGCTTCTGTGGTGTGCCAGTGAGCCTGTAGGAATGCTCAGGTCAGGGCAAGTGGGTTCTCTGTCCCTGAACCCTGCACAAGAACAGAGGAGGAGACAGTGATAGATGCTTCCAGAAGCATAGTCTGAGGACTGCATTCAGGCAGGGATAGAAGATTTAAATGCCCAACTGGCAGGCAAGTTGACTTGGAAGAAACTATGAGTAGGGACCCTAGCAGGTTACTTGCTTTTCCAAGGGGTAGGCACAGGAGGGAGGGGTAGAGAGGGGGGAGAGTCAGGCCAAGGCGGGGAGCATTGACCAGTCTCCAAAGAGCCGGGCTAGTCCCTACCTCTTGTCTAGCAGGAAAGGAAAGGGCTAGGCAATGAGTGGGAAGTCCCCTGGTATCAGGCGAGATTACTAGGAGGGTCTACAGGCTTCCTCTTGCTCCGTGTGACTCCGTCTTTGCTGCCTTCCTTTGCCTCCCAAACCAGGAGTATCCGAGCGGCACGCTAGCAGCTCTGCGCTCCAACCCGATAATTTCCCTGAAGGTTTGTCGGTTCTCTGTGGACTCCAGGCCCTCTTGGCCGAGATGCTTCCTGGGCGCAGAGGCTCAACGTGGCTTATCTCTGGGCCCCAGCATGGAAGGATGGGGCTCTGCGTGGCTCAGTGTGTGGCAGAGGGCCCCCAGACGGGCTGAGTGTGTTCTCAGTGGAGATGGATGGTCGTTCTTAACACCCAGCCTCTGAGGCCTCTGGTGAACCGAGGGTCCTTAAACACATGTGGTGGAGCCCAAGGTCTTAGTCTTCATATGGGTTCTAACCTCGAAGCCATTTCCTCAAGTTCCGCCTATCCGAGCAAGGAGACAAGGAGCGGCAGAAATTACCCCAAATGAAAACGATATTAAATAATGGGACCCCAAGCTGCCTGTTCTCCTAGAAGTGGCTGACCATTCCCAAGGCATCTTTACTGAGTGTGCCAGCCCCAGAGCGAAGCCTCAAAGGCACTTACTGTGTTGCCACACAAGCCACACCCTCAGCCAACTCAGCCCCGGGAGCCAGGCTTAGCCTCCCTTAACCATGGGCCTCAGATTCGCTGACATCAGCCTTTTTGTGTCCCACCAAAAAGGAACCCACAGGGGACCACACGCCAGCCGGGCTCCACGCACCAATTTAGCTCATCCTGTGGCTCTCGATGCTCAGCCCAGTAGCCGCTGTCCACCCAGCAGACCCGGGTGGGGCAGTGTAGTGTCGGGTGGTATTATCACCTGGCCTGAGTAGCCTGGCACAGCTTCAGAGGTGGGCTTAGCCAGGCAGAAGCCCCTCTTCTGGAACTCACAGGGGCTGAGAGCCAGTATCCAGAGCTGAGGAAGGTTGCTTATAGGAGAGTCCAAGGTTAGCATTGTGGTGTCTGTCCCTTGAGCTGAGCCTCAGGGGTACCCTACCCCCAATCTATCCTACTGCAGTGTTTACACTGATCTCTCCTCTTCTTTTCTTTCCACTTGGCCTTCTTGGTGACTTCCTGCATCGTTCTGAATACCTGCGACCTCTGGCCTTTGCCCTCTGGCCTTCCAACTCATATCTCTCCTCAGCTGCTGCCTCTCCTCAATTCAGTGCGGCTGGCTCCACCCCCAGTCATTAAAAGGCGGACCTTTCAGGTAGATACCGTATGGGGCTTCCCCAGGGGCTTGGCACGAATGGGGGTCCCGACAGGCCAGCTGGGCTATCCATTATGCCAGAACCTGCTGCTTCTAACGGTTACAGCAAATTAGACAGCCATTGCCCGGGTGATGCCATAAATGAGGGAATACACAGCACACAGGCCCCCATCACAACATGGCACCTGACAGGCACCAGGCGTTCTGACATCCAATTTTGCAGGCTGACTTTAAGTCTCTCAGTGGGTCATGAGTCAAGGGCCACCATCTTTCTTGCACAGATGTAGAAATTAAAGTCTCAGAAGGTTTCAGCAAGTGGCCTGAGGTCACAGCCCATAAACAGAAGAGTAACGATTTACACCCAGGTCCTCTGTCTGTTCCCACTGTGCCTCGGCTCTGCAAAATAAGGACAGGCACAGTGACTGGGATAAAACTGAGGCTCAGAGACAGACTCCCCCGAAGTTACAGGAGTAGCAAGAAGAGCTGTAGACTTGAGAGCCAGGTCTCTGGTGCCCGCGCTCACACTCCCCGTGGGAGCTTAGACACACAGCCTGCTGCTGACTGCCCACACAGAACCTGGGTGTGTGCAAGGAGGGCGTTTGCAGAGCAGCCTAACCCACAACCTCCAAGAAGGGTTGACCAGGAGTAGGTCCCCTGGGGTAACCCAGCTTTGTCCCTACAGTCTAAGGTCACCTGAGAAAAGGGGCTGCCTGTCTTACTTTTCATCTGCCTTCTACGGCCCAGGGGTCCCCAGGGCCCAGGGAGCGGGGAGTAGCAGGGTGTTGAACTACTTGCCTGGTGAGTCCCATAGCTCGGGGTCATGGGTAGTGAAGTACCTGACTGAATGAGACTGAAACTCATGCCAACAATCAGCTAAAAATACAGAGTCCCACAGCACACGTGCAGCCTGTTAAGTATTTGGCCCATTCCTGTGGGCTACCGATCGCATTACCCACAGAATCCTCGAGAGCCTCCAAGGGCTCCGAGGGCTGCTCAGGAGGTTGCTAGCTGGCCGGGCCTGCTGACTGCCGCTCATCCTGCTGCAGACGGGGCCTGCTTTTAGAGCGTGCTTCTAAACACGCCCACCCCACACTCCGAGCACAGCTACTGTATAGCCCTGCTGGCACTAGCCACTGTTTGTTGGACATTTACTGGTGAGACCTTGCTTGTGAGAACTCTGCCTGATGGATTGTAAGGGGTAGCTCAGTTGGTAAATTGCTTATTGGGCAAGCAGGAAGACCCAGGTTTGGATCCCTAGGTGCACACTGGTAATCGCAGCCCTAGGTAGGCTAGGAAGATGAGGAGATCCCCGGGGGATCCCGGCCACACCACCTTGGCCTAACTGGTGATCTCCAGGTCCCAGAAAGAGACCATATCTCAAATGACAACAGCCCTGAGGAAGGACACTTAAAATTGATGTCTGTCTCACACGTACGCACACATGCACACACGCACGCACATACATACATACACATAAAAGCCATGCATGATTAATCACGTAAGCTGCATACCAGCTCCTTGTGGATCATAGCTTTCATTCAGTTGGTAGAGAAAGACCTTAGAGCAGTGGTTCTCAAGGTTCCTAGTGCTCCAATGACTTTAATAACACAGTGCTGACCCCCAACCATAAAAAAATTTTCATTACTATTTCATAACTAATTTTGCTACTGTTAGGAATCATAATGTAAATATCTGATGTGCAGATAGTCTTAGGTGACTTCCTTTATGTAGGGTCATTTGTCCCCAAAGGGATCATGACCCACAGGTTGAAAAACCATTGCCCTAGAGGGTCCAGAAGTGGACCTGGCCAGCACCTGTTGCTGTATTCTGTACTGCTCTGACCTGGTCCCCAAAGCAGAGTCAGCAGGAGTTGACCTCGTGGCTGCTGCAGATTCTCTGGGGGAGTAATGGTTTTATACCACCAGCCATCATGGGAGATGAGATGGCTTAGCCATGTCCCATTGATAAATCTGTATTGATTGTACATGCTATGCAAGATCTCAGGTTAGCAGAAAGGGGAAGCTTGTGTGAGAGCTGATGCGCTTAGCAGATGGTGCTGGAGACCACTTCCAATGTGCAAGGAAGTGGCTGGCGAGCCCTGCTCCAGAGAGCAGTGAGCCAGATGAAACTCAATGGCCTCTGACCTAGGGCCTCATTTGATCCCCTGAAACAGATAATCAAAACCAGCAAATGCTGAGACAGGAAACAGGGACCCTGTGCTTCCACCCTGCGGCTGGGAGGCGCGGGGCTGAGGTGGATGATGGACCCGCTACATTGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGGAGAGCAGAGCAGAGGAGAGGAGGACTGAGGACCACCTGGGCTGAGCTCTGGCATTGGGCCTGGCCAGGCGTGGGGCTCATGTGCAGGCCAGGGGTTGTCTCTTTTTCACTGTCTGTCTCTGCCACTGCTGCCAGGCTCCCTGCCCTGGCGACCATGTTCCCTAGAAGCCCCCACAGCTTAGTAACTCCGTGCCTGGGTCCTCTTCCTGCTGCCATTGGCCCCTGCATGCATTCACCATCACTGTCCCCACAGCATCGGCATCCGATCACCGCCCCACCGCCTTCCAAGCAGGTTCCACAGAGGCCTCAGCAGATGCATGGCACAGGGGGGCAGTGTGACCGCTGCTCCCAGATCATCTCTCTAACACATGTTTTCTCTAACTTCAG
Seq C2 exon
GGGGAACAAAGCCAGGCTGGCATCCAAGGCCCTCCAGGGCCACCGGGCCCCCCAGGACCAATTGGCCCTCTGGGACACCCAGGACTGCCAGGGCCTATAGGGCCACCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000552:ENSRNOT00000046537:11
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(8.3=55.6)
A:
NA
C2:
PF0139113=Collagen=FE(54.7=100),PF0139113=Collagen=PU(24.1=38.9)
Main Inclusion Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
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]