RnoINT0042223 @ rn6
Intron Retention
Gene
ENSRNOG00000015220 | Crtac1
Description
cartilage acidic protein 1 [Source:RGD Symbol;Acc:621085]
Coordinates
chr1:261531116-261539834:-
Coord C1 exon
chr1:261539666-261539834
Coord A exon
chr1:261531262-261539665
Coord C2 exon
chr1:261531116-261531261
Length
8404 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
CCCTCTCCTTCCTCCCACAGGAA
3' ss Score
14.08
Exon sequences
Seq C1 exon
GGCTTCAGCAACAACTGGCTGCGTGTGGTGCCACGCACTCGGTTCGGAGCCTTCGCCAGGGGCGCCAAGGTTGTACTCTACACCAAGAAGAGTGGGGCGCACCTACGGATCATTGATGGGGGCTCCGGCTACCTGTGTGAAATGGAGCCCGTGGCACATTTTGGCCTGG
Seq A exon
GTGAGTCGGGGCCCATGGGAACAGTAGCAGATTCTCCACAGGAGAAACGGGCTCTGTGACAGCTGTGGGATGTGTGTAAGCTCCCGCTCTAAAAACGTTTTTGTGGGCCGTGTTTTTAGTTTTGTATTTACTGTTAGCAGTGGGAGCATCCATGCATGCGGTGGTCACAGCACAACTCTTGTGGAGTCTGCTCTCTCTTCCACCTTTATGCGGGTCCCAGGGATTGAACTCAGGTCACTGGGCTTGCATGGCAAATGCCTCTACCCGCTGAGCCATCTCACTGGACTATTTGGTGGATTCTTTTGAAATAATAAAAACTATTAGGTATGCCCCAACAGTTACAGGTGCTCCTTGATCTATACTGGGGTTTCCTACTAAGGTAAGTCAAAAGATCTTGATCGGAAAGGCATTGAGTTGCTCAGCCTACCAAAGACGTCCTCAGTTAGCAGCATGGTATACCGCAGAATGTCAGCTGTCCCCTTCATGACTGTTTACCACTGCCCAATGTCCCAAGGGAGGGCCATGATACATATTACTGGACCAGGAAAAAAAAAAAACACATTCATGGTCCTAGTTCAGTTTCTAATTGCATATCTCTTGGTCTTCACCTCAAAAAGTCACAAATGCCAGCACCAGTTGGAGGGCAATCTGTAATAATTCCCTAACTATGTATCCCAGAATGGGAAATTAGACACAGAGATCTCTGCACTGTTATTCATAGTAGTGGTATATCTGTGAGACAAAAAATCAAAAGCAATGTCCAGTGGGCGGTGGTGCACGCCTTTAATTCCGACACCCAGGAGACAGAGGCAGGTGGATCTCTGAGTTCTAGGCCAGACTGGTCTCCAGATCAAGTTCCAGACCAGCCAGGGCTACATGGAGAAGCCCTGTCTCAGAAACAATGCGGGCGTCCTGTGTTTATTGGTTAATGGCTCATGGTTCAGCTTGCTGTGGGACTCAGATTCGACCCGGCCATTAGAGCTGTTTGCTGAGTAAAGAGTTCTTGTCTCCAAAGTCACCTTCCCAAAATGATGAGGTCGTAGAGCTGAGGACAGACGGCTCCCGATAAGGAGATGCTGATGGGCAGATGCTGCAGGGATGGGCATCTCTGCAGGGATGGGCAGTGAGTGTCTCCGTGGCACTGGCTACATGAATCTAATGCACCGTCATGACAGAACCATCCACACACCTGTTCCCATGGCGAAGCCCTGATTTCAGCGTGATACAATCCTAAAGCAAGCCATAACCACAGGGGCAACTGTGTATGCGGACTCCTCTGTGCTATCTGAGCTACCTACTGTGTCTCCGGCTATTTCAAAATAAACCATTTTTTAAAAGCCTGGAGGTTAAAGAAGATGTGAGAACTCCACGGGGAGGATGCAGGGTTTACAATCAATGAGGCAGAGACCGAGGGGCACTGGGGAAGGGGCGAGCCGGGAGTTAACGCACTTGAGTCAAAGATTCCCAGGTGCTACCCAGATGCTTTGCCATGTGTTAGCATCTCGTGGAGTGATGTGATCTTAATATAAAAAGATTAGGCAACGTGTTCTCTAATCGATAAGTGCATACCACCACTAATATTAGGCACACATCGTATGTACACAGGAAGGAAAAGCAAAGAGCATACGCACTTGATTTCATCTGCATGGCTAGATCACTGCAGGGACTGCCACCTGTTCTGGGCACAGTGCAGGGCACTCAGTTCTCATGATTTGAACCTCATGAGTACCCCTGGTGGGCATTATTACCTCCATCTTGCAAATGTGAGAAAAACTGTGGATCCTAACGTTAGAGGAAGACTGCCCAGGCGCTCGTGATTCTCAAATGACAGAGCTGGGATTCAAACCCAGGCCTGCCTGAAAATGTGCTTTGTGATTCCTACCATATGTTCTAGTATATGCATGCACATTCTGGTTTTTATAGAGAACACATAATATTTATGTAGTCTGGGAAAGAAGCAATAAATATTTAGGGGACCCGGGCCTGGTTATATGAGCATGTTCCCGGGCTATTGCGTTTGGATAGGTTAGCCTGGGCCTGGGGCATCTGTCACTCCTAAGGCAGCCACTTGCTATGCTGGCCCTAAAGGTACAGGCTGACTTTTAAACATGGAGTCCTCCCTCTCACAAACTAACAGTAGCTGACACGTAACAATGTTTCACATGCCCGGGCTTTGCCTAAATTCTTCATCAATTCTCTTGGGAATCTGATGAATTATAAGCTGTAGTCTACACTTTACAGAAAACGGAGGTTAAGGCTAAATGCACTGATTCAGTTCACAGCTCCTGAGGATAGGAAAAGGCTGGCTTTGGACTCCTCCTTAGACACTGAGTTGCTGGGCTCTGTGACTCCACCTCCTGGGTCCTCTCTGCCTCTCTCTTCCTGACAGCTATCTGTCTATCTCCTCAGCTTCTGGGTATCCCAGAAGGCCATTCAAGCACTAAGGTGGCTGCCGTCTCAAAGGTGAAATGTTTATCAGCCCCGCTCCACCGGACAGAAAAAGAAGTTGAGGCTCCCAGAGCAAACCAGCAGAGAGGCAAGAGCAGAGCTCAGACTGTCTGGCCTCACATCCTGCTGATGGCCTCTGCTCTTCTAAGATATGTATTGGAGACCTCCCTGGGTCCTTTCTCTGTCCACAATCTGTCATCGCCATTAGAGCCTGCTTCCTTGACTGGACAGCTCACAGGATCATCCACCACCCATGCTTGGGGCTGTCTACACTGCATCTGGCTGGGGGCCCCTCCTGATGCCGCCCTCGACTCTAGGCAAAGAATTGGATTTGCTGTTGGTTTACATCAAATTGCCACAAGGGTCCCACACCCTACCCTTCCCAGGCGCCTCTTTTGTAGGGCTCCATTCCCAGAAGGACCCTGAAAGGAGGCCTATTCTCCAGATCGGACCCTTGTTAGTTGCCTGAGACGGGTCTCAGTCATCAGAGCAGCCTCAGGGATCATTCCAGAAGCCTGAACAGTGAGGCAGGCCAGCTCTGTCCCTGCCTCTTCAGAGCCCCTCAGAATTCCAACAGCTTCTTTATGAGCTGAGCACAGAGTTGTCCTTCCTAAACGATGGGGAAGCCAGCTGTAGGGCAGAGCAGGCAGGCGGAGAAACCAGGCATTGGGATGACTGAGGGAAAAGAACAAGGGAAGAGAAAGAGCAGAAGCAGAATGAAAGCGAGGCAGAGACACAGGGAAAGAAGCAAGAAGAAACGCTCTAGTCTGCTGGGTAAACCCCGAAAGTCTCACGCAAGGCTGACTCGGATGCACCCTGGACTGACATGGAGCTTTGAGAGGATGGGACAAGTGAAACCAACACTGCTCTGGACAGCTTTGCCAAGGAGAAGACCGGACCAGGGCGGGGTGGCTTGCAAAATGGTAGGAACTTAGAAGGCAGGGGCAAGGTTGAGAGCATTTCAGAGGCCCGGCTAGCTTGAACCAAGGCCCAGTGATGGGAATATTCGGTTGGAGGGATAGGGGCAGAGCCTGGAAAGTGGGGGCTGAGCCTAGCTCCCCAGGGTAGGGAGGGGGAGCTGGACAGGGCATGAGAGACAGGAGTGTCCTGTCAGACTCAGGAAAGCCAGAGGCAGCACTGTAGAGAGAGTCAGTGTGCAGGGGCAGTATCCCCCGGTAACACTTGTTCTTAGAGGCCTCTTAAAAATGTTCTCTTGATTGTGAGAACAATGTGAATTGATTATAGGGAAATGAGACAATGCAACAAATCATAAAGAGAAGTAAAAATCACCCACAATCTCATCACAGTGCTTGGAATATTAAGTAAAAAACACAAACATCTCCTCCTTCACCCCAGCCCCATTCGATTCATTCATCCCGTTCATGTGCACTGAACACCTACTAGGTGCCCAGCAGTAACTGCATCGAGAGCCTTGCCTTGAGAACCCCTGTGTTCTAGTGAGAAAAATCATAAAATACACGATGAACAGAGTTAAGTAGGTGAAATAGACCATGTTAAGACTGTATTAGGTGCTACAAAGAAAGAAAATGCCAAGCAGGAAAGGGGAGTTAGGAACTCGGGGAGAAGTGACAACAGCAATTTTCAAATATGAGGCCAGGCTTCAAATAAGCCTTTCTTCCATGCAACGCACACAGGGGCACATATATAAATATACATACTACTTAGGGGGTTTTTGTTTGGTTGGCTTTGTTTGTTTGTTTGTTTGTTTGTTTTTAAGAAAAATGACAATACTTTCTCTACTTGCTTTTTTACTGCCCTGAACAGTGAGAGCCTGGCTGTCCCTCCAGGTCTATGCGTTTCTTTTATTTTTCCTCCAGCGCCTTGGAGCATCGCACTTTACGGCAGCATTCATAATTTATTTACCAAGTCCCCTGTTGATGGGCAGCTAGAATGTTTCCAGTTCTGAGCAGTTGGGCGAGTGAGAAGGTGGATGTCTAGAAGGTGTCTCCGAGAAAGGCCTGCCCTAGGGTTCTGAATGGCTGAGAAGTAGAGTAAGGCTGTGTCCAGAGGCCAGATCTGCAAGATGCCCTCCCAACAGCAGGCGCACAGTTCTGGCTCAACCTAATCCACCCTACTCCCTGGTGGTCCTCACTCCACGAATACCTCCCCACTGCTCCTTTCTGATGTGGTGAACTGGTACTGGAGGGCAAGCAAAGAGGTGAGAACATAGGTATGCCTACCTCAGCACTTCCAGTCCACGGGGATGCTGGGTCAGACTCCCAGAAGCTGCACTTGCTGAGGCACACCTGCCTGCAGGTGCCTGTCTGCATGCTCCGGGCCTTACTAGGTCTGTACAGGAACACTAAGAACAGTAGATTGATACCTTTCATGTAATCCCACCTTCCTCCCTAGAATACCTGAGTTGTGCTACACCAGGCAGTAAAAAACAAAAAACGCTGGGACCTTTCTTAGCCTTGATCTCTAGGGGTCCCCTGAGAACCCATTCAGCTATGCAGGGCATTATGGGTCTTGTTCCTCCTCAGCTGACCCTGCCCTCACTCCAGGAGCCTCACTCCAGGGAAACCTAACCACATTCAGCAGTTCCTGCACAGCTGCCCCCCCCCTTGTCTCTGCTCCTCTGGGGTGCAGACCACCTGCTGGCTTCATAAATAAGCCTTTCTGTTTATAGTGTTGAATACTGCCCACCCAGCCCCCAACATGGCTGCCTCTGCATTTCCTGACTGCCAGTAGGCTGAACCAGTGCACAGCCAAACCCAGCAAATACAAACGAGTCCTGCCAACCCACTTGGCCCCTGGATGCCCCCACTGTGGTCACCCACTCAAGTTCTCCCAACCCCACGCATTGATACCTTCCCACCCTCCACGCCCCCTCCACCGCACCTTCCTTTCAGTTAATTGTTTGTAAGTGACTCAAAGCTGCCTCCAAACCGGCTGGTGCTCATTTAGGGAAAGAAAATTCAGTGGCCCACATAAAAATGCCTTTATTAAAGTGCAAAAATATTCCACCGACTGTATTCCCACCATCTGTTTTGCTTGTAATTCTGAAGAGCACAATTCCATGTGGCTCCCTGGCCTTTGTCCTTTCAAAGCTGCCAGAGGCCACTCCCTGCTGTTTCTGACCTATGTCTCTACTGGGTAATGGTGCCTCTTAGGCAGACCCCCATCACCTACCCACACCGTTCGCACGCGTGCATGCGCACACACACACACACACACACACACACACACACACACACTCGCACACACACTCGCACACACACATGCCCAGCAGAGTGGCTGCGTCGGAGGCCAGGAGCCAGGTCCTCCAGCTTCAGGAACACTGGAGATGCTGGAACAGCAGCCTTGGGATGAGGAATCTTTCTGCCTATCCGAGGACAGAGCCTGGGTCCTGCCCTGGCTCTGATATTCCCAAGTCACTTCCTACCTTGCCAAGCCTTGGTGTCTAAATCCAGAAAATGGGCATGAAGCCCAGAGTTCCTCCCTAGACTCCTGCCCCCCACACCCCACCTAGGAACATTCTTCCATTCTGCTTCCCCCAACTTCGAACTTCTGCACCTTCAGACATAACTTGCCCTTTCACACCCTCGACCTTACCAAGGTGCTCCCAACCCTTTGAACACTTTTCTTCTCTGTCTCTAACCATTTGAATCAGCCCGCTGTTCTCACTGAGAGTCAGCAACTCTGTCCCGACACCTTCCTCATTTGTTATGATAACATTGTGATCTTTTTGCCCACAGCCATCTGCTTCTTCTAGCTTGCTTGAGTCCTTTCCATTCAAGGTTGAATCCTAGATCCCTGTTCAACCTTTGATACATGGTGGCCACTGGGTAGGGGGCAGTGTAAGATGGGTGGAACTCTGGGGTGACTGGGTAATTTCCCTGGCCTCTTCAATTCTCAGTGCTCTGGTTTCTAAGGTGAAGATGTGTAAAGGTGTGAGGAGTGGTACATTGACACCGTGAAGTGTTGGCTCTGGTCGGAGCATGCTGTCAGCGTTCAGCGTTACTACTGAGCTGTCTAAGAGCTGATACTGATCAGAGTACCGAGGGTTGATACATAATCAGTGGGGAGGTGTTCATGATCCAGGGGAGAGAGGCTGTGCTGCCCAGGGGCCGTGAGCCAGCACCCCCAAGTTTCAGACAAATAAGCCAAGGCTGTAAAAGGATGGCTTCTTATTTATCTAACAGCCCCTCCCTGGAGCACAGGGAGAGGACCCAGTCCAGAGCCACATGTCCCAGTGGGGGCTGCAAATTTGAGTTTATGAATATTCCTCAACTCTTTTGAGTTATTTGTGGCTTCAGGCTGTAAAATGTATTCATGGAGCTGTTCTGTTGGCTTAGGTGAGAAACACTTGCTTTTGTCTCTTCTTTATTTTTTTAAGGGAAAATGTTTGCTTTTCAAATGTGCCACTTAATTTGGGAACTTGCACACCCTAAAAATGCCAAATTTCATGTGCCTCACGATTCTGTTTTAAAACAGAAGAATTATATTTGTCCTTCTTAGGTCCTTTCCCAACCTGGCACTGGGAGTTGTGAGGATAGCAGTCAGGCCTGCTGAGAAGCTGCCTCTCACTAGATAGGGGTTTCTCAACCAGTGGGTCCTGACCCCACTGGGGTTGAAGGGCTCTTTCACAGGTGTTTCTGTTACAATTTATGATGGTAAGAAAATTACAGTCATAAAAAAATTAACTTTTTTACAAAACATAATTTTATGTTTGGGGGTAACCACCACATGAGGAACTGTATTAAAGGGTTGCAGCATTAGAAGGGTTGAGAACTGGTGATCTAGATGTAGCGAAACCTGGAACAAACCTTGAGCTGTTCAAGCCCCTTGGGGATCAGTGGGAGGGGCAGGGCTGAAGGTTCTAACCCAGTCCTCTGAACCCTTCCTACGACTGTCTCTGCACTCTTCCAGCCGTGTGTGGGTACCACCCGCCTTCCCTTACAGCTTGAGAGAGGCTAGCAGGTGTGACTCATCAACACCTAGGTCACCACCATTAGCCAGACCTTGCCACAGGGCTAGCCTGCTTCAAGGCTGAGCAGACCTCGGCAGTGTCTGAACACCTGACCAACCTTCCCAACCTGCTTCTCCGTGTATTGATATAGCATGCTGCTGCTGTAGGGGATGTGTGTGACGGATTCACAAGGGACACTGTCTGAGCTTCACAAGGTGTCTTTTGTAAATAGCTCAGACCTGCAGTGGCCTTCCTTAAGCGCCCTCAACCCACCTCTTTTCTGGGTCTTTACTTATAGCTCAGCTCAAATGCTTCCTCCCCAGGAGTTTGACCCTGGCCACTGAACAGGATCTGGCCAGCCCCCCAACACCTCCTCACCCTTTCTTCACAAGGCTTGTCTATCTATGCCATGATTTATTTATTTCTTTGTCTGTTTACCCGCCTCCCAGATGGAAAGGGAAATCCATGAGGAGACATTTTCATTGACAGGAGAGGGGCTTGGCTCCTAGCATTGCTCCATAAATCTGAGGCAGGCTCGGGAGGTCACACGAGCTGGCTGGAGAACTAGGATCTGTCCCCAGGAATCCCCACCATGTTTTCTCAGCACACCAAGCCAGTGACAGAGCCAGGATGTGAACCCCTGGCCTGAAGTCAACCTGCTTCTCAATGGAGCCTTACAGCTCCCCCAAATTCAACCTTCTGGTGCCTGACCTGTTGCCTAGAATGTTCGAATATGGTAGCCACTAGTGTGGCTGTTGAGATGTAAATTCATTTAAATTAAGTAAAATGTTAAATTCAGCCTGCATATGGTCAAGGGCTAGTGCACTGAACAGGGCAGAAACTGGGCTTTTCCTTCACTAAAGAATTGACTGAATGGCCCCACAGAGGAGCCTCTTTCTTACTCATTCCCACAGTCCTTAGGAGAGTGCAGTCATAAGTTACTAACCATTGTTAAATTATTTGTGCGAGTACTCCAAGCGGCCCTCTCCTCTCCGCTCCTGACCCCTCTCCTTCCTCCCACAG
Seq C2 exon
GAAGGGACGAAGCCAGCAGTGTAGAGGTGACGTGGCCAGATGGCAAGATGCTGAGCCGAAGTGTGGCCAACAGGGAGATGAACTCGGTGTTGGAGATCCTCTACCCCCGGGATGAGGACAAACTTCAGAACACAGCCCCACTAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000015220:ENSRNOT00000020568:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.102
Domain overlap (PFAM):
C1:
PF0183918=FG-GAP=PD(2.6=1.8),PF075937=UnbV_ASPIC=PU(53.4=68.4)
A:
NA
C2:
PF075937=UnbV_ASPIC=PD(45.2=67.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
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]