RnoINT0009988 @ rn6
Intron Retention
Gene
ENSRNOG00000018126 | Abca1
Description
ATP binding cassette subfamily A member 1 [Source:RGD Symbol;Acc:631344]
Coordinates
chr5:69857771-69862417:-
Coord C1 exon
chr5:69862174-69862417
Coord A exon
chr5:69861083-69862173
Coord C2 exon
chr5:69857771-69861082
Length
1091 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGG
5' ss Score
7.66
3' ss Seq
GTCTGTCTTCCTTTTGACAGGTA
3' ss Score
11.03
Exon sequences
Seq C1 exon
GTTTGGAGATGGTTATACCATAGTTGTACGAATAGCGGGCTCCAACCCTGACCTAAAGCCTGTCCAGGAGTTCTTTGGACTTGCCTTTCCTGGAAGTGTTCTGAAAGAGAAACATCGAAACATGCTACAGTACCAGCTTCCGTCCTCCTTGTCATCTCTGGCCAGGATATTCAGCATTCTCTCCCAGAGCAAAAAGCGACTCCACATAGAAGACTACTCTGTCTCTCAGACAACACTTGACCAA
Seq A exon
GTAAGGTTTCAGCCCAAAGTACCTTTAGCTACAGGCTTAGGATGCCTGGCCCTTTCTCCCCACCCTCAGCTTGAGAGAAGTTCAGATGGTCTGTGCTTTGATTCCTTCTCTGCTCTTACTGTCTACATTATACACATTTCTATGAACACATGCCAAGTCGATGCTTTCTACTATGTATAGTTACTGTGATGGTTGTGCTGTAGTCAGAATAGCTACTGTTGATTGCCTGTCATGAGCCAGGCCTTCTGCCAGGTGCCTCATCTCTTCTAAGGAACAAGATATATTATTGTAGTAATCTGTGAAACCAATTTGAGATCCCTGTCCTCCTTACCACCAACCAGAGTTCTCTTAATCCTGGAAATAAAAGACACAAATGCCATTTAATATACCTAAACAACACAAGGCTGGGCTTCTCCCTAACTCCATGTGGCTATCCCATTTTACTCTCCGATATCCCTGCATTATTACCTTTTAAAATCTATATTTCATCTCTGCTACCCCAGACATTTGGGGGGGGGAGTGGCCCCTGGGGCCACTTCTCTGACTCTTACACGACTGGATGATTTTCTGTCCTGCAGCTCCTAAGTCTGATCTCTGCTTCCCTGTCATGGTGATTCCGCTCTTTCTTCTCTTAGTCCCGGAAATCTAAAAGTCCCGCCTCCATCTCCCTGCCATTGGCTGCTAGTAACTTTGTTGACCAATCAAAAACTGATTGCATACAGGGACCCTCGGCGACAGGACGCACAGATTCCCGAGTTATTTGGGGGGCCAAATTAAGACAAAGTATTGAAACCAGTCCCCAACGACGTACCGCACAGAGCTTGGCAGTTAGTAGGCATCCAACAAGTGTTTTTTTCCTCTTAATTAATCGTAGATATGCCAAAGTGGATGACTGGTAAGTAGGTATACCGATTGAGAAGTTGGTGATGTGGAGTAATGTAGAGAAGGATTTCAGTGCTTTCGGGGCTTCTCGAGAATTCTCCCTTTCACGCAGGGTTTTCTATTTCGAGTACTTACTCAGTTCTGCGTTCTCCTAACTGACCTCCGATCCAGAGCCCTTCATGAGCGTCCGTCTGTCTTCCTTTTGACAG
Seq C2 exon
GTATTCGTGAACTTTGCCAAGGACCAAAGTGATGATGACCACTTAAAGGACCTGTCACTACACAAAAACCAGACAGTGGTGGATGTGGCTGTTCTCACATCCTTCCTGCAGGACGAGAAAGTGAAAGAAAGTTACGTATGAAGAATCCTGTTAACACAGGGGGAATGAAAGGAAGGGAGAGCTAGGTCTCCCTTTGCACCGGGTCAAGTGTTCCAGAAGAAAGCGTCCCGCGTTTCTGTGGAGTGGAACAAACTGGATTCTGTACTGACACTATTCAATGCAATGCACTTCAATGCAACAAGAACACGATTCCATTACAGGGGCAGTGCCTTTGTAGCCTATGTCTTGTATGGCTCTCTAGTTAAAATGACTTGAAGTTAGTTCATTATCTTATGCAGATGTGAAACTCTGGTGTGGAACCAAGCAGACTCTGGGTTTGGATTCATACTGTTTGTTCCTGTGTATTCTCACTGGGATTGCAACAACAATCCGTCAAGTAGTAATGGCCAGTGATAATCAACGTCGAAGGCATGTACATCCTCATCCACTAAGCCATGCTGACCCACAAACCTGGTTTCCCGGTGACACATCCATTGCTGGCAATGAGTGTGCCAGATTTATTAGTGCCAAGTTGCTCAGAAAGTCTGAAGCACTAAGTATGTCACAAACACTTTTGTGAAAACCGCCCTGCTGTCTGTTGACATCATTAAATATCAGGTGACAAAACGGTGCCGTGTGTGACTAAGTCCCCATTTTCCTTCTCTCTGATGAGCTGCTGTGGTGGCCGTCTTGTGCGAGATGTGGATCTCTGTAACCCAGGTCCTTGGTTCTGCTGTTCACTGTTGCCCATGTCCATGCCCATGTCCATCCCCATGACCATGCTCGTGTCATGCATTACCAGAGCATCTTTCTGAGACTTTTTCAAACACATTAGATCCCGATACGCAACAAAGGTCAGCAGCCAAACTGCTGGGGCTGCAATCAGCTGAGTTCAGGGTGTGGCAGGAAAAATCTGGTGCACTTACACGTGAGAGGTCTGGGTCTGTTCGTCCCGACTGTCTGCTAACACAAGATGGTATACTCCATCTCGAGATCCTTCGTTATTTGACAGAAACATAGTTCTTTCCAGCTGTTGGAATTAGCTTAGAAAACGAAAGGGTGGCATTTTATTTTGATGAAAATGTTTGCATTGCTCGTATTATTTGGAACTTTTAAGTTTTATCAATGCTTCTGGAAGCTCAGAACCAAACCAAACCTCAGTGCTCAGTCGCATAGAGGGATGTGGCCACACTGCCTCATGCCTTATTTTCCTTGGTAAATTTGCAGGTGGAATGTCCGACTAGCCCAGTGACCAGAAAACAATGTTGTGGTTAACATCTCAGACCATATTTTAAGATCCGGTAGAACACTATTCATTTCCAGTTGCAGATTGAGTATTTTTTTTTTTTTTTTGCGTACAATCACTGGGTAGATTCCTGGATGGGAGTGAGGGGGAGCTCGCAGATTTTCTGTGCCATTGACTCAGCTGACTGATTTACAGATACAGGCTGTTTTGTTAAATCCACTGAAAGAATACGGCCACACCCTTGCCTACTTGATAGCATCAGTACAAAAGCCAAGGAGGGTCACTAAACAACCAACTCTTCCCAGGGGAAAACCGCTAGCTTGAAATTTCTTGGATATAATTTATACTTGTGACCTTTGAGACCTTCAAACTATGGGCAAACAATGGGTTTAGCAGGATGTGAGACACCCATTTAAACCTCCGACGATCTCAAACAGTCCATCTCTTTACTCACTAACCAGTCATGAAAAACAGTCAGCTGTTCTACATGGAGCATTTTTCAGACTTTTCTAACCCAAACTTAATTTGCTTTCATCCGCAAGCAATGTGAAAAAAGAGAGAGAGAAAGAAAAACTTATTTCACCAATTCTCGATGTCATTCGTCTTCATACAAAACAAGACATGAGTAAAATTCCGGTATTGGGCAAAGTTCAAGTGAGCTTTTGATATCTCTAATTTCTTCATCTTCTAAAAATTGGGAAGAATAAGAAAGATTTCAGATCTATTCAAATTATGTTTATGTAACACTGTTATGTAACTCACTGCTTGAAAGGAAAAAAATGATGGTTTTGATACTCATGTCAACATAGGTCTCTAAAATGACAAGAAAAGTGTGTTTCCAGGAGCTATTGGCACACCACTATATTTTATCAAAGTTACAGAATTCAAAGAAACAAGTCTCTATTTTTCAAAATCAAACGTTAGTTGACTTCCTCAGCCCACTGTCATTGTGTCCTAACTTTTCAATATACTACAGCCCTGAGAAAAATCTTTGTTTTAATCACTGATTTTTGAGGCCACATTAAAAAGAAAGAATCAAGCAACAGCAAAAATAAGGCACTATTTTGGAAAAGATTCAATTCAGTGTAGATTTAAAATCATTCCTAAAACTAGAGACAATCTGTAGGTATTGTATTACCTTTTATACTATCTGAATAGTTAATCTTCAGTTTTCCTTTGTAAACGTAATTATCTTAGATATTTAAAAATCAATCTTATCTTCAAATAAAATCCCCTATGGAGATGTGGTACGTGAGTTGAGAAATTCTCAAGCGCAAACACTTCTGGTTTACTATTTTTTTTTTAATATTGGAAAACTTACTAACTGTGAATATGAGAAAGACAAAAGAAAGTAAGTCCTCTCGCTAGACATCCTAGCGCAATTCATTTTGAAACAAACAAGGAAACCTCAAACTACTGTATTTAGGTGTCTGTACTGCAAACATATGCCTCATGACAATGTCATACATCAATCGCTCTCTGTAAGCAGGCATTGACTTAAAGGGATTGTCTGTTGTCTTCTCACGGTTGTATATATCAGGTAAAATTGTTCCAAAGAGCCATGTGTTGTGTAATGGGGAACCACTTTGATACTGAAATACTAATTTGTACTCTCGTTACTATTAACTGGTAATAGTGTAATGCCACAGTAATACTGTTCCGATTGAAAATTGTTGCGTCCCTTTTTGTAGAACATTTATATTTCCATATAAGGATGCGGTATGTTCTTTCCCCGTGTACCCTAGGATGAAGCTGTTTTTGTGCTTTTTCTTTATCATTGGCCCTCATCCCAAGCACTTTATGCTGTCTGTAATGGATCTATTTTTGCACTGGAATATCTGAGATTTGCAAAACTAGACAAAAGTTTCAGAGCAGATTTCTAAGTTAAATAATTTTCATTAAAAGAAAAAAACTGAAAAAAATTGTATTGTGAATAACTTTATACGAAGTGTTTTTAAAAGCCTGTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018126:ENSRNOT00000024564:50
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTACGAATAGCGGGCTCCAAC
R:
TCACTTTCTCGTCCTGCAGGA
Band lengths:
343-1434
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]