DreINT0023544 @ danRer10
Intron Retention
Gene
ENSDARG00000074635 | abca1a
Description
ATP-binding cassette, sub-family A (ABC1), member 1A [Source:ZFIN;Acc:ZDB-GENE-031006-12]
Coordinates
chr1:51988841-51993669:+
Coord C1 exon
chr1:51988841-51989084
Coord A exon
chr1:51989085-51990907
Coord C2 exon
chr1:51990908-51993669
Length
1823 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGA
5' ss Score
7.61
3' ss Seq
TTTCTGTCTGTTCATTTCAGGTT
3' ss Score
11.75
Exon sequences
Seq C1 exon
GTTTGGTGACGGGTACACCATCATCCTGCGGGTGGCAGGCGCCGATCCGCGGCTGGAGCCGGTGATGGAGTTCATCGAGCGGGAGCTGCCGGGCAGTACGCTGAAGGAGAAACACCGAAACATGCTGCAGTACCAGCTGTCCTCATCCCTGACCTCCCTCGCTCGCATCTTCAACATCCTCTCCAAGAACAAAGAGCAGCTCCACATCGAGGACTACTCCGTCTCACAGACCACTTTAGACCAA
Seq A exon
GTAAGAATACCACAGGCCTTCTGTTTTCAGTCATCCCTTAATTTGAAGTGTAATCAAGCTGCAAAACAGAAACATTGGATTGACAAAACAAATATTAAAATAAGTTTACCAAAATATGAACATTTTACCAGCATACACTCATTTATTTTTATGAATTTCTTTCTTCGGTTGAATACAAGACAGGATATTCTGTAGAATGTTGGGGAAAAGCGGACATTGACATCCATAGTATGAACTAACAAACACTACCGAAGTCTATGGGTGTTTTTTACTTGATTCTTCAGTTTATCAAGCGGAGGATAAGGAACAGGGTTCGTACGGGTGCCAAAAATATATTTCGGAGCATTTGTGTGAATGCATAAAATTATTGGAGGGCGACTAGTTTTCATTGCAAAATGTTGTGTATTTACGAGACATTCACGCCAAATTTTTCCCTAAAAACGCCAAACGCAGCACTTCGAAATAGTTTAAAACCGTTGACATGTAACTTTATTTGCAAATGTCATCTTAATTGCAGGAACGGTCTTTTCATTTGCTTTTATTCATTTTTATTTATTTATTTTTATCATTTTTGGGTGAAATCTCCCAATAAATCCATGTTTCAAAGTATTCAACAGTTTAAGTTAAAATGTCATATTGTGTTTAATAAAATAGCACAATTGATTTAAATGTAAAAAACTACATACAGCGTATATAAACATAACTTAATGTGGTTGTTTATTGCTGGAAAAGCATAAAAATGCACCTTGAAAGAGCTTAAAAAGGGCTGGAATTTGAAGTTGGAAAAGGTGTAAGAACCCAGAAGGAAACAATGAGTTTTTTATTTATTTTGTGTGAACTCTCCCTTTAATACCATGTGTACATAAACGGGGCCCGAAATTGTTTTATGGGATTTTTCAGTGACATTCAGGTTTAGATGTCAATTAGCTTGTAGTGCATCAATTGCTGGAAACACTAAAAAAAAAAAAAAAAAATTTTTATTCACCAAGAATCCATTTATCAAAAGTTACGTAAAGTAAATTTATGCTACAAAAGATTATTACAAAGATACACCAAGATCTTTTTTTTTTGCAATTAATTTTTTTTGCGACTTTTTCGCATACAAAACTTTTCCTGATCATCAAATCATCATCTTTATATGATTTCTGAAGAATAATGTGACACTAAAAACTGAAATAATAATGCTGAAAATTTCAGTTTTGCATCACACAAATAAATTACAGTTTCCTTTACATTAAAACAGAAAACTGTTGTAATAATTGTAATAATATTTCACAATATTAATGTTTTACGGCATTTTTATTAAATAAATGTAGCCTTGGTAAGCCAAAAACAACAAATCTTGAACAGCTTAAGCACTGGTGTAAAATTTTACATTTACATTTTACATTTAGTCATTTAGCAGGACAAGGAAGCAATTTACACAACTAAGAGCAACAATGAATAAGTGCTATAGGCAAGTTTCAGGTCTGTAAAGTCTAAGAAGGGAAGTATTAGTAGTATTAGAATTTTTTTTTTTTTGGTACAGTTAGTGTGATATTCAGAGAGGCTATTGCAGATTAGGAAGTGAAGTGGAGATTAGGAAGTGAATTGGAGATGAAAATAAAAATACAATTTTGCAAAGAACGAAATCAAATGATTAAAATGCAAATAAAAGCTGCTAAATAACTTTTGGACTTTAATGTTGTAATAATTTAATTTTGTAAATCTGCCTTGCAACAGTACATATTGTAATACACAGCGTTATACAAAATAAAGTACATAAAAAATAGGGGAATGCAATCCATTGGGACTTAATGCATCTTTCTGTCTGTTCATTTCAG
Seq C2 exon
GTTTTTGTCAATTTTGCCAAGGACCAAAGTGACGAGGACCACTTAAAAGACATTTCCATGAACAAAAATGATGCCGTTGTGGACATTTCGAAACTGAACGCCTTCCTCACAGACGAGAAGGCCAAAGAGACAGTGGTGTGATCTGGTTACAAAAACCTTCACGGGACTAGTGTGTCATTTTTTGTACTACTTTTTAGTTTTTTGTTGTATTTCAGCAGTGTGTTTGTGTGCCCGGAAATGGGCGCTGGACCTAAAACACACACTACTGAAACAAACCAATGCAAATCAATGCAAAAAGAGAAGAAGATTGGAGTAAACACTGAGGAAAGTCGAGCCTGGCGCTCACCACTCCCTCATGGTGAACTCAATGAAACTTGAAGCTTTTCGCTCCACAATCGGTGAATGTTCAATCGACGAAAGACGTCCGCGGAGTTTCTTTCGAGAATCAACGAAACACTGCCAATGAGATCCAGTTCAGGGCCGAAGTTCATCTCCTCATCTAACGCAGGCTTCAAAACACTTTGCATTTCAGCAACTATTCTTCTACGTTATTTTTTTAGATATATGCATTTTGAAACTATACTCAAGTGATTTTGTTTTCCGATGTGCAATGTTTCACTATTGTTGTCAAGTGTTTTGAAAGTGTGGTGCCTTGAAACAACACTCCGCTATTGGACAGCAGCCGTAGAGCGCGCACTCTCAGTGGGGTCTTTATCTAACGTCTCATGTGACGACAGAGCGGACGGCTTTCGGAGTTTATTGCATGCTTTACATGGATGCCGTGTTTAGGACGCCATCGTAAGCTCAAGCATGTTGTAGCTTCATTACACTGAAGTATTTTCGCGTGGGTATCAACGGATGGTCGCTGACTTTCGGCGGGAATTGTTTTTTTCGTGTGCGAAACAGGCAGAAGTTCGTATCGTGAATCTGTTCCGAAGCAATTCAAGTGTCCGTGCCAAAACCAGGTCAAGTGGTTCAATATTTTAGCGAAATGATCATATTATAGAGCAGTGTTGAATATTTTTTGTTGTCTTGAACTAAAACAAGAGTTTCCTTGTACAGTAAGGCCTGGAGAGACATCCGTAGGCCTCTGATACAGATTTAAAGGGACAGTACACTGAAAACAAAAAGATGATACTGCCATCGTTTACTTTCTGTCGACGATATTTCGAAGAATGTCTCTCTTTAACTTCCATAGTAATTGTAGCTGCATATAGTTCCATTGTTGGTTCTGACGCATTTATTCCTTGAACAGTTTGATAATAAAATGAAATGTCCTTACCTTTAAAAAGAAATTTGTATATTCCAATCCGTTTATTGTCAATTTAGTCAAAATTTAAAAAGTAAACATTAAAATTAAGTATGGGTGACGTAAAACTGATGTTTCGACACAGTGTTTAATCTCGAAGTGCAAGTATTCCGAAACACTGCATCGAAGCATGATCCGAAACACCCAGGTCACGTGAGTAATGTGATCCAAAACACCCAGGTCACATGACTAAGGTGATTCGTAACACCCAGATCACCTAACTAATGTGATTTGAAACACACAGGTCACATGACTAAGGTGATTCGTAACACCTAGATCGCCTAACTAATGTGATTTGAAACACACAGGTCATGTGACTAAGGTGATTCGTAACACCCAGGTCACTTAACTAAGGTGATTCGTAACACCCAGGTCATGTGAGTAATGTGCTTCGAAACACCCAGGTCACATGACTAAGGTTATTCGTAACACACAGGTCACGTGACTAAGGTGATTCGAAACATCCAGGTCACATGACTGAGGTTATTCGTAACACCCAGGTCACGTGACTAAGGTGATTCGAAACATCCAGGTCACATGACTGAGGTTATTCGTAACACCCAGGTCAGGTGACTGAGCAATACACAAATATGACCACTAGGTGTAACTCTAGAGACGGGTTTCAAAACGTTTCGAGGCTTCGACACATTTGCTATCATGAAGCCTCGCTTTGCTCACTACTAATCAATAAAAACATACTCAAGTCCATCACGGTCAAAAAGTACGTTTGACCTTCTTCCATTCCCCGCAGGTCATCGCTAGGAGAGCATAACTACATTATACACCATCTAGTGGTGTGAAAGAAAATTACAACCAAAAAAATAAAGGCTCCTACAGTAGTTATGTTTTTCTGCTATGGTAGTCGATGGATGTCAGGGAGCAGCATTCTTCAAAATATCTTCTTTTATTTTCGGCAAAATAAAGAAACCACTCGATGGAGAGTAAATGATGAGGCCATTTTCTTTTTTTTGTGCGTGAACTGTCCTTTTATTAACTCAGGATGTGCCTCTTTATCCTGTGTAAACGGTTTGTTTAGGTTTATTTGACCACTTTTACCATCGTGACCAGTGCTCTCTACAGCACCGTTGTTGATCGCCTACAGCGAGAAGTGACCAAACGCAATGAGGTGCTACTGATTGAGTAGATTTTCCAAATCTTTGAGGTGCTGTTTGGTCAAACACCTTCAGAAATTAGACAACAATCCTTAATGCACATTTAACGACGTGGAAGAAGAAACGAAGAAGAAGAAATAAAACTAGTATTGTCTTTGGTCCAAATCTGAAGCACTTTATAGCAATGTTAAACTGCTCTCGATGGTCATCATTCACAAACGGGATGTTTTCTGTTTAATGAAAGATTAATAGGCTATTTTAAAATGTCCCGCCATGGCCATTATTTTCTGTGTTACGATGTATGTGTTTACATTTGAAATATTAAAAAACTATTTCAGTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000074635:ENSDART00000142465:48
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.065
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTCGCTCGCATCTTCAACAT
R:
TTTAGGTCCAGCGCCCATTTC
Band lengths:
343-2166
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]