DreINT0071461 @ danRer10
Intron Retention
Gene
ENSDARG00000060631 | garnl3
Description
GTPase activating Rap/RanGAP domain-like 3 (garnl3), mRNA [Source:RefSeq mRNA;Acc:NM_001128527]
Coordinates
chr5:32778361-32781680:-
Coord C1 exon
chr5:32781566-32781680
Coord A exon
chr5:32778466-32781565
Coord C2 exon
chr5:32778361-32778465
Length
3100 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGA
5' ss Score
6.65
3' ss Seq
TGCTTTGCATGCTGGTCTAGATT
3' ss Score
6.42
Exon sequences
Seq C1 exon
CCATGGGAGTCACAGTCGTTCTGCAGCAGCTTCCCTTATGATATAGTCTGTGGAGACTCATGGGGTCAGTCATTACTGGTCGCCACAGATTCAGCAGGAGTCATGCTGCTGGAGG
Seq A exon
GTGAGAATGCTTTATCACAGCTGGAGAAACTGGCAGACTTCTGAAAATTATATAGAAAATACAGGCTGAATGTAACTTCTGCCAGCCTCTTTTTGACAGATCCACATGGATCAGATGAATGGGCATAAAATTTGAACCGAATGAGTTTTATACTTCCTTAAAGAGGGAAATAACATGAAAATTCTGAAGAAAAAACAACAACGCAACCTTTCATGGAACACAAAATAAAATGACAATGCCTTTTTATATACAGTACAGGGAACAACAACCTGTCAACCTTTTTAATTTAGATATTTTGCAAACTACTGATGAAACTATTTCGATACATAATACATGTCATTTAGTGTGTGTTTTTTACATGAAAAAACAAATAAGGTGCCAGAAAAGTTAAAAAAATTTTTTTTTTTTGAAAAAATAAAGTTAGGAAAGGCATGGGCTGGTATAAGATTCTAATGGTGTGATAACCTTGGATAAAAATCATAGTTTTATCATAGTTGGTTTCACGGTATCACGGTATTGTGATTACTGTTTAAAAGTATGTTCTTTTTAAATGTCTAGGTTAAATACAAAATCTTTTTTCCCCTTTTGAACATAATATATTTTATTTTGAGAAGCATTTAAAGAGCCCATATTATACATGAAATAGGGTCATATCTTGGTTGTAAGGGTCTCCAACAACAGTCTAATATGCATGCAAGGACAAAAAACACTTTCATGTTCTTATAATCTGCATTTATTTTTACCTAATTATCCCAGCGACTCCTGTATGAATCGTTCAGTGATTCATTTGTTCCCAAACCCCTCCTTAGCGCGAAGCTAATCTACGCTGATTGGACCGATGACAGTCTGTCGCGATTGGTCGACTGCCTTCAGTCAGAGAGTGAAATGGCCAATAGCTAATCAGCAATTTAAAAAGTAATCACAGTTCATACACGCTAGATAGTGTAGGCGTGGATTTTAGCTGCCACACACACACACAAAAACACACACACACCTCCGGACGAGAACGCTCCCGCTTCCGCCCGCACTCGCCAGGTTTTAGCCTTAGAACCCGCCCCGTATTCTGCCCGCCGCGCCCGATCCCGCTAAAGAGCGGGGGAGAACAAAACCGAAAATCCCCCAGATATACAGTCCAGACAGCTGTCTGTATAAACACACACACAGCATACCACACACCAAGCATAAAGCTCTCGCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCATACGCGCGCGTGCGCACTAACACACAAGCACCAAGCAGACACATCTTTCTCTTTCTCAGGCAGCCCGCTCCCGTCCCAAATCAAACCCGTTACCGACCGCTCCGGCGATTTATTCGGAAATTTATTCCCGCGCCGCAGAAATCTGGCGCGGGGACAGCCGCGGGTATGCAGACCTCTAACGTTACCACGGAGCTCCATAAACAAAGCAGCACGCGTCGCGTTTTTAACGTGACTTTGCACGCGATAAGAGAATATAGCCAGTTAACCTGATACAGTACACTCGGTTACAAGTAACAAATCACAACTAAATACATTTGCAAGCTAGAGTCAACGAGGCAACAACTTTAACCGCACGTACTTACACTTGAGAAATGGAAGAAACCCATCCTGATGTCCATCAGTAAGTTACTGATCCTTCCTTTAACAAACGCAGATGAAGTATTCTTTGTAGCATGTAGCTTCCAGAAGTTTCCAGTAGTTTCCAACTGCTTGGCTATAATGCTGAGGTTTCATCTTTGGGTAGAGACTCAATATAATATCCATCTGCAATGTGACTTCAATCGACCGGCATGTTTGTGTGCGTGTGTTTGTGGGTGTGTGTGTGTGTGGGTTACTGCGTCAGAGGGCGGGGCCTCAGGTTTGAAATCTCCCGGGTTTGCGCGTGCACGTGAATAACTTGGTTTCATTCGTACGTCATGGCGAAACACCTAATGAGTCGGTATCAAGGCGACTCGTTTGAAGCACTATGAATCGACTCTTTTATAGATGAATCAACCGTTTTAAACACTGTATTCTTACAGATTTAAGCCTTAGCTGGATACATCACTTCACTTAGAACTGTGTTACACACTACATGGAGGGGGATTTTCAAAAACCCATAATATGGGCTCTTTAAAATATTTTGGAAGAGTAAACATGTCAGGCTGAATAAATTATTGAATTTGCTGTCTTTGTTTTAAAAGCAAATTTTTTAAACAATTTAAAACTGCACCTTTAGATATCTTTGCTGCTGAAGATAAAAAAGTTAATAAAAAAATCGTACAAATACCTTAGGAACGATATAGCTGAAAATGTTGACGGTTTTACCGCGGTATACCATGAAAACGGTTATCATCCCATACCTATTAGGAAATCAATGTTTAGTGGAATAACCCTGATTTAAACACTTTCAAAACACAACAATTCAAATATTTGTCATTTTTACCAACTAACATTTTCTAAAGAAAAAAAAACATGATATCTATTTTTGAAATTTGAAAAAAAATTTATTATACCAAAAAATATCAATCATTTACTCAAACCCATACCCAACTAATCTTGTATTTTGGGGGGTCTTTTAATTTTATATTTAGATTTACTACATTTAATAACATTTTATTTTGACATTTTATTTTATATTTATATTTATTTTGCGCCTTAAAATGTACCTTGTAAATTAAAAAATACCAAACTGCATTGATTTTTTTTTTATATTGTATATGTGTAATGCATATGGCACTTCCTCCATCTTTAAAACTTGCTGAAATCTGATTATGTCTTCCCCAGCTTCAGATCCGCTGTTCTCCAATGCAGGTATGTGAAACCAATCCGACAACACTACATATAAATGTACATTATATGTAATACAATACATTTGAATTACTACTGAACGTGTCTTTTAATCAACCAAAGCAAGAGATTCTCAATTTGAGACAGAGTTACCATGCAAACCGCAAACTAATTTTGCTTTGCATGCTGGTCTAG
Seq C2 exon
ATTCACCAACCCTGCCTCCGGTGCAGGTATTTGACAAAACCTTGACCGTCAAACAAATGCACGTGCTTGAACCTCAGGACCTCCTCATTGCAAGAGCAGACAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000060631:ENSDART00000085636:18
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=0.000
Domain overlap (PFAM):
C1:
PF0078017=CNH=PU(7.5=59.0)
A:
NA
C2:
PF0078017=CNH=FE(11.4=100)
Main Inclusion Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
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]