DreINT0134221 @ danRer10
Intron Retention
Gene
ENSDARG00000028099 | sh2d3ca
Description
SH2 domain containing 3Ca [Source:ZFIN;Acc:ZDB-GENE-080102-1]
Coordinates
chr10:10303615-10307066:+
Coord C1 exon
chr10:10303615-10304105
Coord A exon
chr10:10304106-10306950
Coord C2 exon
chr10:10306951-10307066
Length
2845 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAAA
5' ss Score
6.53
3' ss Seq
AACTGTGTGGCTATCTGCAGGTT
3' ss Score
8.28
Exon sequences
Seq C1 exon
TCTCCCGCCACAGACATGGTTCAGGTGGACGTGTGCTTGCCGTCATCCCGCCTTCTCCAGTGATGAGGCGCTCCAGCGATCCCCACCTTTCGCCATCCTCCTCCAATAACAACATTCCCTGCTCAGAAACGGGCCCTAGCACTTACTCCACACCTGCTCATGGGTACCAATCTGAGAGTTTAGAGCAAGGCGGCAGCTACTGTGAGCTGAGACCCGGACAAGCCCCCATTCCTCCCTGCAAGAGCTACGTAGAGAGGTTGAAGGTGGAGGAGGGCCAAAGCCTGGGCTCTGGAGCTCCAGACGGAGTGGAGGGCTTCATGCTCCCCCTGGTGGAGACTAGTTCATCCTTCAAACCAGGGAAATACCAGTCGACTCTTCTGCCACCTGAAAATAAACCTCTGGAGATGAGCGTGTTGAAGAGGGTGAAGGAGCTTCTGGCGGAGGTGGATCCCAAAACGGCCGCCAAGCACATCACCAAGGCTGACTGCACG
Seq A exon
GTAAAAACACAAATAAAATTTTTATTGAAACAACGAAAACATTACTTATAAATGACATTAAAAGATGTGTAAAGAAATTGTAGCAAAACATTGTAAATCAGTTAGATTTTTGATTAGTTGGAGCACAATAGTTTTTCAATTAGCCTACTTATGCAATATTTTTGTCAATATGAAGTCAAAATGTATCTAGTTTGCTAGTGCACATTGTTATTCTTTAAGTGAATATTATATTTTTTAAATATATTTTAAGTTCTATGTTCTATTTGTTTAAATCCCACACACTTTTCAACGCTGACCTTACAACTCCAAAAAATACTACTACAACAAACAAATTGAATTGAATCAACAATTCTTGAGTCTTGAGATTTTTGTTGGGACAACTTGAAGGAATTGTGTAGAACCAAGCAGTTTTTACAGTGTAACAAAATTTTATAAGCATTTTTTGGTCAAGCAACCTCACATAAACCGTAGTAAAATCCATTGACAGAAATGTTGATAAAATTAGTTTACTATGATTTGCGTTTAATGAAATGTGTAGTATGCAGGTGTACATTTTTAAAGATAATATTAGAGCTGAGAGCTGTACTTTATATAAAATTAACTTTATTTTAAAACATAAAACTAGCTGTTATATATGCATTAATAATAATACTTGCTTATTTAATAATAATAAAAATAAATATAGCTGCAAGCAGCAATTAAGGGGCCAAGCACTTCATAGCCAGAATGAGCAAAGCAGTCCAGAGCCAAAATGAGCAAAGCAGTCCAGAGGCCAAAAGGTTAGTAAGGAGCATCAGACAAAGTGTTTTTGAATACATATGAAGTATGTAATGGCCGACAGACAAAATGGCTGACCTGGGAAAATCAGACATTATCGGATTCGGCATGCTCCATCAGATGTAAAGAGACAAATTTTATGAATTTGGGACAATCGGTTAAGTAGTTATAGGCAAAAATAAATACGTTTTTGTATCTCCAGATCACTAGGGGGCAGTTTGCTGAAATGCTGCGGATAACCTCAGACCATAGTTGTCATAAAACACACCAATTTCAGTGTAAATATTTCAACGCATTATGAAGATATCGCCTCAAGACCATTTTTGCAAGCTCTAGTTAGATTTGTTCGCAAGTCAAAAACGGTTCCTCTAATCAGCTTGAATTTCATAACTTTTGGTCAGCATGATCTGAAAATTGGGCACACGGCCTAGAACGAGTTTGATAAACTAGATTTTGATAAAATAAATTATAAATAGCAAGACAATTTTCATGACAGGATGTTATAGGGTGCGTTTGAATCATCATGAACCATGAAATCAGAGGAAAAAAACATCTTGGACTGAATTGAAGTTATAACAATAAACATAAGTGAAATTTTTGACAAGTGGTGGCACTAGAGAGTTTAAGTTAGAGAGTCCAAATTTGTTGTGGTTGAAGATCAGACTGTCCTCTATCAGTGTGCCAAAGTTTGCGCAAATGCCGCAAACGGTTCAAAGAGCTGCCATAGACTCCCAGAGCAGATGAGGAAGAATCCAGAAGAATAATAATAAGAACCGGAACGGATACAATAACATGATAATTAATAGTAATTATATAATAGTTACTTCCTGATTATATAAAACTGATATACATTTTAAATATATTAAAATCTAATCAGTCAGTGAGATGTCAATCTCTTTTTTGAAGAAATAAATTACAATTAAATCAATTCAATATTTATTTATAAAGCACATTTAATAATGACCGAAGTTGACCAAATTGCTGTACTAAATGGAGCACTAAAACAGAGAAAAAAATGAGAAAATAAAATGTAAATGGACAACATGACTACAAAATTATTCTGTTAATTGATTGATTAATTGATTGATTGATTAAGTGATTGATTAAGTGATTGATTGATTTATGTTTTAATGCCATATCAGCAGCACTGGCTATATCCATGGCAAAACATATCAGTTTCCTAACAAACATACATTGTACAAGAAAAACATACAAATAGCAACAACACTGAAATGAGTTATATACAATCTTTCAGTTTGACTAAAGATAAATATTCTAAAATTGCTCCAGAAGGCACCTTTTCAAAAATTTCACTTTTATATTATCTCCATAAATGACAAAGTGTCCCCTGATATCATTTAAAAATACACATTCTAATAAAATATGTTTTATCATCAAAATATTCTTGCACAAGTCACAAATAGGTTTTTCTTCCCCTTTCAAAATTAATACGTAAAAGCAATAATTTAAAATAAATAAATAAACAAGAAGTAGTAAAAGCGAGAGAAAATAGATGGGTCTTTAAAACCTTTAAATGTTAAATGCAAAAATTAAATGTTTGTTTGTTGACTTGCTTTTTTTTTTTTTTTTTCAGATACAATTTTTGGCTTATTTACCACATACCATTCTGTACATGAATAGTTGATGATCCCAAGACCATGTTCAATTCAAGACAATTCCCTTTCCATGCACACACATTCAGATTTCCAAACCCACCCCTAAAAACAATGTAAACAGCTAAAGCCTACAACACACCGACAGATTGAAGTCTTATTGGTTTAAAATCCCTTGATTCTGTTTTCCGGTCCATTAGGGCAGACAGCATTACATAAGGCACATGTGAAATGGACTGATAAATTCTGGAAAGCAACCCAAACCATTCATCTGTCTGTGCTTTCCATTAACATCTAAACCTTTAGGGTTAATAAACTCTTTCCACACTGCTGTTGACCACATTCATCATGTGAGGGGACGAGATTAAGGTTAATTAATTGAGGGGTTTTTTCTAATGCCTGTGAATATATTAGTCTTGAATATATGGCTCTTGTAACTGTGTGGCTATCTGCAG
Seq C2 exon
GTTGCTAGGATACTGGGCGTTACCAAGGAGATGCAGAGGATGATGGGAGTGAGCTCAGGGCTGGAGCAGCTGACTCTTCCTCATGGACATCAGTTGAGGCTGGATCTGCTGGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000028099:ENSDART00000144214:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.591 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0061714=RasGEF=PU(9.6=10.4)
A:
NA
C2:
PF0061714=RasGEF=FE(21.5=100)
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]