RnoINT0124256 @ rn6
Intron Retention
Gene
ENSRNOG00000001516 | Rapgef4
Description
Rap guanine nucleotide exchange factor 4 [Source:RGD Symbol;Acc:621886]
Coordinates
chr3:58868946-58874195:+
Coord C1 exon
chr3:58868946-58869061
Coord A exon
chr3:58869062-58874106
Coord C2 exon
chr3:58874107-58874195
Length
5045 bp
Sequences
Splice sites
5' ss Seq
AAAGTATGT
5' ss Score
6.93
3' ss Seq
TTTTTTTACTTCCTGTCCAGGTA
3' ss Score
9.95
Exon sequences
Seq C1 exon
GACGTTGAGGCGAATACAGTCAGACTTAAAGAACATGACCAAGATGTCTTGGTACTGGAGAAGGTCCCAGCAGGGAACAGAGCTTCTAATCAAGGAAACTCACAGCCTCAGCAAAA
Seq A exon
GTATGTTTGCATCCAACACTATAATTGCCAGACTATGATTAACCTTTTCACATGCCATCGTTTTTACAATAGCATGTTCTCCTCTTTGCGGAAGATAGCAGTATGTATGACTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCGACTAATCACACATCTTGCGGCGTATAATGCATCCATTTCTCTGAGAATATTGTCCTGCTCCAAGGCCTCTCCCTCCATATTGTTCAGCCATAATAGCCCCCAAAGAGAAGACCCCCAAGAGAACAATGCCAGTCGGCATGCCAGGCAGGGCCAGGCACCCGCCCCAGTGATGAGATTCCATGGTATCTGAATGTCCTGGGGAGGTTTCTGATAAAGTGTTTTCCCTTTGCTATCAGAGTGACTGAGGACACAGATGAGACCCTGATTTTGAGGAGAAAGCATTACCATCTCATTGAACTCCTGGGCACTCATCCTTGCCAGTGTCAAACAGTTCCCAAGCTTTCTGTTTAACTGAGGTCATTTCCAGAGCAGCCGGGCCCAGTTTCAGATTTTTCTGTAACTTCCTACCTAAAACCGTTGCATGGAATGTACCAACACATGTGCGATGAGACAAGAGACTTAGCAGTGAGCCTCTTAGGAGAGCGGGGCTAGCCGATTTTTCGAGTGGGGAGTTAATTTTCAATCTGTGTATAAGAAAAGCAGATGAATGTTTGTTTGCTAAAGAAGCATCACCAGATAAGATGTTGAAAGAGCATTTCCCTTTGTTGCCAAGTAAAGTGGGGTTCCCTTTCTCAGCGCGCTCACCAAAACTGATGAATTCCCATTGTTTCGACTAAAAGCCCATGACTCCCATGTTTTCATCTGGGTAAGTCAACATATTTGAGAAGAAGACAGGAAGAAACATATTATTAAATAAGCACAGTATGCTTTGTAAATTTTCTCTAATCCTTACAACAACCCTGTTTAAGGGATGGAGGCATTTCGCTGTCATCGACAAGTCTCAAGGACGCGAAATTCCAATGGGACCCCTTAAACCAATGGCTCTCAACCTTCCTAACACGGTAGCCCTTCAGTACAGTTCCCTATGGTGTGGTGACCCCCCAACTGCAAAATTGTTTTTGTTGCTACTTCATACCTATAATTTTTCTACTGTCATGAATCCTACTGTAAATATCTGTAATCTGACCCCCTATGAAACAGCTGATGGCCCCTGAAGGGGCCAAGACCCGCAGGTTGAGAAACACTGCCTTAAAGGGAAGTTCAACGTAACCGCCTTCCACACCTCTGCTCCCCATTCTTCCTAGCTTATGTTATCAAAGCAGAGTTGTACGCTGCATGGGTTCCAAGGTAGTCATAGAGTGGGGGATGTATATCAGAACATATGCATATGCCTCACCCCTACGGTTATTCCTTACACGATACAGAATAGCAACTATTAATGTTACATTCACTCTCGGTAAGGGTGGGGTACTATCAATAATCTGGAGCAGATCTAAGTAGGAGGGAAGAAGTATACAATGCTATTTTGCATGAGTTCCTGGGCTGCTGCATGTTTGGCTATCAGTGTGCATGCTGGTACCAGACTTACAGACAGACGGCTGTAGGCAAAACACCCCATTCTCAACACCCCATGGTAAATGCGGCAAACCAATTATTTCAAAGGGGGTGGCATTAAAAATGACTGTGTTAAAAAATCTGTTCTTTCACTCACAAAACTCTAAACTTACCACCCAGATTTCATCATTTATTAGTAATAGCTTTTAGCTATTCCTTTTGTGCCAGGGATTGAACCCAGAGCCTTATAGGAGTAGGCGAGTATTCTGCCACTGAGCTATGGCCCTGCTCTATTACCTTTGTTAGTTTATTTCTTTCTTTTGGGCAGTTGACCTTCTAGCCTGCTGAGGAGGGTGGCAAGGACAACTTTCTGTGTGTGAGGGTTTACACTACTTCCAAGATTTATTTATAACTAGATGGTCTTGCAGATGACTATGTTCTGTAGTACTATCTCATGCCTCAGGAAGACTGTGGAATCCAGAAAGGTAAACCTGGATAGTTCTCCTTAACTTTGAAACATTTGATCAAGAGAGGCCCTGGACTTCCCTTTACCTCTTTCTTCATACAAGAGGGAAGAATCAAAAACCTGTGCTCTCTGTAAGTCTTCAGTTCAAGGTGCCCTCCCCTTATGAATTCAAATGAAAAGTCAAGCCAAAGGTGATACAAGAAAAGAGACTGTGTGTCTGATGGTTATTTTAGTACTGTTTTAGTTTTCTACTGGTGTCCTGCCATCCCGTCCAAATTTAAAGATAATACACCCGTGCAAGTTTGTAGCAAGCTGTTTGTGAAATGCACTGGGAAAAAACAGTGCACCACAAAGTCAGCTCCCAAAGGAATGAAAAGCTTCTCTCTCAAGGGGTCACTTCCCCAGACTGACCGGAGCTGAAAAGGGGGAGCCTGTAAGTAAATTTCATGGCTGATGTTTTCATCAACTTTGATAACATACCAACAAAACTTTGATAACATACCAACAACCGTGTCTGCAGACAGACACACAGTTGAGGGTATCTGTCTCTGCAGAAATTGTTCTTTTCAAACTCAGAGGACATCATCATGTTGGTGGCAATAATGTTATTTTTCTGATGTACTTCCCCACCCCACTCCTTTGAAATCCAGGTTAGTTTATGTGCACACATAAAGCTTGGAAAACTGCCTGACTCCACCCAAGCCACTGAACAGTAGAGGTGGCATCGATGCTGATATAAAGTCAGTGGTTTTAAAGATGGATTTACCATGATACCTGCTTTGGGGGATGTCTTAGCCACTGGGTTGTGAGACTTTAGTAATTTAAAATGGTTGTCCTGTTCATATTGGGGCCGTGTTTTTTTCCTTAGACTAGTTTTCCTGCTGAGGTATTCCCAGCTTGTTCACAGGAAGATCAGCTTTCTCCTTCCTCCACCCCTGGCCCTGGCTTCCTTTGTTCTATGCGCAAACTTGACTGGTATTAGGAAAACATTTACTCTCACAAGTTTAAGACTACCTCCTGGCTGATACTATGTAGCCAAGTGGGGTGACTTCTGACTAGAACTGGAGAAGCTTCTGCCAGACATAAACTGACAGAGGCTGCACTATCTGGTGGCAATCACTCTTAACCCCCACATAGCAAGGGCTCAAGTCATAGACACCTGCCTGTTTCTGGCGTGACATAAAGCCAGGATCTGATGTTTTAGGCAAAACGGGGGCCATCCAGAGATTTCTATGCCCTCTTTTCCTCTTGAGTCCTCTGCCCTAACTCCTGAGTTCTATGGCGCTAGGTAAGGAAACCACAGAGCTGAACCACTAGAGGGAGTCAGGTACCAAAGAAAGATCCTGTGGGGTGTGACAGGCCAGACAGGCAAAGCCTTAAAGAAGACACTTGCTCTCTGTTGAGGTGATAGCTTGAGTGGCTTGCCCGTGGGTCTTTTGTCTGTGCGGTCAGGCGGAACTCCCTACCTACATCCAAACAAGGAGAACCAGAGCATAAAGACAAACTGCCTCAGGATTAGACTTCTGACAAACGGACGCATTGCCTGTGGATCTCGGTACCCAGACAGCACGTGAAGTAACTGGGGTCAGTTAAGGGATGCAGTTAGACTCTTATTGAAATAAAAATTGCTTTCAAAGCCTCCTTGAAGAGGAAGGCTTCTGATTACATGGTAAATCTCCTACCCAAAATGGGCTGTTGGCAGCCAAACCTGGTCTCTTCTACACATAGAGCATCTTGCTGCATAGGAAAACAGAAGCAACCAGCTGAACAAACATTTGTAACAAAATCAAACACTCGGTCTCATCTTGGACGCTTACCAGTTTCTCCACCTGCAGGGTAGAGGCAATATTAACTAACAGGAATGAGCAGACAGGGCGCCTCATTCAGCATCGACTTCATTGTTGGGGGCATGGTGAACACCAGAAAGGTGTAGAATGCTCTCCCCTAGGATGCTAGGCTTTCTCTGTTCCCATGACCTCGGGACCATATGCTATCACTTCCCATCCATCCCTCAGGCAGGAGGTAAGACGCTGATGAGGCTCTCTTGCCATCTCTGCAGGACCACCTCCATAGTCTCAAGCAGGCAAGAAAAGCACATAGGTGAGGGGGTGGAGGAAGCTGGGTTTGCTCTGAGTGTGATTCTGTCTCTGCTTTCTGAACACAAGAGAATGCTCTTTGCCTTGTTATATCCCCCTTTCCCATCGCTCCGCCATGCAGGAAGGCCGAGACTGAGTTCTGTTGGTACCCACATCATCTTCATGCGTTCTGCCTACCCACAGCTGGCACTCAGTTTGCCACTGTCTTCACTCTGACTCTAACTCCCATTCGATCTTAAAAGTCAGCTTGCTCTTGTCGATTGGAGGGTACCCCGAATCCATCCCTCAAAATAATGACTAATACCGCCCCCTGACATTGAATAAGTTAAATATAGATTCCTTTTTGATCTATGACCTGTTGGCCATGCTCCCTGGGCCTGTTGGCTTTGGGTTTGGGTTTCTTTTGCTTTATCATTATTAGCTCATTTCCAAAGCACGTAGCAGCGTGGAGTTGGAAAGGACGGAGCAGTCCAGAAATCAGCATGGGAATCCAGTGTGACAGCGACATCTCCTATGAGTGACCCATGTCTAAAGAACGCACTCGGCGTCATTTCCTCCCTCCCTGTCCTCCCTGCCCTGCCCTGCCCTGGCTCAGGTTCATACACAACGTTTCACTCTCCCTTAGAATAAGGCTGACGTGCCTCGGCTCCAGCCATGGGAGCTGCTCTCTCTCCCTCAGATGCTTCTACATAGGGAGGGGAAAGGAGCATTTCTAGTAACTGCTTCTATTGGCTTTTTCTACCGCCTTCTTGTGTGCTGAGGCAAGGTGCGAGATCTCCCTCACCAGAGGGAAATTGCTAGTCACAAGTAGTCCGTATGGTTTCCCAGGATCTCGTTTTTTTCAAAAATATGATTTGTTTCTCCTAATGCGTGCTCACTTTTGTAAAAACTAATGGTCTTTTTTTTTTTTACTTCCTGTCCAG
Seq C2 exon
GTATACTGTGATGTCAGGAACACCTGAAAAGATTTTAGAGCATTTTCTAGAAACAATACGCCTTGAGCCATCTTTGAATGAAGCAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000001516:ENSRNOT00000010630:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.385 A=NA C2=0.161
Domain overlap (PFAM):
C1:
PF0002724=cNMP_binding=PD(2.3=5.1)
A:
NA
C2:
PF0061815=RasGEF_N=PU(26.2=90.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
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]