RnoINT0143673 @ rn6
Intron Retention
Gene
ENSRNOG00000001141 | Srrm4
Description
serine/arginine repetitive matrix 4 [Source:RGD Symbol;Acc:1560213]
Coordinates
chr12:45872336-45877222:+
Coord C1 exon
chr12:45872336-45872640
Coord A exon
chr12:45872641-45877018
Coord C2 exon
chr12:45877019-45877222
Length
4378 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGT
5' ss Score
8.68
3' ss Seq
AGATGTTTTTCCTCCTGCAGAGG
3' ss Score
8.78
Exon sequences
Seq C1 exon
ATCTCTGGGTCGGGGTCCACGGCTGATCTCTTTAGCAAATCGGCCAGCCCGCTCGCCGCCTCCCGAGGGCGCTCGCAGGAGTACGACTCGGGCAATGACACGTCCTCGCCGCCCTCCACGCAAACCAGCTCGGCCAGGTCTCAGGGCCAGGAGAAGGGGAGCCCCGGTGGGGAGCTGAGCAAGAGCCGGGACCTCAACTGCGGCAACACTTCCGATTCAGGGAACTCCTTCACCACATCCTCCCCCCAGAACAAGGGGGCTGTCTTAGAGAATGTCTCTCCCGCCTGCAGGAGCAGTGAGTCAAG
Seq A exon
GTCAGTGTATTTAGGGGTGAGCGGGCCCCCATCTTAGGCACCATTTCACTGTCTCTTTATGGTGCCCCTTTTCTTCCCAGGTGTCTTTATTTGCAGGAGACAGGACATCCCATTCAAATTAGTACTCTCAAGGGCGCTCGAGCACACACACACACACACACACACACACACACACACACACACACACACGACCCAGGGGCTCAAAATTTGCTACTGGGTCTTTATTTTTTGAATTGCAACTCTCAGCTCTGCTCCCAGCCTCTGGTGGCTTCTCAAGCAGACCCTCCCTGAGCTTTTATAGAAATGGTAACTACCTGTCTCTCTAGCCAGCAAAGAGAAGAATACCTCCACCCCATCCCCTCAAAAATCTTAGCAAAAACACCTAATCTGATACTGTTGGCTCTCCTTGGCCCACCGTAGGCAGTTCATGCCTCCTCAAACCAGTCTCTGGCAGAGTAAATATTGAGCTACAAGCTAGAACCTCTGGAAAAAGGCAGGAAAAGCTGCAGTGTCCACCCATATCAGTGAGGGAGGGATGGGAAGCAGATAGATGCCAATTTACAGAGTCTCAGGGAAAGTCTAACATTAGCTTCATCTAAGTCACTGTCAGTTAAAAACGTACCATAATAATAATGAAGTTACCAGAATTATTAAAAAACATATTCACGCCAAAAAACCCTGCACTTATATGATTATAATAGTTTTATTCATATTTCTAAAAGTTGGAGGCAACTAAGTTGTTTGTAAATAAACTGTAGTTTATCCAGACTCTAGAATATGTTTTTAATTCTTTATTTATTTTTATTTTATGTGCATCAGTGTTTTGCCTACATGTATCTGATTGGGGGTGTCGGCTCCCCTTTGAACTGGAGTCATAGACGGTTATGAACTGTCTTGTGGTTGCTGGGAATTGAACTCGGGTCCCCTAGAAGAGCAGCCAGTGCTCTCAATCACCAAACCATGTCTGCAGCCTCTCGGCGGACTCTAGAATATTATTTGGCTCTAAAATATAAGGAAAATTATGCTATCAATGTATACAAAAGAAACACACACACACACACACACACACACACACACATACACACACGACTCCAGTTATGCGAACCTGTGGAAAATAATGGAACTTTTCATGTGAAATATTGGTTTGCATTGTCTGAGAGAGGGAAGATGACTGGCAGAACATGACATGGTCATGAAAACTATAACACACAATACAATCTTAATGAGTTAACTTCTAGGGATTCACCCAAAGTCATGGGATAACTATAACGCCAAGTGTGAGTGTGGGGTAGGCCTTGGATGCTGATGTAAGATGCTGTCTCCTCAGTCCTAATACATGGACTCCTTTGTTGAGGGACGTTGGGTATGGCGGATGAGGCCTTGGAGGCCAGGCTGACATTTAAAGCGCTCCAAAATAAAGTTTATTCATGACGACACACCTAGCTGCCACTGTGAAGTTTGTGTTGGGCGCTTTGCTTGCTACCCATGTTTTTCCTTTGGGGGCAGAACCAAGGGATCCCTGGAGCTAGCTGCCTAGTGAGAGGAGGCCTCTCAGTAAACTCTGGATTTAACTGAGAGACTCTGCCTCACTGAAGAAAGAGGGGAGTGACGGAGGCTGTCTCTGGCATCAGCTAGTACCCACGCATACACACAACCATATCCATACACACATGCATGCGCATACTGCACACACGCACAGACACATAAAAAGAATCTGAAAAAAAAATACACACTGGAACACTAAGCACTAGATGTGCTCTCACAGAAGCGGTTGTTTAAATTCACTGGTCACTTAATCTACACCATTCATTCCCTTACTGATGCCTCAACTTCTTACCAGACACACTCTTATGGCAACACTCAGTTTGGTCAAAATGGTGGGCCCCTTGTCTCCAGTTTATAATTCACTAGGCAGATACCCGAGTAGGGAAGGTCAGCTAACACGCTCTACCCAGAGAAACCCAGGGGATCTCCTCCTGCTGGGGCTTCAAGTCCACCTTGATTCTAAGTGGTCAAGATTTCCAAATGACAGCCACACGCTGATCAAGTGTGGAAGCAGCTGGCAGCTAGCTTCTCCAAGGACACAGCACCCTTCATCTCTAACATAAGACCTAGCCGGGCTCCAATGTGGACCAACAGCTTGGGGCTTTGTGTAGCTTGGCCTCTGGTTTGCCTCCTCTGGGACATCCCTGTCTTCAGCTCCTGCCAATCCCTGCATGGGAGCCAGAGTTGTGTCAGCCCAAAGGTCCGACCTCTCTGAAAGCAGACGGTGACGGTCCTGTATGGGAGAGGAAGGTTGCCACATAACTACTAGCACACTAAAGGGCTATCATTTGAGGGAGTAAAGAGAAAGGGAAGAGAAGTAAAAGTAAAACAAAGAGAAAGTAAAGAGAAGTGATGATGATAATAACAATATTAGTATTAATTAATTTAAAATCCATTAACATCTATTAAGCCAGATAACATGCTAGACACTGCTAACAATGCTTCCTGTGAACAGCTTTCCCCCACAAATTAGTGTCTCCACTAATTATAGTATATAATATATACTATATAAATATGTATATAATTATACACATATCACTATTACAACCTTTTTGTGAAGCAGCGAAATCGAGGCACAGACCTGCAGACCAATTCAGTTAGCAAACAACAGCAGCAGCATTCAAATGCAGGCCCGTCTCTAAAACTAGATTCCACGTCCAGGAGATATATAGCCGTTACCTGCTTAATTTGATATACATAGACAGCCCAATTAAATAATTTAGAAGCAGCCTTTCACCGTAGAAAGTAAATGATGGTGAAATCACGGGTATTTATGCCCTGCCAGCTCTGGACAAAGGGCTCAATAAATATGGACTAAGGGATATGAGCTGGAGACCAAGGGCACCACAGACACAGAGGGAAAGGGGTTGGAGTGGTGACGGGCACGTGGGTATGCCACCAGACAGATCCAAGTTTGGGCCGCTGAGTGACCTTGGATGAGTCACTAGTCCTTCTGAGCCACCTCAGTAATTCGGTCATAAAGGGAGAGCTAGATAAACAGCTATTGGGAGGATTAAAGGGAATGATGGTTTCGAAGAACCTGAGACACGGACGATGACTTTAAGGTGACACTTGACAAGCCGTGTGTGAGGATATTGCAGAGGGGCAATTCTCCATATCCAGGGCAAAAGACACCTGGAATTGTAGGACCAAAGGCGTTGTGTAGGAATGGGAGGAGGGCTAGGCAGGAGGAACCATGGCAACACAAAGGAGACCCTCAACCCAGACTGGCAGGAGAGAAAATGTCCTAGAGGCTTTTCAGGTCAAACCAGAACCATGGGTAAAGGAATAGCTAGGTGACAAGGGGAGTTGCATGCCAACACGTCCTAAGATCTAAAGGCAAAGAACAGAAGAGGACATTTGGTTTAGGAGGGAACAGCCTGTTAGGGTCAAGAGCCAGGACAAGAGGTGAACAGAGGTTGTCATGAATCTACAGAACTCTACCAATGCGATTTGAAGTTGACCTTTGAACTTGACTCCTGCTCATCTTGACATAAGCATGCCTGCATGAGGACCTCAGAAGGGGTTCAGTACATCCCTAGACAAGACAGACTGTAAGGCACAGACCCACCCCCACCTCTTGTCTGTTTATAAACAAGCCTCCATCTATCTCTTCTGGGGTCTCAATCTCTCCATCTGCAAAATGGGCTACATCAAAGTTGCCCAAACTTAAGCTAACCTCAGGTCACTTTCTTGATTTTCTTTTCAAAAACTATATTCACGTTGGTTCGTTTATCGTAGTCATATCACGGCCTTTTCTGTATTGAAATGCAAATCGCTTTCTGAAACACCAAAGCTCCCCGTATAGAAAGCACCTCTGATACTATGATTAAGACAGTGTCTTTAACTCTGATCAGTTACAGTTCCCTGCTCAAGGCCTTGACCTCAGGGCCTGTTCCCTTAGCGTGTGGAGATTACAAAGTGTTAGAGAGGTGCTGAAAAACCGAGAGCACCCAGCCAGGGCTTTCTCGTTCACGCAAGCTGAAGGACTGGACAAGGACAAGAAAGGGGAGGGGTGGCAATCTCTCACCACATGATTTGATGTTATTTAATTAACACTGTGAGGGCTCCCTGGGATGCTCTGAAGCAGCCCCTGTGGTGTGTGGCACGTGTCCCTTACCTGGGGGAGGCTGAATTGGACTAAATATCCATCTACTTGTGAGGTCTTTCCTAAATCTGACACCTGCCAGGCCATCCCTGAAAGGAGGTTGGGGGCATGGAAAGAGGAACGGAGGACACTGTGGCCTGGGCAGATGTGGGGGAGGAAGTGCCAGGTCAAGGCGTCCCCAGAGTAAGGGTGGCTGGGTAACGACAGATGTTTTTCCTCCTGCAG
Seq C2 exon
AGGGTTTCAGTCTCCATGTCTCCAGTGCGCAGAGGTGAAGAAGTCTAGTTTGGTCCCATCCACAGCCCGGAGCTCCCCCATTAAAGAGTGCTCCCGTAGCTCCTCCTACACCAGTACTCGGTCCTCCAGTCCCTCATCCAGGTCTCCAAATCCCAGAGCCTCCCCCGGGTCCACCCGGAGCCGGTCCACCTCCTCTGAAAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000001141:ENSRNOT00000001507:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.980 A=NA C2=0.870
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
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]