RnoINT0143665 @ rn6
Intron Retention
Gene
ENSRNOG00000001141 | Srrm4
Description
serine/arginine repetitive matrix 4 [Source:RGD Symbol;Acc:1560213]
Coordinates
chr12:45880469-45882548:+
Coord C1 exon
chr12:45880469-45880603
Coord A exon
chr12:45880604-45882262
Coord C2 exon
chr12:45882263-45882548
Length
1659 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
CCTATCTCTGGTCTCTACAGTGC
3' ss Score
8.12
Exon sequences
Seq C1 exon
GGAACGGGACCCAAAGTATGGTGAGAAGGAACCACAGCCCCGAGAACGTGCACGCAGGAGGCGAAGGTCCTACTCGCCTATGAGGAAGCGCCGGAGAGACTCCCCAAGCCACTTGGAGGCCCGGAGGATAACCAG
Seq A exon
GTGAGACCCCAGAGCCGGCATTGTGGCTTCCAACCTTCTCCCTTCTGTCCATATGGTTGATGGCTCTGACTAAATCTTCTTTTGCCTCCCTGAAACTAGACTTAAGGATTGGAGGGCGGGGCGCTCCAGAATAGCCCTTCCAACCCCCTAAAATGATATTTGATTCAAAGCCTTTCCTAGTGTGGAATCTTATCAAGCTTCCAATTTGTTCCTGAAGTGGGGCTGGGACCCGGACAGCACGTGAACCAAACTTGTCCTAGAGACTGAAGGGAAGACAACGGGCCGATTTGAGGAATAGTGTGTAGCCTAGGGGGGTGTTCCACAGGGCAAGGCATTGGCCTAGTAGTATAGCCTGACCTTGGTGGAGATAGTCCTATACACTAAAATATTCAGATGCCAGGTTAAAATTAAACTATTCGTGACCATACCTTTAACCACGTTCAGATGGTACAAATGTCGTTATTGGGATTTCCAATACAGCTGAGGCGAGTAAAGATTTTTAGTTAAGACCCAGTTCCTGGGGGCATCTAGAGCCTTTTCCTGTCCTTAGGCCGTTTTTTGCCCACAAAACAAGGCATCGCACCCAAGAATGTCACGTGGAGGAGATCAAAGGGAGTGAGAAAAGGTGACCTCGCTCTGTAAATTTAAACACCGGACACACTGTGTTCTGTCATTAATGACTGAGTGGTCAAAAGAGGTGGAAGTGTGACCTGTGACAGCTAAGGTCTCTGAGGAGAAATGCTGTTGGCAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGCGCGAGCGCAAAGGGTGTGAGAGATATTGAATTTCTCAGGCCATGAAAGCTGGGAGAATGGCTGAATGTTGCTCCCCCTCCCCTCCTCCCCGCCCCCTCTCCACCCCCATTAAGTTATCTTTTTAGATATCTTCACTAATCCCAGAGATCAGCAGGGATCCTGGAAGCAACACTGGTATCCTTCCTGGAGAGGACCAGGAGGCAGAATAAGAACCAGGGTACCAGAGTGATGGATGGAGTTGTCTGCTCAAATAGTCCCTGTCCTCTCTTCCTAGCTTCTGGGCATCCATGAGCATCTTGGTCGCCTGTCACCCATGCTGCCTGCTAACTGTTCATGGATGTACATCATTTTCTTAAAAATTAGTGTCTTCTTTTTCACAGCGACCCCCACCCCCACATTCCCGAATGCACTTGTTTTTAAAAAGTAATGATATAGTACAGTGAGTGGAAAACCAGCCTCTTCTGCCTAGAAGCGGGACCTACTAGGAATAGAAAGTTCTAGCAAAAGTAAAAATAGCAAGACAAAACTTCAATTAAAGTGGCAATGCAGATGCTGTTGCTAGCTGGGAACTCTGATCCCCAAGCCTGATTTGTTGATTTTTTTTTTTTTAAGTGATATCACTTTTTCAGAATTAGAGCAGGATTAAGCTGGGCCTTTGGTCTCAGAACTACCAGAGGTGGGGGTAAAAAAGAGGTAGAGTATTTTTTGTTGTGGTTTGGAGGTTTTTTTCCTGGTTTCCTTTTTCTCACTAAGAGACTGGGAGATAGAAGGATATTGTTTTGTCTGGGGCAGCACTGGGGATCCCTGGGAGCAGAATGAATCCTCATGTTTCCTATCTCTGGTCTCTACAG
Seq C2 exon
TGCCCGCAAACGCCCCATCCCCTACTACCGACCCAGCCCCTCCTCCTCCAGCAGCCTCAGCAGCGCCTCCTCCTGGTACAGCAGCAGCAGCAGCCGCTCTGCTAGCCGCAGTTACTCCCGGAGCCGGAGTCCCAGTCGGAACCGCAGCAGCCGAAGCCAGACCAGGAGCAGGACGCGGACCAGCCGCAGCTCCAGCTCCCGCAGCCTCAGCCTGGGCTCCCGGAGCCGCAGTCGGAACCGGAGCCTGAGCTACAGCTCAGCAGAAAGCTATGCCAGCACGAGGCGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000001141:ENSRNOT00000001507:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF152301=SRRM_C=FE(70.3=100)
A:
NA
C2:
PF152301=SRRM_C=PD(17.2=11.5)
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:
GCGAAGGTCCTACTCGCCTAT
R:
GCTTTCTGCTGAGCTGTAGCT
Band lengths:
343-2002
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]