RnoINT0071196 @ rn6
Intron Retention
Gene
ENSRNOG00000028627 | Hmcn1
Description
hemicentin 1 [Source:RGD Symbol;Acc:1564772]
Coordinates
chr13:67926818-67928857:-
Coord C1 exon
chr13:67928795-67928857
Coord A exon
chr13:67926938-67928794
Coord C2 exon
chr13:67926818-67926937
Length
1857 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGA
5' ss Score
9.45
3' ss Seq
GCCTCTGTTTCTTCTCTCAGATG
3' ss Score
11.43
Exon sequences
Seq C1 exon
GAGATCGCAGTAACCAGTGCCCCTCTGGTTTTATCTTAGACTCAGCTGGACCCTTCTGTGCTG
Seq A exon
GTAAGAATAAGAATGGATAAAATATTTTCATAAATGGTGTCAGCAGTGGTTCTCTCTCCTTTATATTTATTTATTTACTGGGCAAGAGGGCATGCCATGGCACATGGCTCATGTCAAAGCCAAAGGAAAACTTGCAGTTGTCTCCCTCCACCATTTCGTCCCAGGGATCAAACTTTGGTCATCCGGCAAGCAAGCACCTTTACCTGCTGAACCATCACCCTGGTTCAAGTAATAATTATCTTTTAATAGACATCTGCTGCCTTTGCCTAGGCATTTAATAATCACACCTGCCTACTTGATAGTTTAGGAACAGAGATGTAGAGACGTTACAGAAAATGCTGAAGATTGCCTACGAGTGGCAGACTGCATTTGAGGTTAAGTGGGATGACAAAGCCCATGTGCCTTCAATTTGGACACAGTCTCTGCGACCAAGTACAGAATAGAGTGAACAGAGACAATTCATCTAGTGGCTCAAAGGGTGGGAACTATCAGTGAACTATCCAACACAAACTTGCCTAACCACAGAATTGCTCCATCCTAGGACAGAACAGGATTGTTGATCCATAAGTAACCGTGAATCCAGCTTTGTCCCAGCAGGCAATCTTGCAAAAGACTCCCTTGTGGTAAACCACAGCTTAGTCAATGGCTGAGGATTTCATGTTGACATTCATAATGCCAAGGTGACCTTTTGGCTCTCCCACTGACCTGTATAACGTGGTGGCTGGTGAGAGGTGGTGTTTAGACTGCATGCAAGTCTCAGCTCTGGCAGTAATGGCATTGGCAACTGAGAGCATTCCCTTTACCTCTGTTCTCCAGATTTGTCATGCAAAAGGAAGATAGTCTCTTAAAAATTCTGTCTTTGCAAAGTGAGTTGCAACTGCATTTAGAGTGCAGTAAATGTACATGTAATTTAGTATCGTTGCTGTTTTGAATAAAGACTAAACATGTTCAGTAGCAACAATAAGTCTGAGACCCCAAGTTAATTTCTTCACAGCAGTTCCATTCTGTGCCACTTAGAGTATTCTCTGTTATATTCGATCCAATTCCTCAGTATCTAGAAATGACTATTTCCATGCTCTTTAACAGCTCCTAGGAAGCAGGAGTTGTGCATACTTGTTGTTGTAAAAATATAAAAAGTAAAAGGGCTGTCTTTTATCCCCCACTAGGTCCATCACCATGGTGCCCAAGATATCTGCTAGATAGCTTAAGTCTCAGTCAGCAAAGCCTCTCACTCGCTTTGCTCCATCCCATATCACACTGCCGAAGGCCTCTCTCTGAGCCTGACAACAATCTCTCTACCTATCTAGTTCCCAAGGCAGGTTTCCATGCCAGACTCACACATCCCAACTCTGTAGCGGCCCAGTGTCTCTAGCCCCGCACACTTTCTTACACTTAAATCACTACATGAAAGAATACACAAACCTCTGATCCAATTGATAAGATATAATTGCCCACCTAAACATACAAAGCCCAATACACATCCATCCCTTAAGAACTTTCATAACAACCTATAAAGGTACAGTGTGGAATCTTAATGTCAGCTTCATATTGTCCTGCCACAGCTTGTCTCTCTGTCCCTCCTGTCTCTTCCTCCTTTCCATTCCAGTCTTCTCCTCTTCCTTCAAACTTTTCTCCTACTCATCCTTCCTTCTCATGCAATGACAGGCCTCCTTCTATCCTGTACCTGCCCTCACCTATATTTTACAAACTAAATGGGGAGAAGGTTCTGGTGAGGTCACCTGAATCCTGAGTACATGACTAGGCAGCTGACCTTGGGGCAGTGGAATTAGCATCGAAATACAGATGATTCCAGGCAAACCACAACACATACTGACTGGCCTCTGTTTCTTCTCTCAG
Seq C2 exon
ATGAGGATGAATGCACAGCTGGGAACCCCTGCTCTCATACCTGCCACAATGCCATAGGAGCCTATTATTGCTCCTGTCCCAAAGGCCTCACCATAGCTGCCGATGGGAGAACCTGTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000028627:ENSRNOT00000030971:99
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:
NO
A:
NA
C2:
PF146701=FXa_inhibition=WD(100=90.2),PF0764510=EGF_CA=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGATCGCAGTAACCAGTGCC
R:
CTTGACAGGTTCTCCCATCGG
Band lengths:
183-2040
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]