RnoINT0121152 @ rn6
Intron Retention
Gene
ENSRNOG00000006709 | Pzp
Description
pregnancy-zone protein [Source:RGD Symbol;Acc:628643]
Coordinates
chr4:161818843-161820906:-
Coord C1 exon
chr4:161820813-161820906
Coord A exon
chr4:161819018-161820812
Coord C2 exon
chr4:161818843-161819017
Length
1795 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGG
5' ss Score
10.28
3' ss Seq
TGACCCTCTTCTCACAATAGAGC
3' ss Score
7.64
Exon sequences
Seq C1 exon
TCCATAGGATTAAAAATTTTTACCAACACCAGAGTCCACAAACCACGCTATTGTCCAATGTATCAAGCCTATCCGCCTTTGCCCTACGTAGGAG
Seq A exon
GTAAGGGTGTGATTTGTTTGTCTTCTAAAATAACAGGAACCAAAAAAAAAAAATAAGTAAATAAAATGATGCTTCTTTTCTGGCAGGTGGGTGTTTAGAGAACATTTTTATACACACTGAATCTTAGGTTCCTCACAGCTCCTTTGGCAAATGTATTCACAAGTCCCACCCGCCGAATATGGGCATGACTGCTGTTTCTCTCTGCCTGTCCTCTCCTCTCCCAGACTTCTCTCTTCCTTGCTTCCCTCTCCTCTCTCCTTTCCTTGTCAAAATTGGCCTTTTTATCCTAGACGCCAATCACCTCACTTCTTCATCTTCCCTCTGTCCTCTGTAGACACCGCACCTAAGTCAGTCATGCCAGTAACTGAGGCTTCAGGTCAGAGCGAGCACCCCAATCTCGGCGGCTAAGCTTCATGTTGCTTTCCTAGGCTATTTCCATGTCACACTCACACAGAAGCTACTTGTGAGTCCATTTCTTTGCTCTCCCTGAGTCTTGCCTCAAAAGGCCTCTTCATCCTAATTTCCCGGTGTTTTCTTCTATGATTACAATTTGCTTGATGGTGATAAGCATACTCCTGAAAGATACACTCTACTCTAGAGAAGCTTTCCATAACTTCCGAAGGTGCCTTCCCATTGCAGTGAAGACATTTGCACAGCCACTGCCCTGGAATTTCCTCCCCATCCCTGTCTTCCCGTCAACCAATGGCCACCTTAAGTTCCACATGAGGAAATCTCCTGATCAGGTCTCAGCTGATCCCAGAGGTGTATGACGGACTTCTTAAACTTGACACACTTGTTACCTCTTTTCAAATGTAACCTTGGCGAGCACCTGTGTCACACAGTTATGAATATAAAGTGTTCAATGACGGTGAATCGTAGAGAAATTTATCTTAAAGCAATTCTATGGTATGCCGACACATTTGCCATTTACTAAAGACAAAAGCAAATGCACGTACTAATAGGAAGAATGTGCTTGTCTGTATTTGCGTAAGGAATTAAGTTTTAGATGCACATTGGATACTTGAGGATCCGAAGCATCCTCAGTGTTCCGCAGCCTTGATTGATAAGGTGACTTCATACTCACCAACGCTGAGAGTGATGCTTCACATAGAAAAACAGTAGATGCGTGTTTATGGCCATCTCAGAAATCACTGGACATTCTATGCTAACGACATGCTAAAATTCATCGAACGTTTTTGTCAAACTCGAGCCAACTCAAAGAATTGCAGTGTTTTAAACTCAGACATTCTAAATGACACAACCTAAAGATAGACTAGCTTGATGCCTCTGTGGTAGAAAGAAAATATTAGAACTCCTTACTGTTGTAACTAAGCCATTGTGCTTCTAGTAGCGCAGAAACCTTCATATGGAGAGCAAAACGGCTGTAGTTCATAGCACACGACAGCCTGGAATCTGACTCTGGGTATTTCAAGCAGCAAAGGGCAGTGCATGCTTAGGCCTAAAGTTACAGGGAAATGGACAATGTACACTGAGAGGACACCTGATTCGTTGCATCTCTGATTGCTGGTCAGTTTTGAGTCATATTTCTGACCTCTCGCTCCAGCTAATCTCCTTTCTTGTTCTTCGGTGACCACTGCCAGTGCCCGTGACAGACACAGCTGTCATTTCAGAGGAAGACCCATCCTAAAGAAAGCTACATTTGCTTTATTTCTAAAGGAAAATATACCCACATATGTTCGATGAAGCAACAGAACAAATGTATAACATATAGAAGTGATTAAAATATTTTAAAAAGTGACTATTGGGTAGACTGATGACCCTCTTCTCACAATAG
Seq C2 exon
AGCCTCAAGCCTTAGCTATGTCTGCAATCCCAGGAGCCGGCTACAGATCAAGCAACATTAGGACCAGCTCAATGATGATGATGGGCGCATCAGAAGTAGCTCAGGAGGTAGAAGTAAGAGAGACAGTGCGGAAGTACTTCCCGGAAACCTGGATCTGGGACATGGTGCCGCTGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000006709:ENSRNOT00000009467:17
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:
PF0020717=A2M=PU(9.9=15.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATTTTTACCAACACCAGAGTCCACA
R:
TCCAGCGGCACCATGTCC
Band lengths:
254-2049
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]