RnoINT0125963 @ rn6
Intron Retention
Gene
ENSRNOG00000008239 | Repin1
Description
replication initiator 1 [Source:RGD Symbol;Acc:1549707]
Coordinates
chr4:78233332-78236781:+
Coord C1 exon
chr4:78233332-78233525
Coord A exon
chr4:78233526-78234732
Coord C2 exon
chr4:78234733-78236781
Length
1207 bp
Sequences
Splice sites
5' ss Seq
AGGGTAGAG
5' ss Score
0.88
3' ss Seq
TTGTGCTTTTCCATCCTCAGCAG
3' ss Score
7.56
Exon sequences
Seq C1 exon
TAAGGCTGACCTCTCAGCAGTTAGAGGTCTGAGCTCTGCCATGGGGATAGGGATGTCTTTATTGCTACAGTTTTCTCTGACATCCGGGGGCTACCGAAGTGTGGGCCGAAGCAGGCGCTGCAGCAGAAGTATCCCCAGGAACATCCCCAGAAGGAGCTGGAAAAAGCCTCATCCCCAGCTCTGCAGTCTTCAGG
Seq A exon
GTAGAGTTTGGCCTTTCTTGTGCCCTCAAACCAACCCCAAACTGAGCGCTCATGTCTCGTATACTTGCAGAACAGGGACGTACTGGGGAAGGAATCCATTCTCATATCGTGGAGTCTTCCCTGGGTTCAGGCGTGGGTGGAGTGGGGGTTGATGGGGTTGTGAGTCAGTCCGTAGTCCCTCAAGAGAGCAGGTTGTAAAGGACCCAGGAGGCTGCCTCTGGACAGAGGCCATGAGCAGACATGAAAGTCTCTGGAAAGTCTTACTGCCACCCCTCAACTGACTCTGTGTAGGAGGCTCTCAGGAATCTGGGCTCCCTGTGGGGTATAGCCGAAGATGGGGCAGTCCTTGGCCCGGTTTGGGCAGGATCAGGCAAGGGACAGAGATTACAATCTCTTCTTCCCACTCGTTTCTTTACCCCAGCAATCCCTAGCACTCTTAAGAGGTGCTGAGCCAGGGTTCTTCCTCACCTCAGGGGAGGGGCAGCAGACTGTAGGTGTTCCTTGGGTTGAGAAGTGCTTCCCCCCAACCCCCATCCAATGTTCCAATTGCAATTGCTTGGGTGTGGTTGGAGAAGGCTGGCAGGCAGACTGTGGATAGTCTGGATACGAGGTGGCCTGGCATTAGAGCCACCTTGCCCACCTCCTGGGTCTGAAGAAAGGCTGTTCCCACTTGCCCTCCATGCTTAGAGCCGAGCTGGAGAGGCTGAAAGAACCTTCCCAAGGTTTTAGTCAGATGGGTTTTGAGGAGATCTCCGCACACCTAGGTGTTAATGAGGAGTACACACTGGCCTGGATGTTCACCAGATCCTGTTCCCAACTTTGGTTTACTAATGGTTTACAGTGTCACCTCAGGCAAGTCCTACCACCATTTTATGCCTCAAACTTGCTTCATGTGTCAAGTAGGGAGCTCCGATGTGGTAGAAGGGAGTGCCTGCCACAGGGAAAGGCAACAGGAGGTAGGGTACAGTACGAATATTCAAGAATATTTTCTGTAAGTCCTTCTGACGTAAGGTAGATACCATGGGAGAAATCCCAAGGAGTATCAACATGCCTCCCTTCTGTAAGTTTCCAGGGCAATAAAGATACCAAAATAGCAACAAAATAGAACAGCGATGACAGTTCGCAAAGGGAAGCTTTCTTCTTCCTTGGGGTCGGAAAGGAGAAACTGGGGTTAGTTCCTGCAGTGATTGTGCTTTTCCATCCTCAG
Seq C2 exon
CAGAGGAAGAACCGATGCTGGAACGGCGCTGCAGGGGCCCCACGGCCATGGGCCCAGCCCATCCCTGGCTTTTTTCTGGGCCCTCCCAGGAGTCCTCCCAGCCCAACAGAGGGTTGAGGTATCAAGGCAAATCAGTAGCACAGCCAGGAGGCCCAGCCCCAGTCAAGGTCCATCGTTGTGCCCACTGTCGGAAGCGTTTCCCAGGCTGGGTGGCCCTGTGGCTTCACACTCGGCGGTGCCAGGCCCGGCTGCCTCTGCCCTGCCATGAGTGCAACCAGCGCTTTCGCCACGCCCCCTTCTTAGCGCTGCATCTTCAGGTTCATGCTTCTGCAGTCCCTGACCTGGGTTTCATCTGCCACCTATGTGGGCATAGCTTCCGAGGCTGGGTAGCCCTGGTTCTGCATCTGCGGGCTCACTCGGCTTCAAAGAGGCCCATCACTTGCCCTGAATGCAACAAACGCTTCTGGCGACAAAAACAGCTTCGAGCTCACCTGCGGAGGTGCCAGCCCCCTGCCCCTGAGGCCCGGCCCTTCATATGTGGCAACTGTGGCCGGAGCTTCGCCCAATGGGACCAGCTCGTTGTTCACAAGAGGGTGCACGTGGCTGAGGCCTTGGAGGAGGCAGCAGCCAAGGCCCTGGGTCCTCGCCCGCGAGGACGTCCTTCAGTGACTGCTCCCAGGCCTGGTGGAGATGCTGTGGACCGCCCCTTCCAGTGTGCCTGCTGCGGCAAGCGCTTCCGCCACAAGCCCAACCTGATTGCCCACCGCCGCGTGCACACTGGCGAGCGACCACACCAGTGCCCAGAGTGCGGGAAGCGTTTCACCAACAAGCCCTACCTGACCTCGCACCGCCGTATACATACGGGCGAGAAGCCCTACCCATGCACCGAGTGTGGCCGCCGCTTCCGCCACAAACCCAACCTGTTGTCGCACAGTAAAATCCACAAGCGCTCAGAGGTCTCAGCGCAGGCTGCCTCCCACACCGGGAGTCACTTGATTGCAGCGGAGCCTATGGCACAACCTGCGCTTGGGGTGCCCCTGGGGTCCCTGAGGACCCCGGCCGAGGCACCTGCGTCCCTGCATAGCTGCACTGACTGCGGCCGCAGCTTCCGGCTGGAGCGTTTCCTGCGGCTACACCAGCGGCAGCACACAGGCGAGAGGCCCTTCACCTGCACAGAGTGTGGCAAGAACTTCGGCAAGAAAACGCACCTGGTGGCGCACTCACGCGTGCACTCGGGCGAGCGGCCCTTTGCCTGCGAGGAGTGTGGTCGCCGTTTCTCACAGGGCAGCCACCTGGCAGCCCACCGGCGCGACCATGCACCAGAGAGACCCTTTGTGTGCCCAGACTGCGGCAAGGCTTTCCGCCACAAGCCCTACCTGGCCGCGCACCGACGCATCCACACAGGCGAGAAGCCCTATGTGTGTCCCGACTGTGGCAAAGCTTTCAGCCAGAAGTCCAACCTGGTGTCCCACCGGCGCATCCACACAGGTGAGCGGCCCTACGCCTGCCCCGACTGTGATCGCAGCTTCAGTCAGAAGTCCAACCTTATCACACACCGGAAGAGCCACATCCGGGATGGCGCCTTCTGCTGTGCCATCTGCGGCCAGACCTTTGACGATGAGGACCGTCTCTTGATGCACCAGAAGAAGCACGATGCCTGAGAGGGACCCAGGAAGACAGGCCTAGATGTCCTTGGCAACAGGGTGTCAGTGGCCTGGGTGGGGTACCTACACTGACACTGTTAGAGGGACAGGCGGAGATCCCAGAGGGATAGAGGAGACAGTGATCTGGGCTCTGTTTAGGAATGGACTTTCTCCCAGGTGACCAGGGAACCCATTTTAGAATGCCGGGATCTGGGTTTGAGCTAGTCAGGCCCCCAGCTGGTTTTTCTAAAGGTCAACTGAGACTGCCCTGTACCCTGGAAAAAATAGCAATAGCAGCCCCATCTACCCTTTGAGTCCTCAACTAGCCACCAGTGGGAAGGGAGCCACTCCATCCTCTGGTGTTAACGCCTTAATGTCCCCAGTCTTTACTATGAGTTACTTCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008239:ENSRNOT00000011032:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.192 A=NA C2=0.250
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF134651=zf-H2C2_2=WD(100=4.9),PF0009621=zf-C2H2=WD(100=4.2),PF134651=zf-H2C2_2=WD(100=4.7),PF134651=zf-H2C2_2=WD(100=4.7),PF134651=zf-H2C2_2=WD(100=4.5),PF134651=zf-H2C2_2=WD(100=4.7),PF134651=zf-H2C2_2=WD(100=4.7),PF134651=zf-H2C2_2=WD(100=4.7),PF134651=zf-H2C2_2=WD(100=4.7),PF138941=zf-C2H2_4=WD(100=4.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCTGCCATGGGGATAGGGAT
R:
GCACAACGATGGACCTTGACT
Band lengths:
342-1549
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]