RnoINT0154792 @ rn6
Intron Retention
Gene
ENSRNOG00000010694 | Tpbg
Description
trophoblast glycoprotein [Source:RGD Symbol;Acc:621453]
Coordinates
chr8:93491761-93495130:+
Coord C1 exon
chr8:93491761-93491795
Coord A exon
chr8:93491796-93492832
Coord C2 exon
chr8:93492833-93495130
Length
1037 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAT
5' ss Score
8.39
3' ss Seq
TTCTCTCCCTCGTGTCCCAGGTC
3' ss Score
10.45
Exon sequences
Seq C1 exon
CAAGAGATCCACCAGCGGTTTTGTTTCTGTCCGAG
Seq A exon
GTAAATACGCTATGCAAAATACGGAATCACCAAAGGATGCCGGGGAGGGGGAACAGAAGGGGAATCCCTCACCTTCCCGGGGCGCGTTGCTCACTTATCTCCGCCTGGGGGAGTCTCCCAGCCTAGGTACCCCTCGTCTCCCTCCTTAAAGCCCCCACCTGAGGCAGCAGAGGTGGGCTGCGCGGCGGCGATCTCTCCCGCAGCCTCGGCCCTCCCCCGCCCCCCGGCTTGGTTTTTCCCGGTCGTGGAGGTTGGGCCAGGGGCTGGGGTGAGAGGAGAGTCGGCGCCCGCAGCAGGAGCCGGGAAGGCGCGTGGACTGGGGTGGCCCTCGGAGTTGGCTTTGGAAGCGCGGGGCGCGGAGGTGAGCAGTGGGACCGAGCGGCCAGGTTTGGAGCCTGGAGGCGGGACCCGGGCTCCGTTCTATACCAGGGCGTGATGAGAGCGGGGGTCCTGGCTGCTACCCCGCCCACGGTCCCACGGCCGCTTCGTTGGCGGGTTCCCTCCGCTCTTCTGGAGGCGCCTGGACCCTCTCGGGGTCGGGGAGCTGGAGGCCCACGAGTCGAGAGTGGGCGACAGCTCTAGGGCTCTGCTCTCCTTTCCCCACTAATCCAAGGAGGTACAAAAGAAGGGCTCGGAAGAGTCCAGTAACCCGAAACTTCGCTCGCAACCCAACCTGGGAGGGGAGGAGCGGCGGGGGCGGGGACCCCGGAAGGCAGGTGGTCGGCGGGGGCGGTGGGAGCTGGGATCCGGAAAAGGGAGAAGTTTTCTCGCTGGACTCCGCGGGGTCTGCGTGAAGTTCGAGGCGGGAGAAGGGCAATCCGGCTAGAAGCCAGGCGGGAGGTGGCCCGGGTACTGATGGTGTGGGCCCGGAAGAGGAAGGCTTAGCGCTCGGGAGTGGGGACCGCGTCCCTCTGGGGGGGCGGGGGGGGGAACGCGCACAGAGGCTTGGGCTGGGAGGCTAGTGTGGGGGCAACTTGGTTAATACTGGGAAGCCGCGGTCGTCACTGCTCCTCACGCTTCTCTCCCTCGTGTCCCAG
Seq C2 exon
GTCGCCCATCCGATCCTTCCCTGAGAGAGGCGCCAACAAAGGAGTTGAGGAGGTGCCACCCACCCCAGCGGCGGCTGGAGGAGGAGCGCCAAGGCCCGTGTCCCGACCCGCCGTGCGTACTCACTGGAGGGAAGGGCGGGGTACCGCTCCGGGAGGGAGACGCCCGGTGGCCCGGGGTTAGCCAAGTTCCAGCTTTGGCGTCCCTTCCTTGGCTCCCACGCGAGGAAAGTTTGCCGTCGACGCTTGCGGCCGTCTCGCGCCCGCCGGGCCCAGGCGGTCGAGTCTTCGGAGCGGGCACCGTCCCAGCTCCGGGGAACCGCGAGCCGCGATGCCTGGGGCGGGCTCCCGGGGCCCCTCTGCCGGGGACGGACGGCTGCGGTTGGCAAGGCTGGCGCTAGTGCTGCTGGGTTGGGTCTCCGCGTCGGCCCCCAGCTCTTCGCTACCCTCGTCTTCCACCTCCCCGGCTGCCTTCCTGGCTTCGGGGTCTGCGCAGCCTCCGCCGGCCGAGCGATGCCCCGCTGCGTGCGAGTGCTCCGAGGCGGCGCGCACGGTTAAGTGCGTGAACCGCAACCTGCTGGAGGTGCCTGCGGACCTGCCACCTTACGTGCGCAACCTTTTCCTCACTGGCAACCAGATGACCGTGCTCCCGGCTGGCGCCTTCGCCCGCCAGCCGCCGCTCGCCGACCTGGCAGTGCTCAACCTCAGCGGCAACCACCTGAAGGAGGTGGGTGCAGGTGCCTTCGAGCATCTGCCCGGCCTTCGCCGGCTTGACCTCAGCCACAATCCTCTCACCAACCTCAGCGCCTTCACCTTCGCGGGCAGCAACGTCAGCGTCTCGACCCCCAGCCCCCTGTTGGAGCTGATCTTGAATCACATCGTGCCCCCTGAGGATCAGCGGCAGAATGGGAGCTTCGAGGGCATGGTGGCCTTCGAGGGCATGGTGGCAGCTGCCCTGCGCTCAGGCCTTGCACTCCGAGGGCTGCATCACCTAGAGCTGGCCAGCAATCACTTTCTTTACCTGCCTCGGGACTTATTGGACCAACTGCCAAGTCTCAAGCACCTGGACCTCAGGAACAACTCCCTGGTGAGCCTGACCTATGCATCTTTCCGCAACCTGACACACCTCGAAAGCCTCCACTTGGAGGACAATGCCCTCAAGGTCCTTCACAACTCCACCTTGGCTGAGTGGCAAGGCCTGGCTCATGTCAGGGTGTTCCTGGACAACAATCCCTGGGTTTGTGACTGCTACATGGCTGACATGGTGTCTTGGCTTAAAGAGACAGAGGTGGTGCCGGATAAAGCCAGGCTCACCTGCGCATTCCCAGAAAAAATGAGGAACCGTGGCCTCTTGGACCTCACCAGCTCTGACCTGGACTGTGACGCTACCCTTCCCCAATCCCTGCAGACTTCCTATGTCTTCTTAGGTATTGTTTTAGCTCTGATAGGCGCTATTTTCCTCCTCGTTTTGTATTTGAACCGGAAAGGCATAAAGAAGTGGATGCATAACATCAGAGATGCCTGCAGGGATCACATGGAAGGGTATCATTACAGATACGAAATCAATGCGGACCCCAGATTAACAAATCTCAGTTCCAACTCGGATGTCTGAGAACTAGGACTGGCCAAGGAGGACTCTGCATGAGGTGTATGTAGACTTAAGGTCCCTCCCCCCCCTTTACTATGCTTGCTCCACTTCCACCCTCCACCGTAGACACCATTGATTTTGATCCTCGTTATGTAAAATTCTTGGTGTGTTCTGTTAATGTAAGGACATGAACAACTGTGCATATAATGTTTATTTACCCCTTTCCTTTTGGTACTCCTCGATGCCTGCAGAGGGACTTTTTTTTTTCCTCTCAAGTTGCAGCATGGACATGGACTCTTAGTTGAGCTCAAGGCGTAGCACAGATAACATTCAACGGGAGCTGCCTCAATTTCTTTTTTCTTTTTTGAGAAAAGTACTTTATTCATAAATATGAGTTTTATTGTCACCTACCTAAATTATGGAGGAAATATTGCATCCCCAAATTGCCTGCAGACCTTAGCAAGCTCTTACCTAGAACTTGGTAGTGCACAGGAGCACCTGCATCCGAGAGCATGCGTACATTTTACTGTTCTGCATATTAAAAAAATTGCAACGTCAGATAACTTCTTTGACAGACTAAATTACTTTTTTGATTGCAGTTTACATGAAACTGACCCGAGGTTTTTCTTTTTCTTTTTTTATAAACTGCATTGAGACCCAACAGACTGGATTGTTATATAAAAAAAGAAAAATCAATAAAAGAGTCTCAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010694:ENSRNOT00000014326:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
PF0146213=LRRNT=WD(100=7.0),PF138551=LRR_8=WD(100=15.0),PF138551=LRR_8=WD(100=17.8)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGATCCACCAGCGGTTTTGT
R:
TGCCCGCTCCGAAGACTC
Band lengths:
329-1366
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]