BtaINT0069136 @ bosTau6
Intron Retention
Gene
ENSBTAG00000047202 | GRIN1
Description
glutamate receptor, ionotropic, N-methyl D-aspartate 1 [Source:HGNC Symbol;Acc:HGNC:4584]
Coordinates
chr11:105932137-105934097:-
Coord C1 exon
chr11:105933923-105934097
Coord A exon
chr11:105932282-105933922
Coord C2 exon
chr11:105932137-105932281
Length
1641 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGGC
5' ss Score
8.99
3' ss Seq
AACCACACTTCCCTCTCCAGGGT
3' ss Score
8.29
Exon sequences
Seq C1 exon
GCATCATCGGGCTGCAGCTCATCAACGGCAAGAACGAGTCGGCGCACATCAGCGACGCCGTGGGCGTGGTGGCCCAGGCCGTGCACGAGCTGCTCGAGAAGGAGAACATCACCGACCCGCCGCGGGGCTGTGTGGGCAACACCAACATCTGGAAGACCGGGCCGCTCTTCAAGAG
Seq A exon
GTAGGCGGGGCCACTCTCCAAGAGGTGGGCGGGGCCACTCGGTGGGGCCGCCCCCGGAGATGGGCGGGGCCGCTCTTCCAGGGCGGGCGGGGCCGCCCTCCAGAGTGGGCGGGGCCACTCTTGCAGGGTGCGCGAACTGATCTAATGCGGACTTGGTCCCTCTCTTCAAGAGGTGGGCAGGTCCGCCCCTCAGGGTGGGCGGGGCCGTTCTCTGAGTGGGTGGGACCGCCGTTCCCAGGTGGGCGGGGCCGCTCGTCAAGAGGTGGGCGGGGCCACTCTTCCAGGGTGGGCGTGTCTGATCCGTCTGAAGCGGGAGGGGCCACTCTTCCAGGGTGGGCGGGGTCGCTCTGAGGTGGGCGGGGCCGCTCCGTCTGAGGGGGTGGGGCCGCTCCGTCTGAGTGGGTGGGGCCGCCCATCTAGGGTGGGAGGGCCACCGTTCCGGCACCCGAAGAGTCGCTCCAGCCCAGCGTGCTGCGGCTACAAACACAGCCTCCTTCCCCGCTCCTCTCTGTCCCCACTTTGTCTCCATCCTCACCTCCATCCCCGCTGTGATAACCATCTGGTCCATTTCCAACACTGACACCATCGCCTCGAATGTCACAGAAGCATGGCTGCCTCCATTGCCCCTGTCCCCACCTTTAAACACTGCAGCCAACCTGAGACGCCACCCCAGCCACCAGGATGACTAATAGCCCTGGGGAAGAGGATCCTGCCTCAGGCGGGCACTGGGAGCTTCCTCAGGCCCAGGAGGTCAGACAAGGATTTGGGGGATGGCACCCAAGCCTGCTTCCCTGGTGACTCAGATGGTAAAGAATCCGTCTGCGATACAGGAGACTTGGGTTCGATCCCTGGGTTGGGAAGATCCCCTGCAGGAGGGCATGGCAACTCACTCCAGTATTCTTGCCTGGAGAATCCCCATGGACAGAGGAGTCTGGAGGGCTACAGTCCATGGGGTCTTAAAGAGTTGGACAGACTGAGTGACTAAGCACATCCAAGTCTGCCGAGAGCCAGGGTTGGCAAGATACACAGTGAGTGGCTGCAGCAGGGCAGGAGTTAACACACAGAACCCTGGACACTGTGCCACTAGTATGGGGAGGCCCAGTCCATCACCAACACCCACCCCCAAGTAGCAGGTGAAGAGTCCTGGTCCATAGTGCCCACAGCAGGAGCACACACAACTGCAGACATGCAGCATATGTGCACATAGGCGCATGCGTGTATATGCAGATTCGGAGAGGCTCATGGAACATCACACCTGTGCCACAAGTACATGCACAGGGCTGCACCCCATACAAAGATCTTGTGTGTGCACACATATATGGCCCAGTGGACACACCACACACACACACACTCACGTGTGCACATGCAGGAAGATGAGAACTCAACCCAGCCTCTTCCACTCACTGGTGAATGGGCCACCGAGTCCTACCTGGGCTTCTGCCACCTCATCTGTAAAGCTGTGAGAATCAAACGTCCTAGCCCGCAGGAACCCCTCAAAACAGGGTCTAGAGCCAAGGAGCTGCTTGGCTGATGTGGCTGTGCTGTCCATCTGGCACCGGCGGACGGGCTCACCATCCAGGCAGCTCACGGTGGGAGCGGGGATTGCATCCCTGATTGTTCCAACCACACTTCCCTCTCCAG
Seq C2 exon
GGTTCTGATGTCTTCCAAGTATGCAGACGGGGTGACCGGCCGTGTGGAATTCAATGAGGATGGGGACCGGAAGTTTGCCAACTACAGCATCATGAACCTGCAGAACCGCAAGCTGGTACAAGTGGGCATCTACAACGGCACTCAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000047202:ENSBTAT00000065439:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.068 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0109423=ANF_receptor=FE(17.0=100)
A:
NA
C2:
PF0109423=ANF_receptor=PD(10.0=69.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATCATCGGGCTGCAGCTCATC
R:
ATGAGTGCCGTTGTAGATGCC
Band lengths:
318-1959
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development