DreINT0075094 @ danRer10
Intron Retention
Gene
ENSDARG00000025728 | grin1b
Description
glutamate receptor, ionotropic, N-methyl D-aspartate 1b [Source:ZFIN;Acc:ZDB-GENE-051202-2]
Coordinates
chr5:29010868-29013751:-
Coord C1 exon
chr5:29013642-29013751
Coord A exon
chr5:29011014-29013641
Coord C2 exon
chr5:29010868-29011013
Length
2628 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGA
5' ss Score
9.46
3' ss Seq
AATGTATTTTCATCACACAGGCG
3' ss Score
6.89
Exon sequences
Seq C1 exon
TTCCCATGAGAACGGCTTCATGGAGGACTTGGATAAAACCTGGGTTCGATATCAGGAGTGTGACTCCAGAAGCAATGCCCCAGCCACGCTCACTTTTGAGAATATGGCAG
Seq A exon
GTATGAGGCACCTATGATCGACTTCACTTGTTGTCACATGTGATCTATACACATGCACAGTATGTGTATGCATTACATGTATTTCATTGTTTCTGCCATTTACAGAATTAAATAAGTTATTTTTAATGTTGCACAAAACTTCAGCTAATCACAGTTGATTTGTAAAAAAAAAAAAATTATATCCTTTTAAATCTTTAAAATGATTGGTCACACAATTTAATTCTGTTATCATTTATTCTTTTGAGTTTCTTTCTTCTGTCAAACACATACAAAGATATTTCCAAGAATGCAGAAAACCTGCATCTTGACCTTGACTTCCATGGTAGGAAAAACAAAGTCAATGTTAGTCAACTATTGAAATCTATAGAGTTGGGTATTGTTTAGGGTTATTTCAATACTGGTGCTAAATCGATACTTTTAAATTGGTACCGGTGCCTAACCCGATACTTTTGAGCCACAAAATTATGGTGGATGACTCTAGACAAGTCTTTTAATTTACAAAAATATATATTTTAATCATTTTAATTGAAGAATATAATTAAAGTTTAAAGTATACATCAATTCATATTTTGTATATTTGATTTGAATTACATTGATATATTTCTTCTGAATTTAAGATTTGGATTATGCAATTAGCAATACATTAGCTCACTACTAACCTGTGTAAAGGCTGTCATCAAAACCAAGAAACACCTTATTTCTAGAGTTGGGGCCGTTTTACATATAGCGCATAGATTCATTAACATCGTCATTGAACCACCACGCTATCCACGTTTCCGCCGTAGTTTCATGTAATTTCCATTTTTTTTTTTTTATTTTGTAGACTTTAACTGCAGTTTCACTTTCATTCAGCAACATATTGTTAATGCCACGTCACAAGCTGAGGTATTGAATGAAAATATAATGTAAGGACTGGTGGAAGAGTGTTGTTTTAATGGAATTTGATACTGCATGCCGAATGGAAAGAAAAAAACTCCACATTTCGTGACTCTGGTGTCTGTGGTCTTTTAAGGTAATCAAAAATCACTGTTTACATGGCAGACTCTTAATCAGAGTATTGTCTTAAACAGATTAAAATCAGAGTATTGGTGTCTATGTAAATGTAATTAGAGAAAGTGCCAGATGACGTCGCAAGCTGTCAAAGGTAATCCATTCCTCCCCTTTAAGTTGATTCCATGAGCCCTCAAATTTTTCATTAATGTTTGATGTGTTTCGCCCTTTACATGCAACTTTTGTGAAGCATCTGCTTCATGTTGCTGTGCCAGAATCCTTGCTTGTAAAATACAGCCATACTTTAGAATGCTTAGTTTAAGCAAATTTGAAGAACCGTGATCATGCGTGTTGATGAATCTGTAGGGAATCGCACATAAGGATGTGATATACTACGCACATTGCCTAAGTGCATTCCCTTGTTAAGCAACAAGAACACATGCTGATGATGTCCGTATCCCTCAAAATTGTTTAGAATTAAATGTTTAGAGATGGTGTAACACAACATGTATCTATGTGTGCCTTTGATGTATCCCTTGATGCTTGTACATCCTTGTCGCAGCACCAGTGGCACCAAAATTTATACACTGATTCGGTCACATACCAGTTACACAGGAACCAGTGCCTTAATGGCACCGGGTTTCAGTACCCAACCCTAGAAGTCAATGGTTACAGGTTTTCAACCATCTTTCAAAAAAGAAAGTGTTAAACAGAAGAAAGAAACTCAGAAATGTTTAGAACCTTTTTTGAGTTTAGTAAATAGTAAGATAGATTTCATTATTGTGTGAACTATCCCTTTTACCAAAAACTAAACAGGACACCTAAAGCCTGGATCACACTGCACAATTTTTAATAATCCTAAACCATTGCAGCATGACTGCACAAACATGTCTCCCATGTCACACTGTAAGATCTCAGCTGTCATAATGTCAGACTGAATGACATTAAAAATGCGCCAAACACAGAAGAAAACTCTCCTGCAGTTTGACGTCATCCATCCATGACACTTTTCGTCATTTCTCACAGCAAACATAAAGCAAACATAAACAATCTGTAGCAGCAATTTTGCATGCAGCATGCCTCAAATAATAAAACCAGCAAGACAAAAAACTATTTTGACATTTCCCTGCAGTCATTTGAAGTTGTTATGCAGATTGTGTAGCTGAGCCTGTTGTCACACTGAAGAACTGAAGAAAAGGGTTGGAAATTTTCTGAAACTGACAGAACTTCATTGGAGGAAAAATCTGATTGCAATTGCCATTAAGCAGCTGTCTATGAACATGCCAACCTAAAGATCAAATATCACATATTTTAGCCTAAAATCTCTCCCAAATTTGTCTCAGACCACCAAACTGTGGCTGAAATCCCACAGTGTGAGCATGGCTTAAGCTTGATAAGTTTCCAAAACAGAAAATTAATCAGTAAAATTGCAATTATCTTCAACTATCTTGAACCTTTTAGAAAGACTAGATCGTCCAATATCATGTTTTGTCTACTGGTTTACAAATACTCTGAAATCCGGCATACTACTCAGCTAACATAATAATATATAAGTAGGCATATTCACACACAGGGTCTATCCACTGCCAACTTAGTTTAGACTCTCTAGAATTAAGGAAATGTATTTTCATCACACAG
Seq C2 exon
GCGTGTTCATGTTGGTGGCTGGTGGCATAGTCGCCGGGATCTTCCTCATCTTCATTGAGATTGCATACAAACGACACAAGGACGCCCGCAGGAAGCAAATGCAGCTGGCCTTTGCAGCAGTTAACGTCTGGAGGAAGAACCTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000025728:ENSDART00000034849:18
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:
PF0049715=SBP_bac_3=PD(5.0=44.7),PF0006021=Lig_chan=FE(13.9=100)
A:
NA
C2:
PF0006021=Lig_chan=PD(3.4=18.4),PF105624=CaM_bdg_C0=WD(100=59.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]