HsaINT0035490 @ hg19
Intron Retention
Gene
ENSG00000099622 | CIRBP
Description
cold inducible RNA binding protein [Source:HGNC Symbol;Acc:1982]
Coordinates
chr19:1271980-1274809:+
Coord C1 exon
chr19:1271980-1274439
Coord A exon
chr19:1274440-1274647
Coord C2 exon
chr19:1274648-1274809
Length
208 bp
Sequences
Splice sites
5' ss Seq
CCTGTAAGT
5' ss Score
7.52
3' ss Seq
TCCCTTCCTCCTCCTTCCAGGAG
3' ss Score
12.93
Exon sequences
Seq C1 exon
CCGGAGTCAGAGTGGTGGCTACAGTGACCGGAGCTCGGGCGGGTCCTACAGAGACAGTTATGACAGTTACGGTAAGTCACACTCCGAGGGCGCCACGCTGCTGTGGCCTGCGGTGGGAGCTCGGTTCACCTTGGTGCCCTCTCCAAGCACTTTAGGCTGGACACTCAGACCTTGTCACTGTGCTTGCCCAGAAGAGGCGCATCTGTCCTCTCAGAGCCATTTCTATCGCAGGACGCAAAAGCCAAATGAGACTGACCAAAAAGGCAAGGGAGAGCGAGGGCCCGCTGGGCAGTCAGCTAGGTGCATGTGTGGCCGCAGGCCAGCCTCCCTCGGCTGTGGGGGGTGGTTGCTCCCCGGCCGCAGGCCGCGCCCTGGTCTGGCCTCTGGGGTGAAGCTGCCTCTTGTTGCTTCGGTGCCTTTACACTGTGCCTGCTTCTTGTCCTCAGCTACACACAACGAGTAAAAACCCTTCCTGCTCAAGATCGTCCTTCCAATGGCTGTGTGTTTAAAGATTGTGGGAGCTTCGCTGAACGTTAATGTGTAGTAAATGCACCTCCTTGTATTCCCACTTTCGTAGTCATTTCGGTTCTGATCTTGTCAAACCCAGCCTGACCGCTTCTGACGCCGGGATGGCCTCGTTACTAGACTTTTCTTTTTAAGGAAGTGCTGTTTTTTTTTGAGGGTTTTCAAAACATTTTGAAAAGCATTTACTTTTTTGACCACGAGCCATGAGTTTTCAAAAAAATCGGGGGTTGTGTGGGTTTTTGGTTTTTGTTTTAGTTTTTGGTTGCGTTGCCTTTTTTTTTTTAGTGGGGTTGGCCCCATGAAGTGGGTGCCCCACTCACTTCTCTGAGATCGAACGGACTGTGAATCCGCTCTTTGTCGGAAGCTGAGCAAGCTGTGGCTTTTTTCCAACTCCGTGTGACGTTTCTGAGTGTAGTGTGGTAGGACCCCGGCGGGTGTGGCAGCAACTGCCCTGGAGCCCCAGCCCCTGCGTCCATCTGTGCTGTGCGCCCCACAGTAGACGTGCAGACGTCCCTGAGAGGTTCTTGAAGATGTTTATTTATATTGTCCTTTTTTACTGGAAGACGTACGCATACTCCATCGATGTTGTATTTGCAGTGGCTGAGGAATTCTTGTACGCAGTTTTCTTTGGCTTTACGAAGCCGATTAAAAGACCGTGTGAAATGAACCTTGCTCTGACAATTCCCTTGCATTGCACCACACACTCCTTGCTGCGGGCTCCTGCAGCCAGACCTGAGCAGAGAGAGAAGGTGGAGAAGCAGCGGGTCTGCAAGCCTTCCCTGGGGCCTGCAGAGCTAGAAAGGGAGGCCCAGCAGACTGGCGCTGGTCAGGGTAGGGGAGCCAGGCGGGGGACGGGAGCGGGCAGCTCAGGCCTCAGGGCAGCCCTGGGAGGCTTCTGGCAGTGGTGGCCAGAGGGCTGGACTGTGCGGGCAGCTTAGCAGGGACAGTGGACGTGCACCTGACGCTGACCTGGACTGCCTCAGTCTAGAAGCAGGCCAGAGAGCAGAGGCACGTGGCATCCCAGGGCGACCTCAGACGGCCAGCCGGTTAGCTAGTTCTGCTGTTGCTTCACGAGTTCTGAGCATTCTCTGCTAGCCTATGGAAGCTGCAGCCCTCGGAGGACAGAAGTGTTGTGCGCCCAACAGAACCCTCTGAGACGCAAGCTGCTCCCTTGGCTAGCTCATATGTGGAAATAGCCCTGTAATTCGAGGTAACTCCTTCCGCTCGTGTCCACATCCCTCTTGTTGAGAGCTCACTGAAAGTCATGTGCCCGGGGAATGTTCCTGTGACTGTTTTTTGTTTTTCCTTTTTTTTTTAACTTTGTTTTTGTTTTTTTCAATTAAGCTGGAACTAAAGTCAGGCCCAGCCATTACGCTCCCCACGTGCAGCCAGGTGCAGCCTGGGCCCAGTCATGCCTGGCTCATAGATGAAATCCCTTAAGCAGGATTGAAGACCAGTGAACGCCCCCGCCTTTTGGATTTTTTGCTCAATTGACCGTCTTTTCCAGACCTCTTTAAGTCACACTCTTAACTTAGCTTTCTCTGATGTCTGTTGCCGCCATTAGTTTTTTTCTAGAGCCCACACTGGCCCACATAGCTCCATCCCATACGGGTAGCTGGCTCCAGCTGCGCCAAGGTGCAGACCCGCCCTGGGCATGCTGGCCTGTGACGGAGCCTGAGGTCACAGCCCCCTGACTAGCCTGAGACCTTCCTAGGGGCTGTGGCTGTTTCCGGGGAGGCCGGGAGGGGCAGCTGTGAGCCCTGTGGAGGACGTTGGGAGTAACGCTGCTTTGCTTTGGCAGGTTGAAGGGGCCCGGCCAGGACTCGGGGAAGGGTGGCCTGAGAGCAGCGATGACCTCTGGGGTCACTGTCCCAGGAGGGACTTCACCTGGAACAAGAGCTGGAGGCAGCCGCTTGCCCAGGAGGCTTGTCCCCT
Seq A exon
GTAAGTGCTTTCGGGAAGAGTGGCATGTGGCGCTGAGCCCTGTCCCGGGCGGCACCTGGGCGTTTCAGTGAGTCCTGCTCTCCCGCACCTATGGCCCCATGGCGGGCGCCTTTCGGTGTGTGTTGGGTGCAGGGCAGCGCCTCCCGGGAGCGCCGGGTCCCCCGCCTGGAGCCCGCGCCTGTTCTCCCTCCCTTCCTCCTCCTTCCAG
Seq C2 exon
GAGGCGCTTCGCCAGTGAGGTGCGGGCTCAGGGCCTCGAGTCTCTCCTGGAGCACGGGCTGCGGTGCGCCGGCAGCTTACGGGGCGGCCAGTCCTTGCCCACAACGATGTGGAGCCCTGTGAAAGTCGGATTCGAATAAAGGGCCACGTGTGCACCCAGAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000099622-CIRBP:NR_023313:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
NA
No structure available
Features
Disorder rate (Iupred):
C1=0.384 A=NA C2=NA
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
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:
CTGTGGAGGACGTTGGGAGTA
R:
CTTTCACAGGGCTCCACATCG
Band lengths:
300-508
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)