RnoINT0082305 @ rn6
Intron Retention
Gene
ENSRNOG00000003349 | LOC103693323
Description
collagen alpha-1(XXIII) chain [Source:RGD Symbol;Acc:9310824]
Coordinates
chr10:37026875-37028367:+
Coord C1 exon
chr10:37026875-37026913
Coord A exon
chr10:37026914-37027358
Coord C2 exon
chr10:37027359-37028367
Length
445 bp
Sequences
Splice sites
5' ss Seq
AAGGTACCT
5' ss Score
8.49
3' ss Seq
ATCTCTCCCTCCTTTTCCAGTGA
3' ss Score
11.13
Exon sequences
Seq C1 exon
GGCCCCGACGGGTTGCCTGTGCCTGGTTGCTGGCATAAG
Seq A exon
GTACCTTACAGGAAAGGGTCTCGAGGGTGGGCCCGGAGGAGTTGGGATGGGAGAGTTAGAGGGTCAGCGAGGACCATGGAGGACCAGGCACCACCATGAAGAGGTTTGAGTCTCTGCACTGCTGTCTCACACAGTGACTGCATAGTCATGTTTCCCCAAGATGTTTGTGACTTTGTGGTCATAGGGCCAAGGCTTGGAGCTTGGTCCTGGCTGATGTCTGCCTCGCTGGCCCATCTGGATCTTGGTTGGCATTTGGCCCTGCCAGTTCAAAACCATCAGGGGGTTTTCTGAGACTTATTTTAGCTGCCCCACTGAGAGGGGCCTGGAAAGGAAAGGGGGGGCTATGCTTGTTCCTGAACACATCAGCAGGGTAGAAGAAGCTAGTGGGGACCACAGGATCTCCCTAGGTTCCTCCATCACTTTCCATCTCTCCCTCCTTTTCCAG
Seq C2 exon
TGATCCTCGGGCATAGCCCCCAACCTGTACAGATCCGTTTGGATGTTTTTAACTCGTGTAAAAACAAAACAGTAATATATTGAACTTCTTTATGGGATGCGCCAACTGTGTGGCCTTGTAAGATTTGCAAGTGTGCCAACCAGCCCCTGGACCATCTGCACAGGAAGCCGGCAGGAACGCAGACAGGCTGGCTGCTCTGGGGAAACTTGTGTTCGAAGGCCCCCGGCAGGGCCTGGCTTTCCCAGGGAGAGGACGAGGGTGAAAACGCCTGGCTCAGGTGAGGATGGACAGACTCCAGGTCGGGCTTACAATCACCTGATTAGCAGAGACTTACAACAACTGTCCTCTGAAACCCCACTGCCCCAACTTCTCACTGTCCAACGACACCCCCTTGGACACCTGCTGTACCCTCTTGCTTCTGGACTGTGCCACAGGCAGCTGCACTGGGACCCTAGGTTTAACAGGGCAGGCGAAGATTCCTAGAGTCCAGCACTTGGGGAGAAGGCAATGGAAGAACCCAAGAGGGCCTTGCTCCACCCAGTTCAGTAGGCTTCCTGACACAGGAGCTTGTACCCTCTTCAGACCTTGGGAAATGGCAAGACTCTGTGGATACCTCACTGGCAGGCAGCCCAGTGAACCCTGACTGTAGGGTGAAGAGGCCATACCCACTAGTTGGTACTTCCTGTCTCCTCACCCAGAGCAGGAACAGGAAGTGGCTTTGTCAGCCCAAGGAGACAGGCCTCCTGTTCAGAACTTGTATCTCACTGGCCCCAAGTCTCTGACCTAGACCTCTGGTTAGCCTGACAGAAACAGGCCCCCTAGTAAATGACCCTGAAGGCTGGTCCCCCGGCAAGCCTGAGCAAAGCACCTGTGACTGAAACCCCTGCCCTCTCTGGAGAGGCTTGAACACCTATAACGAAGTTTCCTAGCTCCTGCTCCATCACGGCCTCACATCCCTCTGCATATAAAGGCACCATGAGCAATAAACCACAAATGTGCGTCCAGTATA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003349:ENSRNOT00000064078:27
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=NA
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTTGCCTGTGCCTGGTTG
R:
GTGATTGTAAGCCCGACCTGG
Band lengths:
344-789
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]