RnoINT0039486 @ rn6
Intron Retention
Gene
ENSRNOG00000050706 | Col25a1
Description
collagen type XXV alpha 1 chain [Source:RGD Symbol;Acc:1590105]
Coordinates
chr2:235709219-235711272:+
Coord C1 exon
chr2:235709219-235709313
Coord A exon
chr2:235709314-235711233
Coord C2 exon
chr2:235711234-235711272
Length
1920 bp
Sequences
Splice sites
5' ss Seq
TTGGTACAG
5' ss Score
0.92
3' ss Seq
TCCTTCCTCTTCATAACCAGGAC
3' ss Score
9.4
Exon sequences
Seq C1 exon
TTAATCTTTACAAACAGGGATTCCGTGGCGTTAAGGGGGAAAAGGGGGAGCCGGGCCAGCCTGGCCTGGATGGGCTGGATGCTCCTTGCCAATTG
Seq A exon
GTACAGTATTTCTCTTTCCTTCCATCCTGCATGCCATTCCTCTGTTTACTGTGTATTCGTCTGTATCAGTGTAAAGTGCTTCCTTCAGGAGCAAGCTTTACATGATAAGCATACTACATGTGTGTGCATGAACGGGCTCCTCCCCGGGCTCTGCATCGGGGAGAGAGCCAGCATGTATTATCAACGAATGTATATTAATCTTCTAACATTGTTCTCACTACTGGTGTGTCCATTTTATGTTCTTTGGAATATTAACTTACCCAATAAATATTCATAGATTACATCACACAATGGCTCTGCTAGGCCAGAACGTGGGGCTTTTACCCTACTTGATTTTTCCCCTGTCCTCTAAAAGAAAGAAAAGTAATTTTGTCTCTTCCATGATAGTTTTATCAGAGCATAAATAAGGCCAGTTGAACCTTAAGACTTCTATGGTCAAGAGTTAACCAATTTGAAGCCGCACTGTTAAGAGACCACAGGAAGGAAAACCAAACCCCCCTGTACATCTAAAGATGATAATTGTCTGCAGCCCAAACCCTCTTCCTTGTCACATAACCTTTTGCCATAATGGTCTCTCCTTTGAAAACTCACTTTCCTAAAGTAGATGGGACTCCTTCCTCCATTGGCATGACCTCAAAATCCTCCTTATACTAAAATCTAAAATTCTACTGGTTGATCCTTCTCCTTGTACCAATCTGGCATTACCGGTTTCTCCCAAATATTCATAAGGCTAGATTTTTTTTTTTACAATTAAAAAGGTAGCGTGACTATATTCTGTTGAGTACAAAGAAAGATTTATATCATCCCATTCTACTTGGTCTGCATGGCCTTACACCTGACTCTTCAGTTGTAAGCATGATTCTTTAAAGGTAAATGTATATCTCGTGAGTGTCTTATGAGGTTGTGTTTATAGAAAAACATCCAGTCAATTGTTACAGTTAGAAAATATTAATGTGGAGTACTCTGTCTTTTGTTGGCTTGGTGTTCATAAGTCATATTTCAGAAACCTCTTACTTGGAGGAAAACGCATGCCTGCAACTGTGTCACGTCTTCCGGTCTCATTTGTATCTGAAGATGCCTACACCTCAAACGACAATAAGCACTGTAGCATTTAGAAACCTTCGTTCACAATATTAACCGGCTTCTGAAGATTTAACCAGAAGCACTAATGAACGCTGTGAACGGTATCTACTATAACGCCTAGCTAGACTGCCTGTGTTTCAAATGAGTATATTTTTGCAGTATCTATGTGCAGTCTAGTCGAGGGAAAAGCCCTGGAACATGGAGACCTATAAACTTCAGATAGAAATGGCCTGCCATTGATTACCCTCACCACATACCACAGTCCATTGTGACACAGGGAAATGTTGCTCTGACTCGTTTAGTAAAAACAAGTATGGTATGTTTTATGCTGTCAAGAGGCACCGTGCAGGTGTGTTATTTAAAGATTTGGCTGTGGGGCTGAAGAGATGGCTCAGTGGTTAAGAGCACTGACTGCTCTTCCAAAGGTCCTGAGTTCAAATCCCAGCAACCACATGGTGGCTCACAACCATCTGTAATGGGATCTGATGCCCTCTTCTGATGTATTTGAAGACAGCTACAGTATATATATAATCTTTAAAAAAAAAAAAAAGATGTGGTTGTGAGCAAAACGCTGGGGCAACTGTGCCCCGTTCCTTTCCAAAATTAGGCATAGTGTTCTCTGTATTCGTGGTATCTTCTAGGTGTGTGCTCAGTCTGATAATCAGTTTCATTTTAACCAAGAGTGGGTAAAATATTGTGAGCCACTAATTAACACGAGATGCCTATGACTGGAGCCACCTAATAGAAATCATTTCTGAAGTCTCTTAGCCTATGAATGTGACATCATATTACTTGTCTAAGCCTAAGGAATTTTATTTCCTTCCTCTTCATAACCAG
Seq C2 exon
GACCCGGATGGATTACCTATGCCTGGATGCTGGCAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000050706:ENSRNOT00000071463:30
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.894 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(46.8=90.6)
A:
NA
C2:
NO
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]