GgaINT1009836 @ galGal4
Intron Retention
Gene
ENSGALG00000004286 | COL13A1
Description
collagen, type XIII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2190]
Coordinates
chr6:10599129-10600716:+
Coord C1 exon
chr6:10599129-10599185
Coord A exon
chr6:10599186-10600650
Coord C2 exon
chr6:10600651-10600716
Length
1465 bp
Sequences
Splice sites
5' ss Seq
AAGGTTTGT
5' ss Score
7.81
3' ss Seq
CCTTCTGGTTTGATCTCCAGCTG
3' ss Score
8.25
Exon sequences
Seq C1 exon
GAGTACCTAAGTACCACCCTTGCAGCCCTGCGCTCTAACCAGATCCTTACGCTGAAG
Seq A exon
GTTTGTGGGTAACGGTCTGACAGACCAGTTTTGATGCAAAGGCACAAGGCATCCAATATTGCATGTTCCTCTTGCCATTGGGTCCAGAGGGGCAGGGATGGCTGCAGGAGGCTTCAGGCTCTTTCTCTAAATGATCCTACTTGCACCCAAGTCCATTGTTAGATCTTGTCTCTGTTTTCGGAGGGACTCTTACTGCTTCCCTCCATTTTCCCCTTCACCTTTTCCAGCATCCTGCCTCTGCTTCCCTGTAAGCTGTGTAATATTTCAGAATCAGTATATTTGAACACGGCCACCTGAGCAGAGGGTGGCAATGCTGCACTATTGGATGGCCGCTTCCCTTTGCAACAAGACTGTGTCCTAGCTTTTGCAGCCAGAGCAAGGAGTGGCATTTAAAGGGACTAAGCAGCACTGCTGGGGTGCGCGGTCACTGTGGTGGGAGACCTGCAGGCACACCTCCGGGATCCGAGCACAGCTCATGTGGAGAATGGCTGCGCACAGGGGCACAGGCTTTTGTGCTTGAGCACAGAATGCTCCTTTCTCTTCTCCCCGTGTAAATCGAGAACAGCTTCAATGGAAAACTGATAGGAACAGGAAAGCGGATCAGGCCAGAGGAGCATTCCTGGGCCTAGAGCTGCCGTGGTGACTGCCAGGCTGACAGCAGCGTGTATGCAAGTGGAAACTGGATACTGCAGGAGGATGAACAAATGCTCCTGAGCTTTAGTGCATTTGATTGCTGTGTGTCCGGGTCAGCTTTGTGCACTGGTGCAGCATTCCTGACTATAAGCAGTTGGAAGCTGCTGTTACTGTTAAGCGAGAAAAAGCAAAGTGCAGGCTACCAAGGCAGTACCCTGCCCAGGGTTCAGAGACACCGAGTTCTTGTCTTCTCCCTTGGCAGTGTACATGTTCCCAAATGGACCGTGCTGGTGCCCTTGTGCTGGCCCTGAGGCCCTCTGCTGACCCCAGCCAGCCACACTGCTATCTGCACCCTGGAGAAGGGTGAGGCCCCCGGATACTTTCTTGTAAGGGAAGAAGGAAAACAATGGGAAAGCACGCTTGGAAAAAACTTGGAGAAGATGAGCTTTTTGATAGCTGCCTCAGATCTGATGATGAGAACTGAAGAGCAGAGCCAGTGTGGGGGTGTCTTGCAATAAACATTGCCTGGGAGTGGAGCTGAGTCAGAAATCCCTTGGGTGAGCTCTCTGTCCGAGCTGAGGAAGCTGTAGCAGCTCTGTGCTGATAGGCCCTGGTTGGCTCGGACTGGTGGACAGCAAGTCCCCTGTGAGCAGTGCGCAGGAGCCTGGAGGTCTGCCGGCAGGTAACTGTACCACGCGCGGCTGCACACGGTCATTGACTTTCACAGCAATCTCTCTGTTCCCCTTTTCTCTGTTCTTTCCCCTGGCTGCTCTCTGACTCTTGATGCCCTAATGGCCTCCTTTGCCCTGTGACCTTCTGGTTTGATCTCCAG
Seq C2 exon
CTGTTGCCTCTCCTCAATTCAGTGCGGCTGGCTCCACCTCCGGTCATAAAGAGACGCACTTTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004286:ENSGALT00000006816:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.768 A=NA C2=0.909
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0139113=Collagen=PU(4.7=13.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
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]