GgaINT0046087 @ galGal4
Intron Retention
Gene
ENSGALG00000002552 | COL3A1
Description
Gallus gallus collagen, type III, alpha 1 (COL3A1), mRNA. [Source:RefSeq mRNA;Acc:NM_205380]
Coordinates
chr7:595343-596587:-
Coord C1 exon
chr7:596379-596587
Coord A exon
chr7:595376-596378
Coord C2 exon
chr7:595343-595375
Length
1003 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
TTTTTTTTTTTTTTTGGTAGCTT
3' ss Score
7.83
Exon sequences
Seq C1 exon
CCCTAGGAGGATGTACCCATCTTGGGCAGGAATATGCTGACAGGGATGTTTGGAAACCAGAGCCATGCCAAATCTGTGTGTGTGACTCTGGATCTGTTCTCTGTGATGACATCATCTGTGATGACCAGGAGTTAGACTGTCCCAACCCAGAGATCCCCTTCGGAGAATGCTGTCCAGTTTGCCCGCAGACAACACCACAGCCTACAAAA
Seq A exon
GTAAGTTCTCAATATGGTTACTTTGGTGTTGCCAACTTTGATTGATTTTCTTTTATATAAAAAATGTGTCACTTTCTGATCCCTGGCAAATACTTGGAATGGGCTGTTTGCATTATGGTAGTGAATTTGTACATCTTCCAGAATTCCCTGAGCTACTTCCCTGAGCAGGTTGCAATGGTGCAAAGGAGTGGTCCATACAAACATGATGGACATTCAAGCACAGCTTCCTCTCCCTTGAGTCTAGGACCTGCTTTCTGGTCAGCAACTAGAGTGCAGGATTTTTTATTTCAGGACTGAAATCAACCCTGTTGAATCAGTTCTGTCGTTCCTGATAACAAAGAACATGTGGGCTACTTTGTTCAGTCTTCACTTTATGAGAGTTTGGTCAGCCCTGTGGAAGCTGTCCTGCTGACCTTGGGTAATGGATAAGGAAACTGCACCTTGAAAATCCGAGGCAGTTTCAGCTGAATATCCTTTGCTATCTCTTTCAACTGAATTTGTAAAAAAAACTGTTCTAAAATATGAATTAAGATTCAGATATTAATCTATAAATAAATCATTAACTGAAAAAATAGATAATCTAGGAGATTAGGTCTGAAAGACAGTTAAAATTAACTACATCATTACATTTATTAACATGCTTTTTTAGTGGACTGACAAGAATATAAGAAAACTGTCCCTTGTAGACTTACTGCATTTAGTGGCAGAACTCTGCTGACTTCGTTAGTGCCAGGTTTTTACCTAGAGCAGATGTGCACACTTCATGAATGCACCATAATAATGTAGATGAAAGGCTGATCAAAAAAACAAAACAAAACAAAAAACAAACCCTCATCTTCTAAATAATGATGAACAAGAATAAACAAAATGTGTTTCATAAATCTATTTTCAAATATTTAAATGTCTTTTCATCTTGTTTCATTTACATATATTCAGTTTTCGGTTTGGTTTTTGTTTTCTTTCTCAACTTAATTAATTTTCCCTTTTTTTTTTTTTTTGGTAG
Seq C2 exon
CTTCCATATACGCAAGGCCCCAAGGGAGACCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002552:ENSGALT00000004032:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCTAGGAGGATGTACCCATCT
R:
GGTCTCCCTTGGGGCCTT
Band lengths:
240-1243
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]