GgaINT0018949 @ galGal3
Intron Retention
Gene
ENSGALG00000005679 | CDX1_CHICK
Description
NA
Coordinates
chr13:13312551-13314523:-
Coord C1 exon
chr13:13314378-13314523
Coord A exon
chr13:13314247-13314377
Coord C2 exon
chr13:13312551-13314246
Length
131 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
CGATCTGTGTCTTCCCACAGGTG
3' ss Score
13.16
Exon sequences
Seq C1 exon
GCAAGACGAGGACAAAGGACAAGTACCGGGTGGTGTACACGGACCACCAACGCCTGGAGCTGGAGAAGGAATTTCACTACAGCCGCTACATCACCATCCGCCGTAAGGCCGAGCTGGCTGCTGCCCTGGGGCTCACTGAACGGCAG
Seq A exon
GTGAGTGCTGGGGATGGATTTGAGAGAGGGCAGTGCCCTTCCCATTCTGCTTCCAGCCCCCATGGTGCCCCTGGGGTGCTCTTCCTTGTCCACATCCCCTTCTCTGCATGGCGATCTGTGTCTTCCCACAG
Seq C2 exon
GTGAAAATCTGGTTTCAGAACCGGAGGGCGAAAGAGAGGAAGGTGAATAAAAAGAAGCTGCAGCAGCAGAGCCAGCCCACCAGCACCACCACGCCAACCCCCCCAGCCGTGGGCACGCCAGGGCCCATGGGGACCCTCTGCAGTGGCAGTGCCCCAAGCCTTGTCTCCTCATCTCCGCTCACCATCAAGGAGGAGTTCATGCCTTAGCCCCCTCCACCAGCCATAGACACTGAGAGATAAGCACTACACGGCAGAGCTTGTTGCTGAGCGCCCAAAGACACCACGTCCTCTGGGGCATGGTGGCTCTGTTGCCTTCCCAAGAGGCTGATGAGCTCTGTCCTACACAAAGCCCATACGTTAGGTAGTGCTGTTCTCCTGTAGGAAACGTGCGCTGGTCTCCGGTATTGGTAGCCCAAAACCAGTGGGATGAGTCTTTAAGTGGTGCTGGAGGACCCTTTCTGTGGCACATCAGAATGAGCCGGTGGGATGCTTCCTGCACGGTCTTCCTGGTGATCCAGCTGCCTGCTGCTTTGGAGCAGCTTTAGTGAGGCTGGACTAGGGGAAAGGCTTGGCTGGACTCGAGGCAGAATAAATCTCAGCTGAGATTGTCTGCAGGATCTGCCACACCTGGAGCGAGTTGGACAACAGGAGCTGGGTAGGACCCTCAGCAGTGGGGCTGGAGGGGGAATGGGGGCTCCTTAAACTGAGACAATGACAGTGAGTGTCCCCCATGTCCCCCAGCCACCATCCCCAGCTCCATCCCTGCAGCAACTCAGGGCCATCGCGAGACCTGCAGACATCTGTCCCACAGGTGGACCACCCTGCGGAGGTTTTGAGACCACCTTCCAGCATGGAGGAACAAGAACAAGGTTTGCAGTTAGGACACTGGACAGCTCTAGGTTGCCCAGAGGGGCCGCTCACCTACCCATGGCACTGCAGAACCTGCACAGCTCCATGCTGCACCAGGGCACTGCCAGCTGCCGGGACCATCATGGTGATGGGACATGTCCTGGCACAAGATGATGGATAGCTGGCTTCCATAGAGAGGGATGGGTGGATTTGTGCTGTTTTCTCTGAAACACAAAAGGCTCTGGGTTTTGCCCACTTTGTACTCCTCCATGTGCTGCACCATTGGTAACCAATGGCTTTTTTTTCCTGCTGGAAATCCACAGTTAAAATTCCCCTTAATCCTGCTGACTCCTGGGATCTCTACTGGCCCAGCTACCTTACAGCCCAGTTTTGGATGCCCCAAAGGGCGTGCTGGGACACAGGAGGGTTTGAGGCTCCTGCTTGGGTCTGTGGCTTCCCAAGACCAAGGTGAGGGTGTAGAGGCTCTGATGGTTCTCTCCTAGCACCATCATGCTGAGCCCCAGCAGGAACAAGAAGTGGAGGTGTCCCTGTTGCCTGCAGAGCCCCTCACCCATTCCCAGCCCATTCTGGCCCAGAACTCACAGTGTTAGGGGTTTAATACTGGGATTTAAGCTCCTTGACACCCACTGCACCTACAGCCCCTTAATAGGGTCTGCATCCCCCACCATGGGGACCAGTGACACCTCCCTGGGGCCACCACTGCTACTTTGCAGCAAAGGCAGACACCGGTGTTGGCTTGGGACTTCAGCTCAGGGCTTGTGTACAGAAGGCAGAACGTTTTATTTTCTAGGCTTTGGTCAAAATAAAAGCGAGCAGGAGCCCTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005679:ENSGALT00000009108:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.260 A=NA C2=0.695
Domain overlap (PFAM):
C1:
PF047317=Caudal_act=PD(0.1=0.0),PF0004624=Homeobox=PU(73.7=85.7)
A:
NA
C2:
PF0004624=Homeobox=PD(22.8=18.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACTACAGCCGCTACATCACC
R:
GTGAGCGGAGATGAGGAGACA
Band lengths:
254-385
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]