GgaINT0063396 @ galGal3
Intron Retention
Gene
ENSGALG00000002613 | CCBE1
Description
NA
Coordinates
chrZ:8644693-8646051:-
Coord C1 exon
chrZ:8646016-8646051
Coord A exon
chrZ:8644927-8646015
Coord C2 exon
chrZ:8644693-8644926
Length
1089 bp
Sequences
Splice sites
5' ss Seq
CCTGTAAGT
5' ss Score
7.52
3' ss Seq
ACCATGCCTTGTGACTGCAGGGC
3' ss Score
6.61
Exon sequences
Seq C1 exon
GGGGAGCGAGGTGCACCAGGACCGAAAGGGATACCT
Seq A exon
GTAAGTATCACTCACAGCAAGCGATATTGTTTCTATTCTCTACAGCAACGTTTCTACAGCAAAGATATATTGGCTATCAGCAGACCAGCCAAAAGGAAGATAAATTTCTCCTTTGTCAAAATTAGAGTGAATTACACTTTACATGAAGAAAAAAAGTTATTGGAAAGAAAGTAATTTCCATTTTTCTTCCAAGCCTGTTGCCTACATACCTCCGACTTCACTGGATGCTACACTGAAGGCAGTAAGCAGTGGGACATGTTAGCTGGCAAAGGCATGAGAATACATGCAGAGTGCTAGTTAGCACAGTTCAGCCAACAATCATAGAAATGTAAGCTCAGAAACATTTTAAAATCTGCCTCTCATCTCTCTCTGGAATACGGCAAGCTGTAGACATTGAGCAAATCATCAAGAGAAGGATGGGGTGTATATAATCTGTTTTTAAGTGAAACTGATTAAGATGCTGTTTGTCATGGTCTTTTGATGAAATGGATTTTTAGGAGTGTGCAGCAGAGCATCCTCAGTACTGAGCAGTGTAGTCTACTACATGAAGTCAGCTAAAAAGAAACAATGATATTCTGAAATTAGATAGAAACAGGTAGATACTCTCTACATCTTAATTACCAGTGAACATAAGTGCTAGACACCAGTGGGGTTAATCTACAGAAAACTATACAAAGATCAGCATTCCCCAAAGATTTTTAAAACAAATATTACCAATTATTAATTAGTTATTCTATCAGTTTAATAAGAATATGAGGAACCAATATTTCTACCCTCTTTTCCCACAAGGTGTTGAGGTACACTTTAGAGGCAGATTCATCAAAGGAATTGTTTTATAACAAAGAGCTGAGAATCTTGTCAATACAGGCTCTGTCTGAAAAACAAAACAAAACAAACAAAACAAGCAAACAAACAAAAAACAACTTTGCCTTTTGAAAACTGTTTCCTGAGCAGGTGGATTCAAAAAGAGATGCTTAATTTCTGTCAGTAGATATGAAGCAGTATTTTAGTGAATTACCCCTGCAAGGATAATTATTATCTACCCATTTGAAAACCTAAATACGATATGACCATGCCTTGTGACTGCAG
Seq C2 exon
GGCCCACCAGGTTCGTTTGACTTCCTATTGCTGATGATGGCAGACATCAGAAATGACATCGCAGAACTGCAGGAGAGAGTGTTTGGACGGAGGACTCATTCATCAACAGAGGAGTTTCCATTACCTCAGGAATTTACAAACTATCATGACACGGTAGATTTTGGATCTGGAGAGGACTACAAACCACGCGCAGCACCCAGAGACTCCAGGATACAGAAGGCAGCCCATCCTTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002613:ENSGALT00000004114:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.987
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(28.2=100)
A:
NA
C2:
PF0139113=Collagen=PD(12.8=6.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTGCACCAGGACCGAAAG
R:
ATGGGCTGCCTTCTGTATCCT
Band lengths:
255-1344
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]