GgaINT0040499 @ galGal3
Intron Retention
Gene
ENSGALG00000005795 | F1NAB8_CHICK
Description
NA
Coordinates
chr6:18668468-18670610:-
Coord C1 exon
chr6:18670469-18670610
Coord A exon
chr6:18669975-18670468
Coord C2 exon
chr6:18668468-18669974
Length
494 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAG
5' ss Score
9.65
3' ss Seq
TTCTCATTCTTTCCTTGCAGGAA
3' ss Score
13.1
Exon sequences
Seq C1 exon
GACACCATGATATTCCCTTTGCTGTCTCCCATCCTGCAAGACTGCAAGGAATTTCCAAACCCAGAAAAATTTGACCCAGGACACTTCCTGAATGCAAACGGCACCTTCAGAAGGAGTGACTACTTCATGCCATTCTCTGCAG
Seq A exon
GTAAAGAGCTCTTTCTACATCAGATCCTAGACTATCCTCTCCTAGAAGCTCTCCAGAGACTTCAGTGGCTCTGTCATCACGATCTGAACAGTGATGATCTGCTGGTCACTTCTGGGCAGCTCTACCCCATGTACTATGGTTCAATTTACCTCATTTTCTTACCAAGTACCAGAGCTCCTCCAACGCATTCTACAAGAAAAGATGCACAAAGTGGCACTCGTAGCCATGCCACCCCTCTCTCCTAACTAGCCTTAGAAGAGCAATAGAACAGGAAAAAACGAAGCCTTTAAATTGCATCGGCCCACCCACTACTCTCACACTGTTCTGAACACTGAGATCTTAGTTTAATTCTGTTCACTTCCCCAGAGGCATCCTTCTGGGTGCTACCTGCCCATTCAGAGAAGTCCGAACTTTCACGGCAGAGGGGTTCAAATCAGTTACTGGCAAAAGTACTCTACCATCACCTCCTTTTTATTCTCATTCTTTCCTTGCAG
Seq C2 exon
GAAAACGCATCTGTGCAGGAGAAGGGCTGGCCCGGATGGAGATATTCCTGTTCTTAACATCCATCCTGCAGAACTTTTCTCTGAAGCCTGTTAAAGATCGCAAGGACATTGACATTTCTCCAATAATCACCTCTCTGGCAAATATGCCCCGACCTTATGAGGTCTCATTTATTCCACGTTAGACAAGTGAAGACAGCTGCCACCTCCCAAATTCATGAGACCTCTTCTTGAATGATAGTCAATGCCCAGCCTGATAACACTGAGACACTCAGATAATTTCCTAGATTCTTTAGGGACAGAAGACTTACGCTCTTCTATGTGATGCCAGAGGACATGATGCAGCAGAAAACAATTCTCCACAAAGCTTAGGCTCCCACACACTGCCCAAAATAGGTACATATCTTGACTGTTTGTTTTCCCTCATTTATAAAAAATGCATTATGGCTTTAAGACACTATCTGGAAACCCTCCAGTCTCTCTAACAACATGGAAGATTGCTGGACTGTACTTACTGGACCTATCAGAATTAAAACTGCAATTACAGCACTGCTCATTGAGACAAAACAGTGAAATAATTGTGGGATCTCCACGATGCCTTTTAGAAGATGAATGTCAGCTTGAATCTTCCCATTACTTTTATGAAATACGTAAAAATTGCTACAGAAATTGTACAAACTTCAGGTAAAGGGTTTCTTTGAGCTAACAAAGACAGATGGATGTAGGATTGGCATTTCCCAGATTGACCGCTTTCCCTGCAGTGTATAGCTTACTGTGATTGCAGTGACAACACAGCTGAATCCATGCTATGTGGCATAATACAGCACTTGCAATGTCACCACAGTGGCATTAATTGCTTAGGTAAGCAGCCAAATGTTCATTTCTTTCACTGTGTTAATAGTACTGATATACCATGGGTTATTTGTTTTGTGTTATACAATAAGTTCAAAGCATAAAATATCACAGAATGACAGAAATACAAATGAAAGAAAATACATGAAAATATTGCCTACCCTATCGATATTCGTAGCCTGGACCAACTGTTAGAAGTCTTCTTGTCAGAAAGAAAAAAAAAAAAGAAAGAAGGAGAAAGCTCACTGTGCTTCCTTCGACTTTGCCATGGCTAAGTAAATGGCTTGAAAGGCAACCTACGTTCCAGACACCTTCCTCCATACTGAGCAGACAAGGCAGCAGCTTGTGCAAAGCAGCAAGAAAACAGCTGTAGCTCCCAGAGACTTCACCATCATATGGAGCAGGAATCTGAGATCAGAGAAGCGCTAAAGCTGTGCCCCGCAAGTCTCACTTTGTGTCTCACTGTGCTGTGGTACAAGCAGCAGTGCAATAGTTACCAATGGCTGCTTGCACTTCCTCCAAGTTCACCCGATCGAACAAAAGTGGTATTAGCACTTCCTGGGAGATTAAGGATCAGACGTTTAAAAGGGAAGAAGACTTAACGAGCAGGCTTTATTTCATCAGTCTTTGTTGCCTGCTAAACTGGAAAACATTAGTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005795:ENSGALT00000040063:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0006717=p450=FE(10.3=100)
A:
NA
C2:
PF0006717=p450=PD(12.3=91.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTTGCTGTCTCCCATCCTGC
R:
ATGAATTTGGGAGGTGGCAGC
Band lengths:
342-836
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]