GgaINT1010117 @ galGal4
Intron Retention
Gene
ENSGALG00000008266 | COL4A6
Description
collagen, type IV, alpha 6 [Source:HGNC Symbol;Acc:HGNC:2208]
Coordinates
chr4:14058771-14062603:+
Coord C1 exon
chr4:14058771-14059057
Coord A exon
chr4:14059058-14059679
Coord C2 exon
chr4:14059680-14062603
Length
622 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGG
5' ss Score
9.33
3' ss Seq
AACGGACATCTTTATTTCAGCAC
3' ss Score
5.48
Exon sequences
Seq C1 exon
GTTTTGCTGGCTCTTGTTTGCCCCGCTTCAGCACTATGCCTTTTATTTACTGCAACATCAATGAAGTGTGCTACTATGCCAGCCGAAACGACAAGTCCTACTGGCTGTCCACCACCGCTCCCATCCCCATGATGCCAGTGGACAGCAATCAGATCCCACAGTACATCAGTCGTTGCTCCGTGTGCGAAGCACCTTCCCAGGCTGTGGCTGTGCACAGCCAGGATATCACCATCCCACAGTGTCCCCTCGGTTGGCGCAGCCTCTGGATAGGATACTCCTTCCTAATG
Seq A exon
GTAAGGATACCGTTGCTACTGCAGTGGCAGCTTTGCGCATTTTTTACATCTCCTCATCACTGAGACTGAATTAGCTGAGTTGCCCATAGAAAAGCAAAGCGTTTATTCTTTATCAGCACACCACTTGTTCCCATTGATCTGGCCTTTTCATATGCACTGCTCAAGTCCAGTAGTAAAATCGAAGCAGTAGTTCTGCACTGTCACAGATACTCACTGTGCTTCAAACCTTTAAGTGCACAGACACTAATTAAGCTGCATTATTTCCTTAATCCCCTCTGTCTTCTGGAACATTATTTCCACTGCAATCCCCTTGAAGCCCAGTACAGTAAAGTCATTAGAAAACTATGAAGTCAGCTTTATTGTCTCCTAATTCTCCCACTTTGCGACTGCAAAGCTGGATTTCCTTTATACGAGGACTGTATATTCAGCGTAAGCACATGCCTTTGCTTCTTTGTCTCTAGCCCTGACTCGAGACTCAGATACAGATAACCAAGATATACAGATAACCAAGATATACATTTGGTTGCCCGTTCTACTTTTCTCAACTACAGAACTTGAAGCCTGTCCTATTACCTCTTCTTCTGTTCCTTTGCACTCACTTAAACGGACATCTTTATTTCAG
Seq C2 exon
CACACAGCAGCTGGTGCAGAGGGTGGAGGTCAGTCGCTTGTCTCACCTGGTTCTTGCCTGGAGGATTTCCGTGCTACACCCTTCATTGAATGCAATGGTGCCAGGGGAACATGCCACTACTTTGCAAACAAGTACAGCTTCTGGCTGACCACTGTTGAGCAGTCACAGCAGTTTGTCGGTGCTCCTCCCTCTGAAACTCTGAAAGCAGGACAGCTTCGGACGAGGGTCAGCCGCTGCCAAGTGTGCATGAAGAACTTGTAACAGAAATGCAAACAACATGAACAGTCTTTGTTGCTAAAAGTAGGCATCACTGATGTGAAGGAAATGAATTCATAAACCTGCTTTGTGTGTGGTTGATATTGGAATCAAGATGGCCAGAATTCCACAAAAATCGAAAGTAAAGTGCAGGACTTTGCTCACAAGGGAAAGACTGGTGCTCAGAAAACCATTCTGTGGATCACGGTGCTATGCTATTTCTCTACTGTTGTCTGGGGCTTCTTCTTCATTCACGGCTACCTCAGAAAGTCTCTGGGAGTTCTCTATTCAGACCAAAGCATAACTGGCGTCTCACATACACCACTGCCCTGACCAAGGCACGTCCCAACCACCACCAAGAGAGACTTCTCCAGAGTTCTGCTTTATTAGCATCTCCGCAAACAGGACCTGGCCTGGTGTAAGGGAATGAACACGCATTCTCCTATGGAATGCAGAACTACCCAGATTTTGTAATGCATTGTAGGTGACTTTGAAACACTAAGCAGCAGTGGTTGATAACTGACCTGATTAGGGAGATTTGAAGATGAATGTTTTGCTTTGCTTGTAAAACAAACAAACAAAGAACAGGTGGAATGTTCTTTGGCTCCAGTGATAGGTAATCAATTCTAATCCAAGCTCATATCCACAGTTGATTTTGAAGAGCTACTCCAGTAATACATTTTTTATGTGAATTTGAGTCCAAACCACCTCTAGCATTTTTCATAGCCCTAACTATATTCCAGCTAAAAAGTCTCCTTCAAGGCCTGTCCTTATCTCCTTGCAGTCAAATGATGCGCAGCCACCAGAAGCACTTCATTACTGCAAACCTTAATCTTCTTTCAGAGGTAGCCTTGGCACAGTTTTGTGTAACTATTAAAGCTGTGTGTGTTTAAAAAGTAGAGGCCTACTAGCTACCATGCAACACGTCTGCACATTCAGAAGAAAGCAGTTAGTTACGGGATGTACATTCATTATTTCTACAGTCACCATCAGTTGTGTTCTTCCTCTGGACTGCTTGCTGCATTCTGCTCATTTAAAAAATTGCACTTCTATTGTAATCCTGCATTCCTCGAGGGCATAATTAAAGCAAAGTGCTATTGATTGTATTATCCTTGTGTATTTTGAGGGAACGCTGTGAAAAAGTCTGCTGATAGTTACATGAATCCATTAGGTCAGGCTAGCGGTGTTATTATCGATTCCTCTTTCTAATTGTGCACGAAACCCTTACAGATTGACATTCTGGGACATCTGAAGGAAGTGCCTTGCAAATACCCTACTGCCTTGGCTTAAAGATTTTGAAGACAAATTGTCAGACTATTACCATTAATACAAGACTGAGACATTAATGTAAAGTATTTTTTCTCTACTAGTTGCCAGCGCTCTAGCTCTATCCAGCACAATACTTAAGAAAGTGCTTACTTTTAAGCAGATGATGTTTTTACCTTCCATGCCTGCGGTGGAACTAGGTGATCTTTAAGGTCCCTTCCAACCCAAATCATTACATGAATCTGCACTGCTCATTTATACACGTAATATGATGTTATTTTCCCAGATAGAGTCAGGGAGCTCTGTGTGTTCAGAGTTGAACCACAATGGAGATGAGCAGAGTTTGGGATGAGAAATTTTAGTCCTTCATTTAACTTTTCCCTGCTTGTGAGAGATCTGCAGCTGCTTTGGATGTATTTTGCAATTACCTTTTAAGATGTTGTAATGTTCCTGACTGATGATCCTTTTGTGCAGAATATCAAATTTCCTTCCAGCTGTCCTAGTGCAGACTGAGCATATTGTGCTTAACTCCTGGCATAAGCAAATGCAACGTGAAAAAGCTGTGTGCACACAGCAATGCCCACCATGCGCTGAAAATGTGTACAATTAACTCTGGGAATTTTTCAGCAATTGGGCTTCCATGGTGCTATAAGAAGTGTCAGTCAGGTGCTGTTTGCAGACTCGATATTTGTACACCAACACACGCAAATGTGTTTTTTTCAGGATTAGAACTTTACGCATTTAACATGCCAGTATCTTTAGACAAGTATGCTTCTACTGTTGAAGAAGTTGGCTCTGCTGTTACCAATACCAAACTTTCCTTGAGTTCCACAAATGGTCTTTTCCCGCTGCTCACCCAGAAGCCACGCTCGTGCAGCAAACAGCTCAGGAGGAAGGCTCAGCCCTGCAGAGCTCCTCCAGCTGCTCAGAAGGCGTGCAGCTACTCCCTGGGTAGAGGAGGAGAAGAAGTGCTATTTTTTCTTAGCATATAATTTTCAAACTGTGTTTAATAAACATTAAACAAAATGAAACAGGCTCTTCTTAGCTCTTTTCTTTAATATCACGCTGGCCCTGATCAGGAGGTGCAAGTGAGAGGAGACAGCATTCAGTATTTCTCTATGTGTTTTTATTAGTGAAGATGAAACTGCAGTTCACGTTTATCACACTGTCATGACAAAACGACCACCATGGGGACTGTCTGGTAGACCTTTAGCATGGAGTAAAAGATCTTGGCCTTAAATTATTTTAAAGTGTTTTTCTTGGGGCTGCTAGAGAGATACTCTGCCGTATAGAAATACAACCGCCCAGGCTGCTCTGATCAACCTGTAACATTAAGGCACTTTGACCACAACAGATTTCAAAAGGCAATAACTCAAAAAGTAATGATGACGTAATCTGTGTAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000008266:ENSGALT00000013447:44
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:
PF0141314=C4=PD(59.3=66.7),PF0141314=C4=PU(25.9=31.2)
A:
NA
C2:
PF0141314=C4=PD(72.4=96.6)
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:
CCGCTTCAGCACTATGCCTTT
R:
AGGGTGTAGCACGGAAATCCT
Band lengths:
347-969
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]