GgaINT0050842 @ galGal4
Intron Retention
Gene
ENSGALG00000003923 | COL6A3
Description
collagen alpha-3(VI) chain precursor [Source:RefSeq peptide;Acc:NP_990865]
Coordinates
chr7:4799267-4805022:+
Coord C1 exon
chr7:4799267-4799341
Coord A exon
chr7:4799342-4804851
Coord C2 exon
chr7:4804852-4805022
Length
5510 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
TCTCCTGCTTTTCTTTGCAGTCA
3' ss Score
10.44
Exon sequences
Seq C1 exon
AGACCCCAGCGCAGCCCAAAGTGGCTCTGGCCAACATGATGCTGAACGCTGAGCCACTGGAAGGGCCTGAAAATG
Seq A exon
GTGAGTATTGGTACCGGTGGGGAGAGATGGGCTGGGAGCTCTGAGAAGGACCCCCGCGAAAAAGAAAGCTGCAGAGCTGTTGGAGAGGGTTCAAAGGAGCACCACGAGAATGATCAGGCCAGGTTAAATGGGACCTGGGCAGCCTGATACAGCAGTGGCAACCCTGTATGCAGCAGGGAGGTAGAACTGGGTGATCTTTAAGGTCCCTTCCAACCTAAGCCATTCTAGTCTTTCCCTTGCCCACTGCCAAACATGGACTTTCTCAGCAAGTATAGCCCCACTAGGACCAAAGGATCTTCAAGTCCTTTGCTTTGCAGAGCCAATAGAGCACAGGCTAGACAAAAGCCTTCAGCATAAAGGCCTATACTCTGCATGACACCACAGATCCATGCCGGATCCATAGCCCACTAAAACTATTGTCATCTTTGCAGGAGCCTCAGACCAGGCCTAATTTCCATAATGGAGTTAGAAGATAAGCTAGAGCCCAAGTGCTGGCTACTCCCCAAAGGACACACTGCAACCCCATAGCCTACCTCGTGCACGCAGACATTGCTGTAGGCATCAAATATCAATTTGTTTGCCCCCTCATTCCTGGTTTGCCACAAAGAACAGGTCTTGGCTCTTTAGTTTAGCACAGCTCCCAGCAAGGACTTGACCCATAGCCGGGGATTAGCAGGGAAGCAAACACTTGCTTAAATTTAGCTGATAGACAGCTTCCCAGCTGCCCTCTCCATTTTTCTACCATCAGTGGCTTATCACAGCAAACCACTAACGAGCACCCACTCTGCTGATAATCACATTAACATATCTTAGTAATCCTGTTCAATCACTGCAGCTGTTGAAATGTTGTCTCATTGCTTTTGTTGACGTCAAGCTCGCTGTATCAGCCCTATAATGCAATCACATTGTTAGTGCTGGGCTGTAACTCTTCCTCTACAGAACTGGAAAGGTCCGTGGCCTTCATAAAGCTGTCACAGGCACCGACTGTGGATCATCTGACATCTAAAAGTCATCTCTATATAAGCACTTTTTTTTTCTTTAATAAGCCTCTTGCTCACACTGTGGCTCATCATCTTCATCAGGATGTTGAGGAGGAGGGGGAGAAGGGTGTTCTCAATGAGCAACAGGTGGAGGTCTAGGGTGGAGGTCTCAAGGAACATCTTACCTGTGTCTTGATGCATGTCCCATCACTGCTGCGATGCTCTGAATGGCTTCTCCTGCTGCATCTGCAAAGTGCCTCCCATGCATTCCAACCAGCCAGGCCCCCTCCTGGCTATTCCCCTCCAGATGACATGAACCCGTGCCCTGGCTTTGCTTAACCCCTTGTGTGCCAGCCCTTTGGAGACAAGGTGTAGTGCTGGGTGGGTGTGTCTGGATGTGCTGTATGCTCTGCACATCAACGCTCACTTCTGAGTCCCAGGTCTTTTCGTGACCTGTTTGCAGCAAGCACCCCTGCCTTAGGATTTATGGCATCTGGCTTTCAGGGGAAAGCCTTTTCTGGAGGCCTTCAAGTATGCTGCTGCTAACCTGAAGTTTTTCAGCAGGCTGAGGATACTATAAACAGAGCAGAGCAGTGGGGATGGGTTGTTTAACTGAGTCTTTCCTGGTTCTCTGCACAGCGGGAGAGACCCGTACATAAATCTTCCCACAAACCTTGGAGGAAGCCCCAAATTGTGCTGTCCTTATATAGGCAATGCAGCTGCTAGCACTGATGGCCCTTGCTAATAAAAACTCTGGGGTTTGGGCCTAAATTATCATTTCTGGACAGGAAAAATACCTACATTTAAGCCCTGAAGTCTACCAGGTGTGGTTTGCCTTTGAAGATAAAATAAACACGCTTAAGAACTGAAGTTACTGCCAAGGCAAAGACCTTTGGAAACAGACATGGGGGAGCTGTGTGAAGGCCCAATCCTGACCACACCACCCCGGCAGGGGGACGTGGGGTTGGGACGGGTTGGGTTGGTGTTCAGTGAGCAGGGGGAAAAGAAATGGAGTGATGAGGAAACACCCCCAGCAGGAGTATGACCCGCCCGCATGGTCTGATCCAACCCTCTTGGCTTCCGATGATTTTAAATGCTTCGGGTTTTATTTATTTGATTTCATTTTATTTTTCCCTTTCCTGAATCTCTTTCCTTTTTTCAACTTTTAACCCTTCCGGAATCATTTAACCTTTGCACCTTTTGATATGCAGATTTGGCAGACCCTTGCTTGCTGGACTTTGACATGGGCATGCAGTGCAAGGACTATCAGGTTGTATGGTTCTTTGACTACAAACACAAGATCTGCAGCCAGGGTTGGTATGGTGGCTGTGGTGGTAATGCCAATAGATTTGAGACCGAAGCTGAGTGCAATAGCAAATGCTTGAAGCCATGTAAGTACCACACGGGGGTTAATCCTTTCACTTTTTATCGACGTTTCAAATAACATTTGAATCAGAGAGAAAACATCCTTTAAACACCAAACCAACACACTTTTTCCTCCAGCAGCAGCTGAGAAAGCCATGCAGCAGCCACCCCTTGAGAAAAGATTATCGCCAGGTAACACGCCAAAAAATTAATCATAAAATAAAGCACATCCATCATTCATGTTCACCATTTCATGGCGTGCATCCATGCTTGCCCATTACGAGATCATCAGCACAAGGACCTTGGTTTGCATTTGCTCCCCAACGTGGCCGTGCCCCGCCATCCGCTTTGCATGAGCAAGTCACCTGCATGCCTTGTCTCACCCCAGAAGTTGTGGTTGCACGCCCCAAGTGCAAGCCATAGCTAACACAAAAACACACTGGATGTTGTAAGAAGTGTGCAGCAGCGTGGTCCCAAAGCATCTTTTGTTATCACTGCATGTCTAAGCAATGCCATCGCTCATCAGCGTGCCTTTGTTGCGGTGCGAAGAACTGCAAATACTTTGCAAGGGAGATTACCCCATGTGGCACAGGTCTGAAAGCTGTGGAAGGAGCCCACAGGAAAGTGGTAACAAGCTCCTCTTCTCAGGGTTTTTCTCAGCCCCTAGGTTTCAAGACCTGGGAAGAAAGCAGGGACTTGCAGTCACCTGTGCTGGCAAAGCAGTGGGATGGGATGGGAACCTGACCCTCCAAAACCTTTCCATCATGGCAGTCTGCCCTTCTCAGAATCTTTTGGGGCCCTTTGCAGAGAAAGGGGAGAAAGCTTGAAGCAAAGTGAGCTCTGAGACTGACTTTAGAGGCTCATGCAGAAACTAATGGCTTGAGTTGGGAGCAGGATTTCACCCTCGCTGAGCGGGGAAGCCTTGCTGGTGGGTAGCTCTCTAGAGCAACACGTCTCTGCTAACCCCATCCCAAAGCCTAGTCCCTTCCGATCATCATCACATGCCTTGATGATGTTTCCAGCAACTGTTGTTCAGCTTAGATTGATATTTCATGAACTTGGCACCATTCTGCCCTGGGCGGATAGTCAAGAAAAGCAACGGAGGGGCCCTGAAAGGATGCTCATGTCTCTGCCCACCCCGCGAGGGTCTCCCACTCTATTCATCGCTTTCTCTCCCTTCTCTTTTTGTTTTCTGCAAAACAATATGTTGTGGAAAAAGAAACTGAGCTTTTAAGATGCTGGGCATTGGGTCAGGCTCTTGGTTCAGCCCATCGCAAGGTCCGGAGCCAGGTGCAACACTGAGAAATGCCTGTTTCCCAAAACCTAGAGCTCTTTGGGTGTGCTTCACACCCATCTCTCCTTGGAATCAGTGCTTGGTTACCCTTTAATTATTGCTGTTTATAGGTCTATATTTTTTTTTACTATAAAAAATTAAATGTAGTTTGAATGGAAGAGTTGAAAGATGGGGTATGATGACATCCCATAGTGCTCTGAGTCTGGAGGGTGACACCAACCCACACAGTATGAATACTGGGGCTCATGAATGGAAGGTCACTCTTCAAGGGAATCTTCAGCTAACAGCACAGCAGCTTTCCTGAAGCCAGCACTGAAATCAGAGCTGCCTCCAACGCTGCTGTTGAATTTCCCCATCCATTAGTTGATCCTGAAAGCTCCTGCTGCCATCAAAGAGGACGATGGGGTGAAGAAGTAGGGATGCTTTGTCCTTGTGCTGAAAGAGAAAAATACAGGATCCCTCCCACGTGCTGCGTGATGGCTGGCTGGATTCATGAAAGGGTGCACAGGGTTTGAAGCAGAGTCATTCTGGTGTTTACATCTGCTGGCGTTTTGGAAGGCAGGACGGAAGGGAGAAGGGCTTTCAGCAGAATAAATAGGAAAGGAGAAGAGCTTGCCAAAGGGATGGGGAAGCTTTTGGCTGGAGGAGCCCGATAACAAAGCTGAATTGGAAGTTCAAATATTGATTTCAAATTCCTAGGAGAAGCAGAGATTTAGAAAGGAATCCCACTTCAACAAGCTGCTTTTAGATCACAGCAAAGCAAACTGTGAACAAGAGAGTCCCTTCCAACACTTCTCTCTCCGAAGGATGCATTCCCAGCTCATACCTCAAACCAGCCAGCAAACCTCTGCTCGGTTTGATCCATGCAAGATCGGGCGGTGACCTGCTCAGCTCCATGCCTGCAGCAAACGAAGAAAAGAGAAAATGCAATCAAAAGGAGAAGACAGAGAGAGTTTAGGCAGGGTCCTGCCCATCCCTGGGGTCTGATGGGCATGTGACACTGATTTCTCCCTCTCCCTGTCCCGCTGGCTGCAGCATTCCTGTGCTCTGAGCAGCTGCCAGCACCAGCCGCAATTTCCTTTCAAGCAAACCTGCCACCAGCACTTTCTTATTTTCTAGGATTTGCTGCCAGACCTACTTTCTAGTCAGGATTTCAGGGATAATACTCTGCATCCTTCTTCCCATGAACATTTTGAAAGGGTTTAGCATGCATTGTCTATCCTCAAACTCCCAAAAAACTCGCTTGCAAGTACAGCCTTCCATTAATTCGCCCTTTATTTCTATATTCTTCTCTATTCTCCTTCTGGATATGTGGGAACTGTTTCTGGTGGGACAGAGTAGCCCGTCTATAGCATCTATACAAAGGGTATGAGGTTATCACAAGACAACTTCAGGAGATGGATTTCCTGGCCACTCATTGCTGGTGTGCTCTGTGTACATTTTTGGGAGAATGATGGCAAAAAATGGTTTTTCCCTTGAGACCCAGTTCTGACACCTGCCAGCTCATTTCCTAGAAATCGAAGAGATCTGCAGACAACTGTTGCCACGTGGCACACGTCCTTCTCTCTGCCTTTACTCCAGCATTGTGCCATGGATGCACACTGGCAACACAGCTGATGGCTCGAAGAGCAGGGTTGGCATCCTCTTGGGCTCAGTGTTAGGCAAAGACCTTCTCTTCGTCAACACAGAGATGGGGTTCAGCCACAGGAGACCAGGCAACGTCTAGGCTTTGGTTACCTCTTCTGGTCTTGTATCTACTATATCTATCTATCTGGCATTTCTCTACCATGCACATGTCCTGAGAGAGCCTGTCTTTAGCCCAGGACCCCAGACCTCTAGCTGACTCTTCCTTCTCCTGCTTTTCTTTGCAG
Seq C2 exon
TCATGGACATCTGCCTGCTGCAGAAGGAGGAGGGGACCTGCAGGGACTTTGTGCTCAAGTGGCACTACGACCTGAAGACCAAGAGCTGTGCCAGGTTCTGGTACGGCGGCTGCGGAGGCAACGAGAACAGATTCAACACGCAGAAAGAATGCGAAAAAGCCTGCAGCCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003923:ENSGALT00000006250:42
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.154 A=NA C2=0.006
Domain overlap (PFAM):
C1:
PF115933=Med3=FE(12.0=100)
A:
NA
C2:
PF115933=Med3=PD(1.0=3.4),PF0001418=Kunitz_BPTI=WD(100=91.4)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]