GgaINT0043083 @ galGal4
Intron Retention
Gene
ENSGALG00000004286 | COL13A1
Description
collagen, type XIII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2190]
Coordinates
chr6:10631307-10635363:+
Coord C1 exon
chr6:10631307-10631393
Coord A exon
chr6:10631394-10635324
Coord C2 exon
chr6:10635325-10635363
Length
3931 bp
Sequences
Splice sites
5' ss Seq
TTGGTATGT
5' ss Score
7.12
3' ss Seq
TTTCATTCATGCTTCTGCAGGGA
3' ss Score
8.94
Exon sequences
Seq C1 exon
GGGGAGAGGGGCAAGAAAGGCTCTAGAGGGTCTAAAGGGGATAAGGGAGACCAAGGAGCGCCTGGATTAGATGCACCCTGTCCGTTG
Seq A exon
GTATGTTCTGTTTTATCAAATGTATTGTTTTAAGATGTGTTGATGGGGAAGAAAGGACCTCCTTTGTGCTAGCTATGGTTCTTCTTTGGACGCATTCAGTGTCATCATGTCTACATAAGAGCAAAACTGGTTTTGTTGTAACAGCCAGTCAATGTGATTGCCTGAGAATGACACAGGGCACTTGAGCCGCATTACCCAGACAGGAAGCACATCTCAGTTATTTTCAATGGAATATGTTTCTGCCAAGATACACTGTCTATAAATCTAGATGAATAAATATATGAGTATATATACATTTTCATCTAAACTCATGCATTGCAGTGAACGTGCTGCCAGAAATGACCATAAATCCCAGGAATGCTCGTGCATCGTCCTTCTAGAAATTCACATGCTGGAATTTCCAGTGAAGATACGAAGAACGGATGATTTGAAAACAGATGAGATACCGTTCCCATCATCTCCAGTTTAACTCAGTTACACTGATTTGTAGATGGCAGAAAAACAGGAAGCAGATCACACAGATGAACTGAAACAGAGTACAGTCCCGTGTGTGTTCTGGGTATGCAGCAGAGTGCCCTGTGACAGTCCCAGTGCAGGACTGTGCCTGTCCTCCGGTGCCATGGAGGTGACTGGCATCAACTGAAATAACGATAGTGGTTGATTTCATAAACAGGGTCTCCGAGGTTTTAAAGGCGAGAAGGGTGAGCCGGGGTTACCCGGGCTGGACGGGCTGGATGCCCCATGCCCATTGGTATGGTGTACCTTCCCTTTCCTGCATGTTTGTTTGCTTTTATATCTTGGTTGTTACTTTCTGATGCCTCCATGTAGTTGCACGCCCTAGAGACGTATGACAGCTCCTTCCTCACCTCTCTCTATCCCACCTCCCTCACATCGCTGTTGTCAGAAACAGTCTTTTCCCTTCTTCCTATGATTCACAGCTGCTGCCAGTGTTACTTTATGGCATGAGGAAAAATGCAACAGGAGTGAGAATTTAAATGCTGCTTCAGTTCTCACTTTGCCTTCACTCTGAGAACTTCTGTTAGACTAACACGTGAAGGGTACCTCTGCACTAGCTTGGCTTCCGAGCCAAGGAGCTGCAATGCTTACATCCTTCATTAACTCTAAGTGCTTGTGTGTGGTTAGCAGTTTGACACTGCTCTGTGTTACTTAGTCACCCTGAATATTGACTGGAAAAATACAGCTATTAGTGTCCCATGTGAGATGTTACTAGGCACTTATCTCCCTCAGCTCCCAACAGATAATTCCTGTTTGTGACTCTTCCCTGAAATGAAAATGGCACCCACAGCATCCAAAAACTTGAACTAGGAATTACCTATTTCCCCATATCTGTCTCATTCTAATATTAGAAAGTGATCATTGTATTAGTTATTTAACCCAACTACTGTAGCACTAAAGGTATTCGGGGACACTTAACCTCAACTGATTTCTAAGTATCCCATTGAAGAACACCAATTTATTCATTCATGGAGATCATCTGTGGACATGCTGCATTCAGGTGAGGTTGTTGCCCCTCCAGCTGTCTGCACCACTCTGTAATACCCTGAGACTTGTGCTCTCCTACCCTTCCCGCCCCCATTTAGCATGGCTAGGTTTGCTTGAGGATGATCTTCCCAAACCTTACGTTCACTTAAAGACGTTTGCTTTCATTTGCAAGAGATGTGATATCAGTTCCTTCAACTAGCTGGAAAAATGTATCCCAAGGAAAAACTCAATACCATATTTAGCAGGGCTTTCTGGTTTCCTGGGGAAATTAGCCCTGGAGTTGCCATTATGAAAGCCTCCATTACTTGGCCTTTGTGAACTGCTAGCATTAGTGTTCCTTCCAGCACTCCCTCCTCAGTATGCTGCCATTATATCTTCATAGCAGCATGATGACTACTTGCAAAGCCTCTGTTTTGGCAGTGGAAATCTGCCACTCTGTCAATTCCAGGTAGTACAGAGCAAATCCCAGAAGTGAAATCATGCCTGCAAAGGAACAAAAGCCATGTGTTTCACCTCCCACTGCCAACAGCCGGAATCCCTACAGGGCAAGTTTGGGCCGAATACAGCACCTAATTTCACAGGTGCCAGGGATTCTGCCTGTGCCCCCACAGACTGCCTTTTGTTTGTCTCTGCTTTTCATGGCCACATTACAATGCACACCTCTTCACACCTATTTTTGTTAAGGAAACTTGACAGAAAATCTGGTGAAATACAGATGCTGCTATTTTTATTTGCACATACAGCATACTGGCATGCAAACTAGCTTGAGAACATGAGTAAGCATGGGTTTTGATCCAGCTTGGTTAAAAGCTTAGCATCCTGATGACGCATTCACGTGCATAGCTTATAGAGGCCATGAACTAATGATTTACACATCTGATACGTGGATGGAGATACTTGATACTAATAAGCATGTCCCATTTCCATTCTCTGTAAATTAGCCTGCAACAAACACTTCCTTATGACCCTGGTCTTCCTTTGATCCCTACACTATAACTCTGCCTTCCCATTCCTTCATGCACCTAACTTTCCATTTCCTCCTGCAACGCACTGCACCAGTCACTCCTATCACCACCAGAGTACCAATGGGAATGCCACACGTTACCCAGTAATTAATTTATCTAAAGTTCAGGATTTCCCCATAGTGGGAGGAGAGGGGGATGAAACTATACCACAAGGGGGACCCTAGTCCAAAAAATACATCCAGAAAGCAATATGGTTGCAGCATCATGACACTATCGGTTCATGAGTCTCTTGGAAACATCTTTCTGATAGGTAGTTTTTGTCCCAATATGCTATTGTGCATTTGCTTTTCTATTTGTTTTGTTTTGTTCCCTTCTCAAGTGGGATGATGTACTTTCTCATGAGGTACTTGAGGAAGTGAGAACTGAGTCATTTGACTGAAGAAATGTGCCTGCCTGGCTCTTTGTACAATCTCACTGCCTGCAGTTGGGTTCTCCTGGGGGACAGAAACAGCCCCAGAGCTTGACATGCACACACAAGAAGTATTTGACTTCAGTGTTGCAGGTGTAGCTCCTTGGGCCTGACTTTTCAGCAGTTCATCTCCTGCTCAAGAGTACATTATTATCAACATTTGGTTCCAGTTTTCTCATGTTACGTGCTAATTAATGGCAGTAATTCACGAAAGCATTTCCTAGCTGCTTAGTCTCACATATTTTAGTAGCAAAGTCCTTGAAGTATCCAACCTTCAACTTAGAAAAATAATAAAATTGCATCCTGACCTTATAGTCCAAGGTTTTGGAGTTGCAGAGTTGAGGGGGTATTTTATAGAAATCTCACTGACTTTATTGAGGCAAAAAACATAAAACCAACCATTCAAGGAGCCAGATGAGTTCCTGGAGCAGGAGCCTCTCAGAGGCAGGAGGGGACAGCTGAGCAGTCTACCATGTGATAAATCAAACTTTTCAATACAGGGCCGGAAGGAGATGGAATTTTTTTCCAGGCCCTCCTCAGGAGCCAGAGTTAGCACTACCCCTGGGGTTTGGCTTGCCTTGCTATGCCAGGAGTGATAACCTACCTCAGTGCTATATAGCCAGGCCTAGGATATAGACCTGCCATCTTGTGTTCTCCATGGCCAACCTCCTGCTATACTTCCCTAGCTGAACAGGACCTCCTCTGTTCCTCTCCTTCCCTAAGGGAAGCCTGATTAAGCACCCTCATTGGAGAAATGTGCACAAGCTTATGGTATGAGCCTGCAGGCAGCCCCTCCAGCCCCAGCCTTGCTTCCAGCTAAGCTGAGCCACAAGCCTGGGTCACTGCAAGGGCGTGAGGAATATCTGTGTGACTATTCCTCCAACGCTGGTTCAGACTGTTTGTTGCAGCTGTAATAGTGAACCCATTTCTTCTTTCCTCATTCTTTGCACTGTTTTCTGTGCCCTAAACTGCTATTTCATTCATGCTTCTGCAG
Seq C2 exon
GGAGAAGACGGCCTTCCGGTTCAAGGCTGCTGGAATAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004286:ENSGALT00000006816:40
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(41.2=100)
A:
NA
C2:
PF0139113=Collagen=PD(10.3=53.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
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]