HsaINT0038058 @ hg19
Intron Retention
Gene
ENSG00000197467 | COL13A1
Description
collagen, type XIII, alpha 1 [Source:HGNC Symbol;Acc:2190]
Coordinates
chr10:71690156-71695147:+
Coord C1 exon
chr10:71690156-71690308
Coord A exon
chr10:71690309-71695105
Coord C2 exon
chr10:71695106-71695147
Length
4797 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
3' ss Seq
GGCTCCCCTTTGGCTTTTAGGTT
3' ss Score
9.1
Exon sequences
Seq C1 exon
GGACCTCGCGGTAAACCAGGAGACATGGGCCCTCCTGGTCCCCAAGGCCCCCCAGGAAAGGATGGACCTCCAGGAGTGAAGGGAGAAAACGGGCACCCAGGGAGCCCAGGAGAGAAGGGGGAAAAAGGGGAGACAGGACAAGCAGGCTCACCG
Seq A exon
GTGAGTGGCAGGGCTGGCTGCCCTTCCGTGCATACACCACTCCCAAGCATGACGCCAGCTTTGCAGGGCTTTGCACTTTGCATGATGTGAGCTGCTGCCTGGGCTAGAAACCTGGGGCCAGGGCTTAGGGGTGGAGGATTCACTCAGCTTCCCCTCAAGTCACTCACTTTATGAAGGCCAGTTTCCCGACTCAGGAGACCTGAGTTGTGCTCTGTCATCTGTATCCTTGGGAAAGCCACTCACTGTTGCAGAGTCTCCGTCTCCTCATCTCTAAACTGGCGATAATAATGTTTTCCCTGGATACCTCACTGGATTGTTGGGAAAGAGATGAAGACATGGTTTAGAGCTGCCTCTTTGGAAAGTGTACAGAAGCCCTATACCCGGGAGAGGCTGCATGTACAGAAACGGGGCCTTCGCCCAGTCCACTAGGCTGCTAACTTGACTTAGGGGCCTTCTCTGGGTCTCAGGGGTTTCCATCTGTGAAATGGGTGCCATCCTAGACACCTACCCTTGGAGCAAGGGAGCCACATCCTGTGCAGGCCACAGTTGGTCACACTCAGCAAGACCACCTTGAGCTCCACTAACAGAAATCATTGTCAGTCTGTAGGGTCTAGATGGCCCAACTGGGGAGAGGAGAACATGGTGGCCAGAGCAGACCCAGAGTGGCAGGATTGCCTAATCCAGCTGGGCTCCTGAGGTTTACAGTGAAGCCAGAGGGCTGGGTGTCAAGGTTGCCTGCAGGCAGCCACAGATGAGGGTCCTCCTGGGGGCCACCAGCCTAGTGGGTGCCTGACACTGTGACGAGGCTGCCCTAATCCCAAGCCTGCCGACCCAGCCTGGGAGCAGGCAGGGAGGGTCCTCTTAACAAGCAGCTACTTCATTTGAGTGTAAACAGGAGTTGCATCTTCCTTGGCTCACGGTATGATGGCCTCTAGGAGCACCAACCTAGTTCGACGGTGCTAGAATCTTGGTCTCAGAATTCTCCTCTAGGAAGTGGAAAGAGCCTCAGAGGTCAACCAGTCCCAAGTCTGACCCAGTGCAGGACTCCTCACTCAACCGGCACAGGCAGGCAGCTCACTGCCTCCAGACCTGTCCACTGCACCATGGGGCAGCCCCAGGATGGAGGGAGCATTCCTGGATATGGTGTGGAAGCTCCCTTGTCAGCCTCCCCGAGTTGACCCCTCAGAGCCTCTGGCCTCTGGAGCCATATTTATTATCTATTGCTGCATAACTAATCACTGCAAACGTAGCGGCCTAAGAAAATACACACTTATTGGCACATAGTTTCTGTGGGTCAGGAATTCAGGCACATCCTAGTTGGGTCCTCTGCCCATGGTCTCATGAGGCTGCAATTAATGTCTCAGCCAACTGTATTCTCATCTGGAGCTAGGGATCCCCTTCCAAGCTACTGGTATTGGCAGAATCCAGTTCCTTGCTGGAACAGAACTCAGCTCCTAGAGGCCACCTACAGTTCCTGCCACCTGCGCCCCTGCCCTCCCCACCTCCCGCAGAGTAGACAGTTCACATTATAGCAACTGGCATCTTCAAGGACAAGGCCAGCAGTAGGGTCTCTCTAGTGTCTAGTGCTAGCAAGACAGAGCTGTGTGCACGTGTGTTTGTGTGTTCATGTAACATATTTGTAACATAATCTTAATATATGTTATATGTCACCATCTGTATGACATGTATGTTATAATCTGCAACATAATCATAGAAGTGAGGTCCCACCACCTTTGCCATGTGCCTTACTCCACGGCTAAGAAACAAGTCACAGGTCACCCTAAGGCCTGTACGCTGCAGAGTCCACAGAGAGTATCAGCCTCTCCTCCCCTGTACTAGAGCCTCAGATTCTGTCCTGCAGGCTGACACCTCCACATCCTCCATGGTGTTCCTTGTTGACCCCTAGACCAGTCACGTCCCAGTCTAGTTTGTCACAGATGTGAGGGTGCGTCTGTCCCAGGCTTTCACAAGGGCTGGCATTCATGCAGTGGTGTTTTGTGCCCACAGGGAGAGAAAGGAGAAGCCGGGGAGAAGGGCAATCCAGGAGCAGAGGTACATGAGAGATAATTTGACAGAGACTCATCAAGCGACAGTCTCTGCAGCATGCACAGTATTTCTGTGCTTTAGAATGAAGCTTGCAACTGCCTGATGTTTACGTTTACTGAGCACCACCATAGGTCAGGCACTGATCCTCTGGACTGCTCCAGTCTTCCCAAACCACATCTCTCAGCAACCTTCACAGAGCACCTCCCATGCTTCCATCCTGGTGCTAGAGTCTGGAGATACGAAAATAAACAGAACTTGCCGGGCACGGTGGCTCACGCCTGTAATCCTAGCAATTTGGGAGGCTGAGGCAGGCGGATCACCTGAGGTCGGGAGTTTGAGACCAGCCTGGCCAATATGGTGAAACCCCATCTCTACTAAAAATACAAAATTAGCCAGGAGTGGTGGCAGGTGCCTATAATCCCAGCTATTCGGGAGGCTGAGGCAGGAGAATCACGTGAACCCAGGAGGCAGAGGTTACAGTGAGCCAGGATTGTGCCACTGCACTCCAGCCTGGGCAACAGAGTGAGACTCTGCCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAGAACCATCCCTCCACAGCTCACAATACCCCATAATGGGCACTAGCATGGGAGCAACTCAGGGAATCGGGCAAGCATCCCAAAAGACTTTCTATTTGGGCAGAGTCTTGACGGCTTTGTAGGAGTTTGCCACAAAGTTTCAGAGGTAGGCTTTCCAGATAGAGGCATTATTCTTTTGAGAAGTGTGGTGAAAGGAAGAGAAAACAGAATGGCTGAGTGAGAATAGTCAGGATGGAGGCAAGGTTTTCAAAAGACAGCAGAGAATCAGGCATATTTGCGGGCTCAGGGGCAAGAACCCGGAAAGCAACGGAGATCAAGGATGCGTGAGAGACAGGATGTTTGGTGGCGGGGTCTGGGCAACCCAAATAGCACCTCAGACCCATGGGAGAGACCACCAAGCCTTCTCAGTCCCCATCAGGGTGGGTTCACCTTGCCAAGCCCCGTCTGAATGTAGTGAAACAGGCCTGATTGTACAATGTGTATGGTACTTGTTTCGAAATGGATAGCCTCCTAAAGAAATGATCCTAATTCAGGAAAAGCATTATACGCACATTGTCCCTCCAAGAAGTATTTAAAATAAACATTAGAAACACTCTAAATTTTATCAAGAAGGAAAGGATTAAATAACTTATAGTAATAATACTAATAGTAATAATAGTCACCACGTCTGAGCACTTCCCTCGTGCCAAGCACCGCACTAAGCCCTGGGTATGTAACAACTCATTTTCACTCCACCCAGTGAATAGCACAGCACCGTTACCAGGAAGCTGGTGGCGAACATATAAAAAATGGAAACATCAGTTTCACAGTAAGTGAAAAAGAGTTGAAAACGAAATTTTATACATATATGAAATCATAAGCATATACATATATGTATATACAATTCTACACATATTATATGTAAATATCAAAAGTATATACATATATTCAAGCACATCTGATACATCAAGAAAATGTTTAAATTTTCTCTTTAAAGAAAATTTTAAAAATTCTTTTTATTCTTTTTATTATTTTTAAAATTACCACCCAGGTAAAATTGACTTCTTCTGGAATGTGTCCAGTTCTGTGAATGTTAATGCATGTAGAGATTTGTATAACCAATACCATGATTAGGATACATAAACCACTTACTTATAATAAGAATTAAAATGGTAAACTTTTGTTAAAAATGGGAAGCTTTTTTTAAGAAGGCAGAGTTTCCAAAGACTGTGTTCCCTCCAAGGAGACTGTGATGGAGCGACAAAGTCCACAGGTCCAGGAAACAATAGGGACCTCCTGTCTGCCCAGTGTAGGGGTGCCCTCTGTCGTGGCCTGGCACAGGAGTCACTCCCCTGGCCATGCTCCAGGGAATTCTACCCCTGGGAAGACGAGGCACCTGAGGAGAGCCCTGAAGCCGAGGCGGGGTGAGCAGCTCAGAAGGACCCAGCAGTGGCTGCCTGTGGATGAAAGGATGTGTGTGTTCATCAGAGACAGAAGCTGCAATGGGCACCACCCTCTGTAGAGGAGGCAGCCCTGAGCTCCTCCATCTTCACTGTCCAGTCAGAATCTCCTCTAGCACAATCTGCATCTGCTCTCAAGGGAAACAGAGACCAGCAGTCCCCATCCTGTCTGTAACAAACCTTGGGGACTTGAGGAGCAATCTCCAGGAACAGCTCAGTCTCCCCACATTCCAGATAACCAATCTCTGCTTCTCTAAGCCAAGGGTCTCAAACTCAAATGTCTACAAGGGTCAGGCCTGCAAAAAGTGACTGCAAGAGCGCTGGATCAAAGACAATAAGGAGTGGTGAGGACTGGGGTAAACTGAAGGTGTCATGCCCCACCTAGAGGGGAAAGCTCTAATTCCACTCCAGGCTGTTGTTGCCATGCATGAACAAGAACCTAGTGCTGCTAGATCTTCTGGTGTTTTTTTTGTTTTTTTTTTTCCAAGAAAAATCTGGAAGAATAGATCTTTAGGGACAGTTCCTGGAAATTTGCTTTTTCAACATTGAGCAGTCCACCGGGTTGCTATGAGTTTTTGACCTGTTCTGAGCCTTTTTTGGGGGATACTGTGCTGGGCAGTCACTGGCTGACCTCCAGTGGGCAGCCATGTCCTCCTCTGGCCTTGCAGTCTCCAGCTGGGCTCTAGGCCCTATCAGGAGGGAGGGCCACTTCAAATGTAACAGGGCTCCCCTTTGGCTTTTAG
Seq C2 exon
GTTCCTGGGCTGCCAGGGCCAGAGGGGCCTCCCGGACCTCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000197467-COL13A1:NM_080805:26
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(37.7=45.1),PF0139113=Collagen=PU(71.0=86.3)
A:
NA
C2:
PF0139113=Collagen=PD(1.6=7.1),PF0139113=Collagen=PU(21.7=92.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
Other Skipping Isoforms:
Associated events
Conservation
Rat
(rn6)
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]
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)