HsaINT0038056 @ hg38
Intron Retention
Gene
ENSG00000197467 | COL13A1
Description
collagen type XIII alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2190]
Coordinates
chr10:69889414-69894578:+
Coord C1 exon
chr10:69889414-69889440
Coord A exon
chr10:69889441-69894551
Coord C2 exon
chr10:69894552-69894578
Length
5111 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGA
5' ss Score
9.48
3' ss Seq
TGTGTGTTTGCTTCCCACAGGGT
3' ss Score
11.03
Exon sequences
Seq C1 exon
GGCCACCCAGGACCAAAGGGCGACATG
Seq A exon
GTAAGAGCCCAGCTTTCCTGCCTTCCCGAGATGGGTGGGGGTTGGCCCAGCCTCACAGGCACAGCCAAGCACTGCAAAGTGGGTCCCACAGGGACAACAGGAATGGCTGTCCATGCTGGTCACTCCCCAGCTGTGTAAACCACATGCCCTGGATCCTCACATCAATATGCAGGGAGGAGAAATGGGCAGGGGCTTCTCCATCTGAAGCATGAGGATGGGAGATCCAGAGAGAGTGCACACCTGGCTGGTAGCACACAGAGGTCGGTGTCCAGCTTACTGCTCTCAAACCACACTCGCATGGGCCTTGGGAGACAAGGTTTCATCTGCACTCACAGGGGACACTTTCTCTAGGAGACACCATTTCTACTGAGCCTGAGGTCCCTCAAGGCCTCATAACCCCTTCCGGGTGCTGGCTGTGCCCTGAGCCACCCCAGGACTCCAGGGGTTCCTGCCCCACTGGGGCTGGTGGTGCCCAGTGGATCATCTCAGCTGGGGGTGCCACATGCATCATCCCAAAGGCCCCTTCCCCTCTCCCTTCCTGGGAGTTTCTGTTTGGAGGTTGGGCCACTTGGCAAGTCAGGAGCAGGAGCAAGGTCTTCTCTTCCATGTCACAGCATCCCGCGGCCACCACCCAGATGGATCTGCCCAGGGTACCTGGAGTGCCTCAGGCCCCAAAAAGGTGGAGAGACAACATTTGGCCCAGCTTTCTCCTGGCCCCTACCTTCTGCAGAGCTTTGGAAATAAATTTTCTGTCTCCACAGACCATCCCTTCCAGAAGGGAATGAGGGGCTGCGCACTCTCACGGTGGGCCAGATCTCAGCAGGGACTGATGGGCCATTAAGAGCTAATGGGCCCCTGCTCCCACACTGTGGAGTGTATTTTGGTTTTCAATAAATCCCTGCTTTAAAAAAACAAACAAACAGACAGACAAACAAAACAGCCCTGGGCTGGGGTGCATTTCTGCCTCCTAAGATCCAGGTCGCACCTACTGTGAGGGACCACCTCCTGCTCCACAGGTTGGTGGGCCAGGAATTTGTGCAGGGTGGTGAAAGCAACGCAGCAGGCTCCCCCTGTCCCTGTTCAGTGGGGGCCTGGCTCATGCCTTGCTCCAAGCGCTGGTGTGAAGACAACCCTTGACCCATGACTGGGGCACTGCCAGGGCATGGAGGGAGGCAGGTAATCATGTGGGTGGAAAGGGGGATGGTGGAGTGTTGGCTGCAAGGCCTGGGCTCCAGCCTAGCTCTTCCTAACTTGCCAGCTCCCTCTGGGCCCCAACCTGTCCTCTTGACTCAGATCCAACTAATATTTATTGAGGGTTTGCCACGTGGTTGGCACTGGGCTAAGCACTTTGCATGACTGTCTCAATCCTCAGCGTAACTCTGTGCTCCAGGTCTTGCTAGAATCCCCTTTGACAGGTGTGGAAACCAAGGCTCAGAGAGTCTAACTAACTTGCCTGAAGTCACACAGCTGAATGTCCAAAACAAGATCGAAACACAGTTCTCAAATTCCTTCCCTCCCTTTTTTTATTAAGGTTTTATTACCTTCCTCCCTTTCTGTTTCCCTCACTCTTTGTCAGCCTTCCTGCCACCTTCCTTCTTTTAATGCATTTTTTATGGAGTATCTAAAATGTGCTGGGCACTGCTTCAGGTGCTAGGGATACAGACGGGAGCAAGAGAGAGACTGTTCTTGCCATCTGTAGCTCACAGTCTAGTAGGGAGACATCCTTTTAAATGATCACTCACATAACTAACAAGTTGCTTTGCAATGAGTGCTATAAAAAGATAATCCTTAGTGCCCTGGAAATCTTGGTATAACAAAAACCTCACCCAGGCCAAAGGTCGGAGACGGCTTTTCTGAGAAAGAGACTTTTGAACTAGTGCCTGAAGAATGAGCATTCAACCGAGAGAAAATAGAAAGGGGGATGGGAATGTGCTTTCTGGACATGGGAGAATAGCACGTGCAAAGGTCCTGAGGTAGGAAAATCCTTGACATGTCTGCAGAACCGGAGGAAGGGCACTGGAGGCAGAAGGCCCTGGAGGCAGTGGCAGAAGAGCTGGCGCTGGAATCCAGGTTCCCCAGCAAGGTTTCCTCTCCATCACAGCTGCCTCCGCTGCAAATGCATTTCCCCCCGCCCCTACCCCATTCCCAGGCATGCTGTGCACATGCATGGAGTAGTGGAGACCGAGGCAGGAAGAAACTGCCATGCCACATTGTTATAGAGGCATAAAGGGCTTGGGGTGCTCATCCCTTCAGCCTGAGCTTCTTTCCCTCTCTGGCAGCCTTATGCTACCGTAAGGCAGCCCATGGCCCCCCAGAAGTAATAATAATGGTCATCCTCTAGGCAGCACTCTGTCATCCTCATAACAGCTTATCATCCCCACTTCATGAGAGGGGAAATTGAGGCACAGAGTGGCTAAGTACATTGCCTGAGGCCACAAAGCTCCTAAATACAACAGCTGAGATTCAGACCCATGCAGTGGAGTCTTACCCCTCGATCACACCTCCTCTCAGCAGCCAGCACTTTGTCCTGGAGGAAAGGGACCCTTCCATGGGGCCGCTTTTCCTGCCCTCATTCTGCCACACCGTCCCTCTGCCCCACACACTTGACCGCCTGTCCAGGGATCAGAGCTAACTCAACAGAAAAGGCAGGCCCACCCCCTCTCTCGTGAGCCCACATCAGTGGGATAGATCCCCTGTCTGCCTCATCAAATCCAGCAGGCCACAGAGCATCTGATTCCTGTTTGGCTTGGCATGGGTACCCGAGCTGTTAGTTGCCCACCGCTGTCCAGCATCATTACCTTGCCCTGCTCTTCATCTGTCTGTCTCCTGCCCCAGATGCTGTCCCCTCCACTGGCGTCCCACTGGGGCACTGGCACTCACCCTCATTGTTTAACCTGTGTCCTCACCTCTCAAAAGGGAGTCACCTCTGCCCCACCCCCCCACTTCACATTATTCCCAAGAACCTGAAATAAGGTGTTGAAGTGTTGGGAGGACACAGTTGTATAATAGTGTAGTTGGGGGGTGGACAAGATTGGGGGTCTGAGACTCAGGAATGACATAAGGGCTGTAAAGCAAGGCCTGGACTGAGTCCAAATCTCACCCACCACCCACAGGGCTGTCGAGTGAGGAGCGCCAGGCACTCAGAACATGCTTGGCACCCGAGAAGCAGACAGGCGCCTTAGCTATGCCTCAGTGGCGGTTAGCACAGGCCTGCTGGCAAGTGCTAAGCACATCACCGGTGGCCATGGCCCTTAAAGGGGCAGGTGCTGCCTGGCTGAAGATAACTGGTACCATGTGTTGTTGGACCTCGACATAATTAAGAGAAACTTGAAATCCAAATTTTTATTTGCACTCTGCTTGCTCTCTTAAGTATTGGCAACTAGTTGAAATAAAACCATGTGGGACAAACAAAATCCCTATGAAGACCACGATTGTCCCCTGGGCCACCGTTTGGGATGTCTGGTTTCAATTGTCCAAGTCTCTGCAGTCCTGAAACTCCGCCTGCCCCTCCCCCATCACACTTATATCTCTGTCCTGACAGAGGATGACCTGGTCACCTGTGGTCTGGGCCCGGGTTCCCTGCCGGATGAATCATGTGCTGCAGAACTTCATTCTAAGCACTCTGCCAGGCCGAGCGCGGTGGCTCACACCTGTAATCCCAGAACTCTGGGAGGCCAGCACGGGCAGATTGCTTGAGTCTGGGAGTTTGAGAGCAGCCTGGGCAACATGGCAAAACCCTGTCTCTACAAAAAAATGCAAGAGTTAGCCAAGCACGGTAGTGTGTGCCTGTAGACCTAGCTATTTGTGAGGCAGAGGTGGGAGGACTGCCTGAACCCAGGAGGCAGAGGCTGCAGTGAGCGGAGATCACACCACTGTACTCCATTCTGGACAACAGAGCGAGACCCTGTCTCAATAAAACAATAAAAGACCAATAAACACTTGGCCAGCCACATGGGCTGGGAGTGCCACATGGATGGTCCCAAAGGCCACTTCTCCCTTCCAGTGATGCTCTTGGGAGTTTCCCAGTTTGGAGGTGGCCCTGTTGGCAAGCGGGGAGCAGGAACAAGGCTCTGGCACATCACAGCATGCTGCGGCCACCTCCCAGATGGACCCACCCTTGGGGATCTGCAGTGCTTCAGGCCCCAAAGAGACTGGTGGCTCAAAGGGACCTGCTTATGGCTCTAGCCAAGTCTAGAAGCCCTGACTCCCAAGGTCTGGCCCAGTTCTGAGCATTTGGCAGTGGAAACAGCTGGACCTTGGCCGTCAGACAAACCTGGGCTCCTGTCCCAGTGCCACCTTTCACTGAGCCATGGGGCCTTGTCTCTGTCACCTCACTCGGGAGCTGGAGTGGACACAAGCATCTCCCTCACAGACACATACCTGAAGAGCCAGCCTCAGGGTGGATCCTCAGCCCATAAGGCATTTGTTTTCTCCTCTTCCCTCCACCAGCCTTGGTGCAGCCTCCTAAGAGAGCCAGAGCATGCGGGGCCCTCCCCAGACAGCAAGGGTCCCTCCCAACCCCAGCTCCTTTCCTAGCCCTGCATGGACAAGACAACCTTGAAGGAAACTTCAAGACCCCTCATATTCCTTGGAGAAGTCCAGAACATGGCTTCAGTTGCCAACTTCCTGCTTTCTCTCTTTTGCTGAAGGTTTCTCTAAGGCCCCCATTGTCTGAGGCACCGGCCCAGCACCCCCAGGCCAGAAGTTCTTCTGGTTCAGTGGGCTTCACTGCAGCCTGGGAGGCAGGAGGTGGAATGTGCTAGTGTCTCCCAGAGGCTTGATGCATGTGAGGTAGGGGGTCCCATGGAGCAGAAAACTCCCTGACCTCTAGGTAGAGCCCCTCCATAGCTGGCCCATGAGATGCTGGTGGTTGGAGGAATGGATGAAAGATGCCATCTGTTCTTCATCACAGCCCTAGTCCTGCCCACTGGGGGGTGAAGCAGCTGAGACTCTGTGAATAAGACATCTTGAATGTGGTGGGCATGGGAAGACCTGGCCATGGCTGGTAGAGCCCAGCCTTCGGGATTCAGCCCCAATCCCCACCCAGGCAGGTGTCCCTGATTGCCTGTCTTCTGTCTGCCCACTGACCTGTGTGTGTTTGCTTCCCACAG
Seq C2 exon
GGTCTGACGGGTCCCCCAGGACAGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000197467:ENST00000398978:9
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(13.1=100)
A:
NA
C2:
PF0139113=Collagen=FE(13.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
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]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development