GgaINT0090628 @ galGal4
Intron Retention
Gene
ENSGALG00000016195 | COL22A1
Description
collagen, type XXII, alpha 1 precursor [Source:RefSeq peptide;Acc:NP_001132911]
Coordinates
chr2:144142255-144146972:-
Coord C1 exon
chr2:144146895-144146972
Coord A exon
chr2:144145919-144146894
Coord C2 exon
chr2:144142255-144145918
Length
976 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGT
5' ss Score
9.8
3' ss Seq
GCATTATGTTTTTATTTTAGGCC
3' ss Score
10.06
Exon sequences
Seq C1 exon
GAGAAAGAGGAGCGAAGGGTGAGAAAGGAGATGCTGGCATTGGCCAGCGAGGTGAAATAGGTCCTCCAGGAATTCCAG
Seq A exon
GTATGTTTTTTCAGAAAGTTACACACACACACACACACACACACACACAAAGTATATATATAACTCAGAACATTCACAAAGACAAAGGTATCTTCTACATTAGATAAATAATCAAGTTGACATAAATAATGGCATTATGCTATTTCCATAGCTGGTGGCCCAAAGGGAAGAAATAAAACACTAGTATCATATCTAGCCACCTTTGTTTCTTCAGCCCGATTGGCAAACACAATGAACCATGTCAGTAACAGTTAGGTTAACTGACCTTTCGGACAAGTCCAAAGTGAGGCTTTATTTACTAGGTACACAGTGCGGTGCCTTATCTGCACTTGCCAGAATCTTTTTGTGACCAAGCTGAATGCAGAGATCCAGGCAGCTTCAGCCTGTTAAAAGATTCTATCTAACACCTCTGTCTCAGGCACACAGCTCAAGCCTTATCTTTGCTGATAAACAAGAAGCAAATAAATTTTGTTTCTAATTTGTAATTAGGAGCCATCGATCAGCTTTACATTCGCCCTGCTTTGGTGGGAGAGGAAATTATGGAAAAAATTCATTGCTCTATAGGCTGCATCAGGCATGCCTGTCCTGCATTGCCTTAAAATGACAATGAATCCACTATACTTCATACAATGAGTTATCTCCCAGAGGTGGCTCTTTCCTCAAGTTTTCCCATTCTCACCACCTCCCTATGAGAACTATTTGTCATTAATTGGCTTGTGCAGCTGCACAACTTCAACTATATGGTGAGAGTATAGTACAGTTGTGTAATCCAATTATGCATACAGGGTGGAAATCTCGCATTCAGAGGAGCCATGTTTGCCATATTCTCATAGAAAAATGTCAGCCAGACCCAAATCTGTGGAAGGTGATGCCTACCTCCCAGTATAGGCAATAAAGCCATCTCCTGTGATGCTGTACTACTAAGTACTGCACTCTGAAGGTGCCACTCACCAAGGGCATTATGTTTTTATTTTAG
Seq C2 exon
GCCTCCCAGGGGAGCCTGGCTATGCCAAAGATGGGATACCAGGACCACCTGGCCCTCAAGGTGAAGCTGGGGTACCTGGTCTCATGGGCCCACAGGGACCTCCGGGAGCCAATGGACAGTGTGACCTCGCTCAGTGCGCTTACTATGCAAGCCTGGCTGCCAGGCCCGCCAATGTCAAAGGGCCCTAGGATAAAGGGAGTATCCCCAGACTTGTTTTTAAAACTTGAATTCATCCAGCCTACCAAGAGCTCTCAGATGTCTTCAACTTTGTTTCTTTCATGGGAGGCCTTCTAAAGCCAACAAATGCTGCCGGTCGGTCAGATTATTTTTATGAATTATAATAATTATTATTATTATCTTTGATGTGATATGTGAATTTGTTCTTGTTTCTCTAACACCAGGGCATATTAAAACATTAAAAATGTGGTTTTTTTTTTCTTTTGAAGAGCATACAACATTGATGCATTGTGTAGCAGTTTATGCAAAACCATTCTGATACCACTTTTTTTTTCCTTTTTGTGGTTAATTCTTTCCAAAGCTTTAGCCTTGAAACTGAAATTAAATCCTGCACTGTGCAGCATGGGGCATTAACTGTGTAATCACAATATTGGTGCTAGCTGCCATCCACACAGAGGACAGGAAGATAAGGTCATGCCAAAGCTGGGGAAGAGATCTCCAATACACTCAGCTCACAATGGACAGACAGCTATAGACAGGCAAGGTGTTCTCTGGAAGATCTCTTTTACATTTATTATTCTGTCCACAAAAGAATCAGAATTCTATAGAAGCCAATTTTTTGGGACCATGTGAAATCTCACAGTGAGGCCTGGATCACTGTTCCTTGTGCAATAACTTCAGTAGATGAAGGGTATGTTCATATCAGATGGAGCTTATCTTCCTTCTGTCAGGGAGATGACTCTGAAAAAGCCACAATACTATCCTCCATCAGCTCAGGGCTGCCAATTCCACTTTTCACTGTCAATGCACACACAGCCCTCTATCACTGCTTCACCCAAGAAATCTGCCAGCACAGCACAGAATGTCTTCCACTGTTAAAAATCTCAGGTAGCAAAGTGTCACCCGACTTCACTGTTTTGAATGATACACCAGGACAATAACTTGGAAAAGTTGTGTTTTAGAGGGAGGTGAGAGATTAGAGGCTGGTTTTCATCTCTCATGAAAAGGTCAGAACAAAGAGGTGTTCACAAACTCTGAGGAAATTATGCTTGAGAGTGAAAGCCAAAACTCAGACATAGACCATTTTACATATCAGCTAATTGCCAAAATCAAGCTGGGAATTCACTGGGAAAATAAATAGGGGACAGTGTCTGAGAAGACATTCACAACTGGTCACTTTTCAGTCTAACTTCCTGACAGAGACACGTGAAAGTGTGTCAGCAAAGGAGCCAGATTTCCAGAACTCTTCTGTATAAGCAGTTTGTATTGAGGGATCAGAGTAATGAACAGGATACAGACACTAAGTGCTGAATCTGTTTCGAAATCTCATCTGGTCTTTTGGAGAGATAAATGTGGCCCCCTGCCCTGCTGGCACGTTCACCATGTGGCATGGTGCTTCCAAACTGGTTAAGCCAAGCGGAAGGCACAACTGTCTATAACCATCCCAAAATCAGACACTGTAGCTATAAGCCCAGAGCTAACTATTTGCAAGACTTGGAGTTTTTTTCTTACCCAGAAGATTAAACAGAGTCTTTTCTATGTAGATCTCAGTGGTGATCTTTTTGCTATTTCCTATGCAAGTAAATTCTTTTATTGGATTTTACTGTGTTTCTGTCTGTGGAAAGATCAAGCATAGTGAAAATATCATGAAGAGCATAGTGCTTTTTAGTAACTCTCAGTAGTATAATGTTATTGTAGAGCATCTTATACCAACTTTCTACAATTCAGTTTTAGGCAAGTATGTTGATCACATAGTATTTAACATCATCATTTTTTCTAGTCCAGGATGAATGAGATTTTATTCCTCTATTGGTGATGTAGAATGAGCTGCTTACTCAAGAGAGACCTCTCAACATAGCATGAGCCATCATTTTGAGTAAATGTCATGGGAATGAGCAGGTTTTATGGAGGTCAGGCATGTTAATTGTCCCATGTTAATGTGACATGGCATGATGAGTGATAAGCTGACAGTGGGACTAGATCTTAGTGGTCTTTCTCAACCTTAATGATTCTGTGATTATATGATTCCATGATGTGAAAGTACCCAAACTCTGCATCGTGCATGCATGCACTATGCATGGCACAGACTTTAATACGTTCAAGTATACCATGTGATGGGTAAATATATAATGATGCTCTATTGAACAAATTCCAGGGTCTTTCATCTCTCTGAAATGGTGCATTGGAATCTAGATAAAGGAGATAGGAGATTCTGGAGTTTTGTTGTTTTGTATTTTTTTATTTTCATTTCATCTGCAAGTCTCTTAAAGCCATTGCTAGGAGCAGTCTGTGTTAGAAAAATGAAACACATCAACATCTTCAATAGAAATTAAAAGATCTGCAGTGGGCAGCTGTCCCCAAAAAAGGAGAGACAGCCTAATTCCCTTTACTCTAGCATATTCTCTATTTTATTGTTACCTGTTCAGTCCATTCCTGCCTTTGCGTTCTGAGTTCAGTGGATGCCATTTCCCTGCTTTTTCTTAAACCTTGTTTCCTCTACAGTCAGTTACACGACTTTACCAAGCACAGTCTGTCAGTAGTGAGGAGTATGCTGCAGACCCAGATCAAGACTGGTGCTTATAGCCAGCCAGTGCTGTCTGCCAAACAGCTTGCAAGGCAGCAATGGATGCAGGAGGTGAAAGATAGGGCAGAGGTAATGAGTGTGGCTGCTCTACTAACCACTCTTGAACAAGATGAGGATGTGGCTTTTGCATCTGAATGTTCCTGGCTCAGAAACAAAGCATTTGGTACATCACAGTGAAGTTTATTCAGTGTCGGAGACTTAATCCCAGGAATCCACTGTTATTTTTCTATGAATTTTTTTGGCCAGCCATGTGATAACAGGGAACTTACTGATAAGATGGCATTAGAGAGCCAGAGAATGTATTGTCTACATATTACCAAGGTGCTAATGATACACACATTTTATGATATTGCTGTAGTGTTCTTTTTTAATCAATTGTGTAAATTATTACGGTTATAGCAAACAAACTATTATTCCATTATATATTTTGCCTGTCAAATAAATAATTTAAAATTTTTAAGAGATTAATTTCGGGAAAATAGTTTTTTGTGTTACATTATTTAACAATTTACACTTGTATTCTGAGCTGCTCTAAATTAGCTTTTTTGGAGCTGTAGCAAGGAATAAATTATTTTCCTTCTTTGCTGCTTTTGAGAGGCTCATCTCATTACAGTCTTGTGGTGGTGTTTTTCTGAGCTGTCCTTTTCACACCTCTCGTTAATATGGGATAATTAAACTGTCTAAGGTTGAACTCAGTTCCACATGTTTATCCAGAAATGTGTAATCAAAGCAAAATAGTGCTGCTCAGGACTGAAAGCAATGTGTGTGTTTTTCCAGAGATGCAATAAAAACGCAGCAGCAGCTAAGCCTCAGATCTGTGCTCTGAGCACAGAACTGTCAGGGAGATGAGCACATTTTAAGAAAAAAATGCAATTAAAATTAAAATAAAAGAAAAAGAAAAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016195:ENSGALT00000026109:64
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.823
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(22.0=48.1),PF0139113=Collagen=PU(25.0=51.9)
A:
NA
C2:
PF0139113=Collagen=PD(73.2=65.1)
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:
GCCAGCGAGGTGAAATAGGTC
R:
CGGCAGCATTTGTTGGCTTTA
Band lengths:
348-1324
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]