GgaINT0105271 @ galGal4
Intron Retention
Gene
ENSGALG00000016843 | COL4A2
Description
collagen, type IV, alpha 2 precursor [Source:RefSeq peptide;Acc:NP_001155862]
Coordinates
chr1:138384201-138387983:+
Coord C1 exon
chr1:138384201-138384487
Coord A exon
chr1:138384488-138387728
Coord C2 exon
chr1:138387729-138387983
Length
3241 bp
Sequences
Splice sites
5' ss Seq
ATGGTATTT
5' ss Score
3.85
3' ss Seq
GCCCTCCTTGTCTCCTCTAGCAC
3' ss Score
9.93
Exon sequences
Seq C1 exon
GGCTGGCTGGCTCATGCTTGGCTCGTTTCAGTACAATGCCATTCCTCTACTGTAACCCTGGGGATATTTGTTATTATGCAAATCGAAATGACAAATCCTACTGGCTCTCAACTACAGCACCTCTTCCAATGATGCCTGTGGCAGAAGAAGAAATTAGGCCATATATCAGCCGCTGCTCTGTGTGTGAGGCCCCAGCTGTGGCAATTGCTGTCCATAGCCAAGAAGCTTCTATTCCTCGCTGCCCTGAAGGCTGGCGCAGTTTATGGATTGGATATTCCTTCCTTATG
Seq A exon
GTATTTGTTCTCCAGTGTGGCATTTTGTATGGCACTAGATTTAAGTATGAGTCTTAGATACTAGGAAGGCTGCTCTGTCTTAGATTCAGTAACATCAAAATGATGCTTCATCCTGGGGACCTGGGGAACAACAAAAGTCATCCCTAGGAAGTAGAAATAGGAAGCAAAATTTATGTGAATTGCAGAGAAAATGGCCAGAGTGGCAATTTGGAGTCCTTTGTCAGAATAGCATCTGGAATCTTTATATACCAAAAGTGTTTGAGAGCAGAACACCGGGACAGCTGTGGCTTAGAAGGTAAAACCATGCTGAGGTGCATCCATAGCCTACAAAGCATTTTCACAGCTACAAGAAGAGTCGGGGATGTACCTCACTATTAAGAAGCTGATCTGGAGGAAAAACAAGATACATCCCCTTCTTTTGGATACTGAAAATCACTGCTATTTAGATTTAGATGCAAAAAATGTTTCACTTGGTCTGGAAAGAGAGAGAGTCTCCTGTTGCTTTAAAAGTTAATCTTCAATGTATTCTCCCTAAGCGGCTGAGGCCCCTCGGTGTGCTCAGCGCAGAGCAGAGGAGCTGAGGGGAGGCCTCATGGCGGCCGCAGCTCCTCACAGGGAGCGGAGGGGCAGCGCTGAGCTCTGCTCTGTGTGACAGCGACAGGGCCCGAGGGAACGGCATGGAGCTGTCAGAGGAGGGGCAGCTGGGGGTTAGGGAAAGGGGCTGCACCAGAGGGCGGTGGGCATGGAACGGGCTGCCCGGGGCTGTGGGCACAGCCCCCAGTGCCGGAGTTCAGGGAGCCATGTTGTGAAGGCCGGAAAAATAGAATCAGATGTATTTGGCAGAAATCATCTCTAGTCAGCCTTTTCCACAAATTATTTGCTTTTCAAAAGCTTCAGCTTTTTTTTTTTTTAATGAAAAGGAGAAAAAAGAAAGAAATTTGTTATTTTTTACTTAGTTATAGAAACAAGATTTGAGACCTTTGACCTTTCTCTTGCTTCTCTGATAAGCCCTTGATAGCAATCTCATAGTTCCTTCACAGGAATGCCAAGGATTAATTGTTTGTAAAGGTAAACATTCAGCATTGTTAAGGGCAAAGCTGTTACCTTTAGCAAGAAGCTTTTGCCTGGACAAAGTCTGTGCCAGCACCACAGAACATACAGTGAGAAGTGTTTTAGAAGATTCAGATCTTCAGTTTCCCATCTAACATTCCAAAGCGACTGAAGTGTTTGACATACACATTTTTTTGCTTCTCATGCAACTCTTGAAAGAGAAGTGAAACATGCTTGTGGTTATTTCAAGCTATGCATTGTTTTACTTCCTTGGCTGAAATTTGTCACCTCCTTCCCTTGGGTGAGGCACAATCATGAAGGGGTCACCATGGACTCCTGTCCAAACAGCCTTGGAGATTGGTAAGATTTCATGTGGAAAGGGCACACAGCTGTAGTGCTTCCTAGAAAGGTGTAACCCTTGCAGAGGGACAAGAAGCTCTAGTCAGTAAAAAGGAAGCTGTTAGAGACACAGAGTTGGTGTACACTGAGCATAGGAATATCACGGTCCTTGCCCTGAGGTTGCCGAGCAGGATTGCTCCCAACCCAGTGCTTGGAGATCACCTGCAATTTTTTTCTGGCTGCTTTGTAGATACAACTGCAGAGGCCTCAAAGCTGTGAATCATAGAATCATTCAGGTCGAGAAAGATCTTAAAGACCATCAAGTCCAACCACAACCTAACCATACAACTCTAACAGCCCTCCACTAAATCATGTCCCTGAGCACCACATCCAAAGGGTTCTTAAACACGTCCAGGGATGGTGACTCAGCCACCTCCCTGGGGAGCCTATTCCAGTGCTTAACAACCCTTTCTGTAAAGAAGTGTTTCCTGATAGCCAACCTAAACTTACCCTGGCACAGCTTAAGGCCATTTCCCCTCACAGGGCATGTTCTCCAAGCCCTTCGCCAGCCTTGTTGCCCTTCTTTGGACCTGCTCCAGCACCTCAGTGTCCTTTCTGTACTGAGGTGCCCAAAACTGAACACAGTACTCGAGGTGAGGCCTCACCAGTGCCGAGTACAGGGGCAGGATTACTAGTTCAGCCCTTCTACTTACCAACTTTGTTTATCTAGAGGGATGCTAGAACAGTTTCACTCTGAAGCTTTATAGCTTAGTACATCATCTTGCAATTTGTAACACAGCCCATGGGTTGTGTTTGAAAAAATAAATACATCTAAAACCCCAGCAACATGCAACCCTGCACACAGGTCAGACTCTGTCACTCCACTCCAAGGTGGCCACTTGTGTTCCTTATGGATATGAACATGGTGGGCCTCTGAGCATAAACCAAGGCAGTAATGGCTGTTATGTACTTTTATAATATGGCATTTATTAAAGCGTAAGCAGGCAAACGTATTGAATATACCCAGCAGATTTCTTCCTACATTCACAGAACTATTTAGCAAGTGTATTTTCCATCTGCTTTCATTTATATTGCAAACTCCTTCGGTTTTTAAGTGAAAATTAAACCGTGTCACTTCTGCAACTGTACAGCCCTGGGGCAGACCGGGAATGCCTGTTTTGTCAGAGATCCCTTTGACAGAACACAAGTAACATTCGTTTGTTACTACTGTCTGTGTCAAAGGTAGCAGCTGAGTGGTTTCAGATGCATAAATTTGGTGTAATTCACAGTTAATGATAGAGGGAGCCTAGTTATTTGTATAGAAGCCAAAACTTTGTTTCCATAGCGCTCCTTATATGCTATGTGGAATAAATAAGACTTTATAATGACGGTTAGTTATATGGAAAATCATCCTTCTCAGTGATGACAATCAGAAGAACAGGGCTGCCCATAGAGGTGGTGGAAAATCCATCCTCGGATATCTCAACAACTTGACTGTGCCCTGGAACAGCCCAGCGCAACTTTGAAGCTGGGCCTGCTTTGAGCAGAGGACTGGCTGAAGTGATGCTGAAAGGGCCCTTTCTCACCTACATGATTCCTCATTTGTAAGCTTTGCAACAGGGAGAATCCTAACCCTAGAAAAGATGTTTGTCAGAAATGGCGTCAACACTTGAGATAGTTCCTTAGTATAAAGCATAGCCAAACCCTTCAGTCTTACACAGCCGCAGGATCGGCCGCTCTAGGTTTAAGAATTAGGAGCACTTCTAGTGCTTTTCCTGTCTTCCCACGCATAATTTGTTGATGGCATTGCCTGAGGTTGTGCTCTGAACGCTGCCCTCCTTGTCTCCTCTAG
Seq C2 exon
CACACTGCGGCTGGTGATGAAGGCGGAGGACAGTCGCTGGTCTCTCCTGGGAGCTGCCTGGAAGATTTCAGGGCTACTCCTTTCATCGAGTGCAATGGGGCCCGTGGAACCTGTCATTACTTTGCCAATAAGTACAGCTTCTGGCTCACTACGATTGACCAGCCCTTCCAAAGCAAGCCATCGGCAGACACACTCAAGGCAGGACTCATCCGAAGCCACATCAGCAGATGTCAAGTCTGTATGAAAAATTTATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016843:ENSGALT00000027208:46
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0141314=C4=PD(59.3=66.7),PF0141314=C4=PU(26.3=31.2)
A:
NA
C2:
PF0141314=C4=PD(71.9=96.5)
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]