GgaINT1019725 @ galGal4
Intron Retention
Gene
ENSGALG00000025723 | NKX1-1
Description
NK1 homeobox 1 [Source:HGNC Symbol;Acc:HGNC:24975]
Coordinates
chr4:83983652-83989486:+
Coord C1 exon
chr4:83983652-83984067
Coord A exon
chr4:83984068-83987898
Coord C2 exon
chr4:83987899-83989486
Length
3831 bp
Sequences
Splice sites
5' ss Seq
TCAGTAAGT
5' ss Score
9.14
3' ss Seq
CGGCTGTCTGTTTTGCGCAGAGG
3' ss Score
7.49
Exon sequences
Seq C1 exon
GTGACAGCCCCCGCAGCCGCGGCGGGCATCGGCCTGGAGATCCTGCGGCGTGCGCGGGGAAGGCATGGACAGCCATGGGGAGCAGCGGCTGTCGGCCGGCGGAGAGCTGCCGCTCTACTCCTGCCCTGGGAATAGGGACAGACAAGGGGACAGCCAGAGCAACACTCCCGGACAAGAGGGGGCAGTGGCCGCGCTGCCCATAGTGCACAGAACCACCTCCTTCTCCGTGCTCGACATACTGGACCCTAACAAATTCAACAGCAAAAGGAGGCAATGCGCGGTCTTGTACAAATCGGTGGCGACCGAGTTCACGCTGGGGGCGGAGGATAAGCCCGAGGACTCAGGGACGGAGCTGGCCGAGCCAAAAGCTCTCGCCGAAGATTTCGACACGTGCAAGAAGTCCGCAGAGCTGATCA
Seq A exon
GTAAGTAGGTGTGGGGGCTCCCCGGGACGGGGGCTGCGCCCGGACGCCCGGGAAAGGGACTCCTCGCATGCTTTTACGGATCGCCCTCGGGAAGCGGCGAGCCGGGGGCACTCGGCTCCCGAGGCTGTGCGAACGCTGCCTGCCGCGCTGCAGGGAGGTGCAACTGCGTTTTAGGCCGGGGGACGGCGAGGCGGGGGCCGGGCGCAGCGCTCCGCTACGGGCAGAGCTTCCCGTGCGCGGCCCCGCTGCCTGCGTTCCCCATCGCTGAGCTCGTCGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCGAAGCATTTCTGACTTTTATGTACGTTCTCCCCAGGCTCGGAACCCGCTCTTCCCTTCCCCCCCTCGCGTTGCTCTGGGCGACAGATTCAATTTTCTCTCTCCCCTTGGCTTTTTTTAGGACAAATCAGACTAATTGTGACAAAATGCTGGTTATCTCTGGAAAAACAATTAAATTCCTTCGATTACATTTAAGGTAAAATGTGCTTAGCAGCGTAAAGAGGCTGGATAATGGGGGAAATCGCCCCAGAGTGGCATGTAGGACTGCCTGGATCGATATCCTATTATCGAATTGTGCATATCTCTTTCAAGCACCTTGCAAACTCTTTCCTAACATCTAAATTATAGGGTCAAAATTCGGATAATTACTCGATTAAAACCTATTACACTTATTAGGGCTCGCTATTGATCGGGAATTGCATTCGACCCAAGCTCGAGATTGCTTTTTTTTTCTTTCTTTCTTTCTGGGTCCAAATATCCCGAGTTTGTCACCTCTAAACCCCGCGGCTCCGGGCACAGCGGAGCGCTCCGGGCAGAGGCAGCTCCGGGAGCGGTGCGGGGAGCGATTCGCGTCCCGAGCGCGGAGCGGTGCCGGGGAGAAACTTCTCGGGAAGGGGGAAAATGATTTCCGTGTCTGGGCCGGGAGAGGGGACTCCGAGCTCTCCCATCCCGCCACGATGCGGCTCTTTCCGTTCAATTAGGCAGAGAAAGCGCTCCGGAATCTCTTCCAGCTCCGGTCTTTCAGAGCGGGAGTGTTTCTAAACCCTAAAGCAAAAGCGGGAGCGGAGCGTTGATGGAATTCCAAAGAGATTTTTCTGTACCCGAGGTAATTCTTCGTCTAAGCTCGTCCGACTTTTGTCATAGCAAATAGATCCGCGCGACCCGAAAGACGGACGAGGTGAGCCTATCGCTAATCTCGCACTTTTATCTCCAGACAAGGAGAGAAACGCAACGCCATCACTTCTCTAACAGCAAACGCATCGGGGGCGGCACGGAGCGGAGATCCGCGGCCGCTGCGCGCGTTCGGCCCTCACGCGTTAACGTTGTCGCAACCGGAGCCGGGGACCGCTTCAAATCGCCCAACTTAATTCCCCTCTTCCCCCCCACCCGCCTCCCCCCGCCGTAATTAACGGCGGTGCTTGGATTTAGGAGAGGTGTTCCGAAAAGCAGCCGTAGCGCCGACAGCGGAGGGCTGCTGGCAGAAGGAGGGCGGCCGTCACGGGGCGCTCGGAGAACTGCGCGGTCCGGGGGAAAAGTCCGCGTTCGATTCACACTCGGCATCTTCCGAGCACAAAATCACGGCCGCGGCGTCCATCTCCGCCACGAAAAGCACCCGTTCTACATTTTGTTCCGCTTAAAGGAAATTGTAGTAGCTTAAATAGAGCCGCGGAAGGGATTTCTTAGTTTACCGGAAAAAAATAAACTCCCAACCGGGACCGGCAGTTCAATGGGTGTGGAAGCGCTCGGTCCGGACCCCGCCACGCACACAGATACACGCACTGCTTGTATATATTGTGTATCTATCTGGCTGCGGCCAGAACGGCACAAGACGACGCGTAATAAGTTCTACAGGTGGTGGGACAGCCGTCCTCACCACGGGGTCGGATGGGGGAAAGCGATCCCAGCCGCACGTCTGTGCGGCGGCGGTCGGGAGGGTTCGCTCTTCACTCTTTGGTTTGCTGGGGAAGCTGGAAAGGATTCGGAACAAACCCGCGTTATTAAGGGATGTTTTCCGGGTAAAGAGGATCACACAAACTTCTCTGCCCCTTTTTCTCCCCGAGGCAGCCACAGCGACGTCAGCCAAAATGAGCTCCTTCGACAGACATCCTTTTAAAACACCCTTAACGTTGCCTAATGGTGAGGGTCCGGCGTTAGCGTACGGACAGAGCGGGGCATGCACTAACGGGTTCGGTTCGGGGGGCATTAAAACCGACTAAAACACGCACGGGGTGAGGGTGACAGATGAGCGATCCATTTTCTCTTGCACACCTCGGTTAACCGAATACAACGAGCCTTCGCTTCGGGATCTCCCGGAGCTGCGGCCGCGTTGTAGGGCCGAGAGAGGGAAGCGGAGGGGTGCCTGAAACCCGCAGATAAAGGGCCGCGGCTGTGGCTCTGAGCCCCCGGTGCCTCCGACAGCGCCGTGGCCCCGCGGCACACCGCGGGCAGCGCTCTCCTGCCGGCAGCCGGAGCAGCCCGACGGGCGGAGGAGGCGGCTCTCCCGAAAGCGCTCTTTCCTTCCAGGCTTCGCAATGACAGAACCATCGGCAGAAAGTCCGATAGCCTTAAATATCGGATAATTGCCCCGTTCTCCAATGAAGACCGTTAATTGGAGCGTCCTATAAACCCAAATAAATGAAATGACCGTTAACTAGTTTGTACATTACACAAAATGAGTTTAATTAAGTTTGTATCTGCTCCGCTAATCAATACAAGTATTTACTCCACTTTAATACCTCCATCTCACGAACTGACAAGAGGTCAAACTAGGCGGAGAAAGGGTTAAAAATGCTGGAGCAAAAGCCGGCAGCTTCGGTGCCGACACTTCCCTAACTAAAACTGCTAAAAGCGCTGACAGCCTCTCTGCCCTCCTCCCCAGGGCTGCTCGCTCGGCCCAGGCCGTCAGCCCACCCCACAGCCCTCTCCCTGCCCGAGCGGGGAACGGGGATCCGGCCCGGCGGCTCCAGCTCAACGCCGTTGCCTCCCCGAAGGGGCCTTTCCGGCCATGTTTTGAGGATGAGGTTGGAAAAGCGGCCGCCGCTCGGTGCCAGAGCCTGCCCTGCCAAAAGCGTTCCCGGGCTGCACGGGCACCGTGCCGGCCCCAGAGCGCAGCCCCCGGCGCTGCCCATCAGTGGCAGCTCCGAGACCCATCCCCGCCGCTTCCGAGCCTCGCACCCTATGAGCACGGCAGCCGGCCGGCAGGGCCGCGGATATACGCATCCCCACCTCGGGCCACGGGCTTCCCCCGTTCCCTTAACAGCAGCAGCAGCGGGGAGGCCGAAGGGCGTCGGGGCCGCGCGCGGTCGGGGCTGGGGCTGGCGGAGCTCTAACGGCGGCTGTCTGTTTTGCGCAG
Seq C2 exon
AGGACGGCGAGCTCTACAAGGCCGAGGAGTGCGACCTGGACTACAGCAGCCGGCCGAGCCGCAGCCCCGACAGCGAGCTGCAGGACGACGAGGAGCTGTGCAGCGAGGAGAGCAGCAGCAGCGGCAGCACCGGCAGCGGCTCGGCGGCTCCCGGCGAGGCCGAGGCGGGCCCGCAGCACTCCGAGGCTCCCGAGGCGGCCGTCGGCCCTCCGCCGCCCCCGCCGCCGCCGCCCCAGCAGCCGCCGCCGCCCCAGCAGCCCGGCGGAGGGCAGCAGCAGGCCAAGCCCAAGAGGAAGCGCACGGGCTCGGACTCCAAGTCGGGCAAACCCCGGCGGGCGCGGACAGCTTTCACCTACGAGCAGCTGGTGGCGCTGGAGAACAAGTTCAAGTCCACGCGGTACCTGTCGGTGTGCGAGCGCCTCAACCTGGCGCTCTCGCTCAGCCTCACCGAGACGCAGGTGAAGATCTGGTTCCAGAACCGCCGCACCAAGTGGAAGAAGCAGAACCCGGGCGCCGACACCAGCGCGCCCACCGGCGGCGGCGGGGCGGGCGGCGGGGCGGGCGGGGCGCTGGGCGGAGGGGCGCTGCCGGGCGGCCTCAGCCCGCTCAGCCACTCGCCGCCCATGGGCAACCCGCTGTCCATGCACGGGCCCGGCAGCTACGCGGGTCACCCGGCCGGGGGGTTGGTGTGCGCCGCCCAGCTGCCCTTCCTGCCCAGCCCAGCCGTCCTCTCGCCCTTCGTGCTGGGCTCGCAGACTTACGGCGCTCCGGCTTTCTACACCCCTCACCTATAAGCGCGCGCCTCCTCTTTCCCTCAGCCCTCAGCCCGCGCTGCCCTCGGCGCTGAGGGGCCGCCACGGCCCGAGGGACCCTCAGCGGAGGGGCGCGGTGGCGGGCTGGGCTCTTACCTCAGCGCACGGAGCATTGCGGACCGGACCGGACCGGACCGGACCGGCGCAGCGCCGCGCGGGACGGCCGAAGCCCCCTCGCCTGCAGGGCTTTGGGTTTCTTTCGTTTTTACGTTCTGCGTTTCTGTATATTTCTGGTCGTTACGGGAAAAAAAGAAAGAAAAAAAAAAAAGAGAGAAAAAAAGAAAAAAAAAGTTTTAACTTTATAATTAATGTATAAGGGATGGGAATGACGGCGGGAAGATGATACAGAGAGCACTTTGTTTGCCGAACGCTTTAACTCAATCAATAAACGTGAAGGAACCCGTGGTGCCGGCTGCTGCTTCCGGGCGGGGCTGCAGGAAAACGCCCACAAAAGGCAAAGGGAGACGATGCGGGGCTTTGGTTTCTCGTTGCGTTTGCGTTGGGAACAGCGCCGCGTGTTCCCCATCCCCAAAGTTCGTTTGTCCTCTTAAGGCAGCCGGCGGTGCCCTCCCGTGTTCCCGTGGCCGTCTTTCGCCGCCGACCTCCGTCCTACAACGTTAGGGCCGCCCTCCCCCCCCCCTCCCCACTCTTTTTTTATGTTATCCCCTCTGTCCCCAGACGGAGAGTCCGATATTTTGGCTTCATGTAAATGGAACACATCGGTTCTTTCGCTCATATCCCGCCCCTTTAACAAATAAAGCAAGCTTCCCATCGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000025723:ENSGALT00000044880:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.669 A=NA C2=0.686
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF136221=4HBT_3=WD(100=63.4),PF0004624=Homeobox=WD(100=21.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
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]