RnoINT0071672 @ rn6
Intron Retention
Gene
ENSRNOG00000001577 | Hoxd3
Description
homeo box D3 [Source:RGD Symbol;Acc:1588601]
Coordinates
chr3:61658245-61666909:+
Coord C1 exon
chr3:61658245-61658542
Coord A exon
chr3:61658543-61666285
Coord C2 exon
chr3:61666286-61666909
Length
7743 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
TTCACTTTTCTTCTTGGCAGGTT
3' ss Score
10.49
Exon sequences
Seq C1 exon
GCCGCTTTGGGCCTGGGAGCCGACCGGCGGGCGGGTGGACCGACCAGCGAGCAGCGCAGGCGAAGCCAGCTTGGGGACTACAAACTCGTTCCTCCAGCGTTTATTGGTAGTTGAACCTCAGCCTGGTTCCGTTCTACCGGGAATTCCGTGTACTCTGGTATATGGCCGAGTCTGCAAGCGCGCAAGACCAGGGTTGGGACACTGTTGTCTGCAGACAAAGGGGGAAGGCTAGCTCTGCCCCCCACTGGCGCCCACTCTGAGACCGAGGACACCAGGTTTATGATAAATTGGGATCCAG
Seq A exon
GTAAGCAATTGCATGACAAAATGGAAATCTTTGGGCACAGGGCTGCTTGCTGCCCTGAGCGGGATACTAAATATGATTTATTTTGTGTAATCTGTGATCTTGATTATTGCCAATTGGTGAGGCAGCCCGCAGACCTATATACACTTCTACATATACATCGAGGACGGTGATTAATCGTAACGAGGTGCGCTTTTATGGGGACATTCCCCGCCTACAAAAGGTTAAGAGGACACTACCTTACCATGCTTAGAGGGTGGCCGGCAGCATTGGGGAGGGGGTGTAGCAGTTTGAGGAATGGGTTTGTTAAGCGGACTAGGGGCTGGAGTTAGTATTTTGAGGGTAAATGTGTAGTTATGAGAATGGACTGAAAATGGAATGAATAAAAGAGACCTTTTTTTTTTTTACACTGTCACTGCCAAAGTAATATGGAACATCATATTAATTCTGTGTCTTGGGCTGCTGGGCTGGGTGCAGGAGGGTTGATTTATCCATATTTAAAATAAACTGTGTGGCCAGCCAGCTCCCTGCATTGTTCTGTGGGCCACCTCCACACGCTCAGCCTTTCCCTCTTGCTGTTGGCTTCCTCTGTTCCCCCATAGGAATTAAAACGTCTCTGAAATTAAGGACCCCCCCCCAAAAAAAAACTACCCTGAGGAGTTTGAGAGGGTTCTCCAGTGTCTCAGCATAGGCTCTGGCTGTTACAATGATGAACAGGTTTAGTGTTTCTGGGTCCTTCTGTCCAAATAACCCTACACGGTGAAAGCTAAATCAAATTGGTTCCTGCATCCCTCATATCTTTTGTTGACTTGTTCCTCGTGGCTTCAGGCTAGAAATGTAGAAAACAAATATCACAGGTCTTTTCCCTCAAACAAGGCAAGAGTGAATGACCCTGTGAGCAGAAGTGGCCAAATCATACTGGACTACCCCAGGGATGGAACCCCAAAGCAGAAGCACTGTCTAAATTTAAGTTGGGACAGTCTCTGGTGGGAGGAGGACTGAGTTCCAAGGTCCTGGCCATCAAAGGGAGCAGGAAAAGTTGTTTTGTCACTTAGCTGCACTGGGCTCCATCAGAATTTGAAGTCGGTGGACATTTTTCTTTGCTCATTGCCTCTGAGCTGCAAGCCTGCCAGCTTAGTCAGCTGAATCCAATTACAGCAAGCAGCATTTCATTTGGCCCCACGGAGCACTCACTTATAACTTCCCCGAAATTTTCAATAATCCCCACCAAGTCTCTTCTCCAGGCCCTCTCCTGAAGAGGTTTCCCTGGATAATGCTGGTGGGTGGGGTATGGGGGTTATGTCTGAAGTTAGATTCCCCGGACAGCTAGACAGCTTAGCCGTCAAGATTCCCTTCTGCTTCTGAAGTTTCTGGCTGGGAAAAGTGTGTTGGAACTCAGGCAGGACGAAGCCAGCCTGGTTCAGGCCACGATTGGGGGCACCTACAAGCCAAAACTAGGCCAGTACTTGGAGCAGGGCAGGGAAGGAAACGTAGGAGAGAGCTTTGAGAAAAAGGGTGCTTTGCTTATGACCCAACTAACTTGGGGTCCTTTCTGCTTTCCACTTCCCAAAACCCCTGAACCCAGAGCTCAGAGAGCACCCCTCACCCAGGTACGAACTTACCGGGTTCCTCCACGCCTGGAAAACAAAATTTAGCTAGATGCGTTGGGACTGCGAGGATCTTCTTCTCAGGGAGTGATCCTACTTCTAAAGAAGCCCTTCTAAAAAAATAAGTAAAAATGATCAATCTGAGCAGGTTGATGTCTGCCCATGAGATTGTATTATATAAAACGGTCTGGGGACTGCGGGCCACCGGTTTGAGCATCCTGATAACTCCTGCACCTACACTATGTCACCCTCGGGGCCCAGTCAAGAGGATTGGGGTGTAGAAAGCAGACAAATGAGGATCCTTCCCCAACTCAAGTCGTCTGGGAAGCTGAAGTCCGGGCGAGAAGTTAGAAGTCCTACCGGGCTGGGATCTCTCTGAGGCGCTTCCGCTGGGTGTTCATTAAGGGGTGAGTTATTGCAACAAGAGCCAAAGGTCACTTCAAAGGCTTATGGCTATGCTCTCTAGTCTTTAGAAGCGCCCTGAACGCTTTGTGTGGGGTTTTCCCGGGCGCAGTTTAGTGTTTGCAAACTACTGAGTCGACAAATTGCACAGGGCAGATGCAAGAGAGAGACTGCGTCTCCCTCCTTTCACCTGACCGGAGGCCAGCGCTTGCTGAGCAGCCGCAGTGGTGAGCGGTTTGGCTTGGTCATAGTTTGGGGTTGGAGATAGGGAAGGTTGTTGGTTTCTTAGGCGGTTTATAGCCTAGTCCCGATTCAGAACTGAGCAGCCCAGAATGCTGTGTATTCGCTAACACATCCAGGAAAGCGAGCTGAGCCAGAGATATAATGTGCAAATCAGGATATAGCAAGCGCCTCACTCCCGGTTTACTAGGGCCCTGAGGGCGCAGCTTCAGTTAACATCCTCCCAGGTGCGCCTACGTATCTACCCTCCTTTCCGGTTCCTCTAACCTGTAAGCTTCTTTCCACCTCCCAGGGCTTCTCTGAGCGGGCTGACCCACTTGGCTCACCCTCTGGTCCTTTCCTCGTGCGTTCAGGTCCTCCCCACCCCCTATCCAGCCAAAGATTTTTGCCCTTAAGCTCCCCTGGATCCAACTGTGTCTTCATTCTGCTGGGGCCAAGCGTCTGGAATAGCTGCAGGCATCACATACAATAGTCACATTGATTGTGACACCCTTAAAGGGGGTAAAGGCTCTCCTGGTATGTTTGTAAGTCAGAACCGGCTGTTACTGAGCTTTCCATTTTGTTCCAGATCTGCTTCCACAGAATACCTAAGAAACCCGAAGAGCCTACAAAAAGAGTTAGAGATAAAATTCAAGGAAATACACATGCAAAATTGTGGTGAGTGGGGGTGATTTAAATAAACAAAAAAAAAAAACAATTTGCGCTACATTTCCATTCCACCCCCCTCCTTCAACTCAGGGTAGCCATCCCAGGATTCATACATCAAGACATAAAACAAAGGGTGGCTTTGAAGTGGATCACCTCAGTGTGAAATGCCGCCTGTTACATGAGAACCGATCATCAGCCTTCAAATTTATGGTGCTTTAATAGAGTGCGTCCGCTGTCTTAAATGCAGGGTATGTTACAGTACTGAGTTATCCGGGCTAAACAGGAGTGATTTAGAATGGGCGTCCTGGGCTTCCCAAAGGGCAGAAGAGGCTCAGGCTGAGGGGTCGGGAGAAAGTGGGCAGTCAATTCTCTTCTCAGCAAACCCGCTGAAGACTTGTTTTCCCAGAAGTAGCAGCCACCAGGGCAAGGAGTGTGATCGCTCCGTTCCACTGAATTAACGAGAATGCCCAGTAAAACTCGGGGCCTCCAGGAAGAGATCCGTGGGTTATTGGAAGACCCGGGTTAGGCAAAATAGGGAGTGGAGGTTAGAACAACTTAAACCTCCAAGAATTTGAAGAGAAACTGACACAAGAAGTGTCCATCATCTCCCACTTCTGGCACCCAAGACTGGCACCGACTGACGGTGGCGGTCCGCTATTCACTACCTCAGCAACGCTAGACACAGCCAGAGGCTGTGGCCTCCCTCCTAGCCCAAGCCTCCCTCTTCAGCGGCCTTCCCGTGGCCGCCGCGGGCGGGCGAGCGAACGCCTGGCATCCATCGAGCCTCCTAGAGTCCGAGACCAGGCGAGCAGCAGGTCTGTGTTCCTCGGCCGGCCGGGCTTGCGATCCTCTCTTTCCAACTCGGGCTGCGGAACACAGCTGCTACTAGGCCAGGCTGGCGCCAGCCACTTTATATAATCCCGCAGCTCGCACGCAGGGTGTGTAAACGGGAAAAGTGCGGAGTAGGGGGATTCTTTTGCTGTGCTGCCTCCTACGCGGAGCCTGCTTTCCATTTCTGAAAAGTGCCGGGCCTTGGGAAGTGTTTTTCTTTTCATTCCTTACTGAAGCGTTTACTGCTGCCGTGGTCACAGTCATAAATTTTGTTACAAACCACAATGACAGGTGCATTGATATGCACCGTGAGAGCTCCAGCTGCTTAATAACCCTGTCCCCTGGCCGCTGTGAGCGCCTTTTATTTATTCGGTATCATATTAGGTATTGATCTGGGCAGAATTAAGTGCAGTGAGCAAGTATCAGGACTCCGGTGCTTCTGAGGCTAGGCCAGCTGAGTGGGCCAGCATGGCTGGAGAGCGAATAGTGCGAGCTCTGAGAGGGTGCCTGGCCTTCCTTCCTTCCTTCCGGTTGGAAACCAGTCGGCCCTGTCTTCTGGGCCTGCCTTTAAGATGGGACATGAGGAGGAAGAGGAGGAGGGAGAAGAGGAGAAGGAGAAGAGGAGAAGGAGGAATTAAGAGGAGGCTGAGAGGAAAACAGAGGACTACTCCAAAATAAGAAGTCCCTGCTCAACTTCCCCTCCCAACCCCGCCTCCGCCCCACATTTATGGTCTTTGGTGCTCTAAATGAGGGGAAGGTACCAGAAGGGGTTGAGAAAGAAAGCCTTGAAAGGCGGGCGTGATCGAAAAGGGGGGGTGATGCGAAAAGATGATATTTCCACGTGGAACAGGTTCAGACCTGTGAGCTCCAAAATGATGTATGGTGACCTTCACTATTTTGTGACTGCTATGTTTGGTCACAGCGAGGTTCAGCAAGGAAGTAGGGATTTCTGTTGTCAGAGTATAATACTGATTTTATTCCCGGAGTCTTTGCTAACAATGGTATGTCTCTAGGCTTCCTCTGAGCGTGTCCCGTTTGCGAAAGTTGGTTTCTTGTTGTAGTGTACTCTGTGTGGTTGGTTGAGTGCAACAAGATGCCAGCAAAGAGGTTCTTATTTCCTATCGCCGCCTCTAAGACGTAACTAAAATCATTCGCAATATCGTTACCTTGGGGCTGTAAGCGAGAATCCTCGGGACATGCTAGTCCATCGAAGTAGATCTAGGAATTCCCTTCAGGACAATGTAACAGGGCTGTGTAGGTGACCTGACTGTAGTGTTGTCGCGCTCGAGGTTGCTGCGTGCTGCGCGTTTTACGCTTGAGACGTACTGTTCTGTATAGAGTGACGATTTCTATTCGGACATGCCATCAGAAGACCCACGCTGACTTTGTTATATGCAACTTAAAGGGGGGGTGATCGAAAAGGGGGGGGTGATCGAAAAGATGAGCCACTGAACAGTTGACCATTGTCCAAATGATTTATGACCCAGTGCTGCTTTTTAGGTTCAAGCAGAGTTCACAAGGAGTAGGGATTTCTGGAAAGAAATAAACTGATTTTTTCCCCCAGTTTTGTAACAATATTCTCAGGTCACCATGCTTTGGAAGAGGGGTTTCTTTAGGGCTCTGTCTGGTGGGTGCTGCAAAGGCTGTTTTTCCTTCCCCCAAGAGAACAAAACAATTGCTACCTTGGCTTGTAGAGAAACTGACGGACATTAGGCCATGAAGTAGATCTGGAATTCCTTCAGACAATGTAAACAGGCAGGAGATGACTGTGGTTGCGGTGCTGTCGTGCTGTCGCTGTACCTCTGAGACTTTTTATAGAGAGAGATTTCTAGGGACATGCCACAGAGCACAAATACTATGCAAAGTCATCCATCCCATAGGCTTGCTTAGTTCCTCAAGAAGCTATTTTAATGTGGCTGGTCCACCATCCAACACAAACTTGGTCAACAAGGAGGCAGGAGGGGGATGTTTTGCTTCCACAGTTGTCAAGGAATAACAAAGCAGCAGCAAATTCTGGTGGTCTCAGAAGCCTGATGTGACCATTTAGACATCTAGAAGCACGAACCCTGAAAAACCCTAGAATTTTGCAAGCCGGCATGCCAGGTCCTTTGGCCTGGGGCAAACATGTAAATATTAGTCACAGAATGAGCATTTAACTGTCCATTTGCTATTTGATAACTCTAGCAGTCAGAGATTGGTATTGAAAACTAATCAAACAAATTAGTCTAGCTTTGTTAAGTAGATATCTTAAGTGCACACATTTGTATATTCCTGCAACCCACTGAGAAAGGCCCTGTCTCTCACCTAGATAAATGACATATTTTCTTATATTCTAAGAAAATGGGGAATGATACTACCAAAGGAAGGCTAATTTGGAGAGGTTTTTTTTTTTCAGTTGGGTGGGCTTTCTGGTGAAAATACAGGGGGAATTTAATGCAAAAGTATTTTGGTTCCTGGGTTTAAATCCGATTGGCCAGAAGTTGCATGATGGGTTCTCTCATGATGATGGAAGCCAGGGAGAGGTTTGGGAAAGAAACTTTGCCTGAAAGATGAAGCCAGAGAGCTGAGCTGTGAGTTTTCTTTATCAAACAGACAAAAGTGATTGAATGATATTAGTTATACATTAACTCCTCAGGAATCTTTCAGAAGGGGCAGGAAAAGCATCTCCCATGAAGAGTCGAAGCATACAAAAGAGGAAGAATTTTTCTTACCCCCTCCCTTCTTATTCTGGGTCCATTCATCATGTCACAAGAACTTCTCTCATTGGTTATAAGTTGGGTGAGAGGTGGGGCAGAATGGAAGGTCCAGAGAAGAGGTCAATAATAGTATCTGTTTATGTAAAGATCTAAAAATGATAGAGTTATGACAGCATTCACTATTCAGCCACAGTGCAAACATTTCAAAATCTAAATCACCCATTTTCAGGGACACCCTTTTAAAAGGGGGAGGAGGACAATGTAAGGGGTGTGGAAAAGTATAGGTGAAAAAAGCATTCCTTTTAAGCTTCAAAGTAAGTCTGAGAGCCTTTAAGTCTTTGTTTTTTACTACCCAGTTCTCTACCTAGTTCTCTAGTTTACTATCTTGGTTTCATAGTGCTGACCCACAAAACTAGCTGTGTGGATTCCCACCCTGCCATCCAAGAGGACTGTCTTGGTCTTCAAAAAAGTTGGTGTGGTTTTGACACCACATGGAAAAGATACTTTGGAAGGAAGCTCTGGAAACTCTGGGAGTGCAATAAGGCTTTTTCTTTCATCTATCAAAACACCGAGACTAGGGTTTTGGGGGTAGGGGACCCCACAGAGCACACACAAAGCCCTGGGGTTGATCTCTCTCTCTGTCTCTGCTTCAGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTTTTCTCCAGAGCTGAGAACCGAACCCAGGGCCTTGCGCTTGCTAGGCAAGCGCTCTACCACTGAGCTAAATCCCCAACCCCCTGGGGTTGATTTCTAACACCATGCAAAAACCAAACCCCAGGATTATCCAAAGACTGACTAACCCATTCATCTAGCTATTCCATAACAATTTATTGCACTTATTACACGCAGGGCACTGTGCTTAGTATTAGTAATATGTAGATAAATAAAGTATAGTCCTCTCTTTTAGGAGTTTATAGTTTAGGGGAAGAATCAGCCAGTCCTAAATGGTTTCTGGAGCAGCCTCAAAAGCTATGTTAACAATCTTGGAGAAAGACAATTCTCCAAGAGAATCTTGGGTTGGAAAGAGATGCTTCCCTAGACTAAAGTTGAGCTCAGGAGAAGGAAAGGTTTTTTTTCCCCTTACATTTAGGAGAAATGTTCCAACTTTTTCAAGAGTTTATATAAACTGAGCTCCATAAAACCCCCAGTCCAGAACCTTGCCCATCTTCCCGCTTCAAGGTGAGTGGGAAGCGAGGAGGAGCATACTCTAGGCCTTCTATACTGATTGGTCTTGGCAATGACAGTCCCTCTAGGATCTTTCACTTTTCTTCTTGGCAG
Seq C2 exon
GTTACCTGGAGCTTGGAAACTGGCCCAGCTCTCTCAAGATTAGCAGACACTGGCCTTGGTGGAGAAGGAGACAGTGGTAGTCAATGTTATTTGAGCAGGGTCAGCAGGCCCTGGAGCTTCCTGAGTGCACCATGCAGAAGGCTGCATACTATGAGAACCCAGGACTCTTTGGAGGCTATGGATACAGCAAAGCCACTGATGCATATGGCTATAGCACTCCTCATCAACCCTACCCACCCCCTGCTGCTGCCAACTCCCTGGACAGTGATTACCCAAGTTCTGCCTGCTCCATCCAGAGTTCTGCACCTCTTCGAGCCCCAGCCCACAAAGGAGCGGAACTCAACGGTAGCTGCATGCGGCCTGGCACTGGGAACAGCCAGGGTGGGGGTGGAGGCAACCAACCTCCTGGCCTGAACTCAGAGCAGCAGCCACCGCAACCTCCCCCTCCACCACCCACCCTGCCCCCATCCTCACCCACCAATCCCGGAAGCGGAGTGCCTGCCAAGAAGACCAAGGGTGGGCCCAATGCTTCTAGCTCTTCCTCTACCATCAGCAAGCAGATCTTCCCCTGGATGAAGGAATCCCGACAGAACTCAAAGCAGAAGAACAGCTGTGCCACTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000001577:ENSRNOT00000033511:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.829
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
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]