GgaINT0029756 @ galGal3
Intron Retention
Gene
ENSGALG00000003005 | F1NWX4_CHICK
Description
NA
Coordinates
chr10:4554464-4557757:+
Coord C1 exon
chr10:4554464-4555436
Coord A exon
chr10:4555437-4557375
Coord C2 exon
chr10:4557376-4557757
Length
1939 bp
Sequences
Splice sites
5' ss Seq
AGTGTAAGT
5' ss Score
8.46
3' ss Seq
AATTGGCTTTTTTTTTCCAGGTC
3' ss Score
10.02
Exon sequences
Seq C1 exon
TGCGGATGGTACGTATGAAGTTTCGCTATACACAAACGCAATTGTACAGAACAATGGAAGCATTCGCTGGCTGCCTCCAGCAATTTACAAGAGTGCCTGCAAGATTGAGGTTAAGCATTTCCCATTTGATCAACAAAACTGCACCTTAAAGTTCCGGTCCTGGACATATGATCATACAGAAATTGATATGGTACTTAAAACTTCCATGGCAAGCATGGATGACTTCACGCCAAGTGGAGAATGGGACATTGTAGCACTCCCAGGAAGAAGAACTGTAAATCCTTTGGATCCCAATTACGTTGATGTGACATATGACTTCATTATTAAAAGGAAACCTCTTTTTTATACCATCAATCTTATAATTCCTTGTGTGCTAATTACATCCTTAGCCATCCTGGTGTTCTACTTGCCTTCAGACTGCGGTGAAAAAATGACCTTATGCATATCTGTGCTGCTTGCTTTGACCGTGTTCTTACTGCTGATCTCCAAAATTGTTCCTCCAACATCTCTAGATGTCCCACTGATTGGGAAGTATCTCATGTTTACAATGGTACTGGTGACCTTCTCGATAGTTACTAGTGTCTGCGTACTCAATGTCCACCATAGATCTCCAAGTACTCACACTATGCCTCCATGGGTAAAGCTGGTTTTCCTTGAAAGACTCCCAGCCTACCTGTTCATGAAGCGTCCAGAAAATAATTCTCCACGGCAAAAGCCGTGCAACTGCAAAAAGACAAGAGCAGAGAATCTCTGCATGGACCCAGCAGACTTCTACAAGAACTCTACTTACTTTGTGAACACAGCCTCTGCCAAAAAATACGACATGAAGATCACTGACACTCTTGACAATGTCAGCAGCCATCAAGATTTTAGGTTAAGAACAGGCACAAAATTTTCTCCTGAAGTCCAAGAAGCGATTGATGGAGTCAGTTTTATAGCAGAGCACATGAAAAGTGATGACAACGACCAGAGT
Seq A exon
GTAAGTAAATCTCCAAACTTCTTCCCTTGTCCCCCTCTGTAGCGTGTGTTCCTTCAGGAAGGAGATTTGTACTCTCTAGTTACCTTGAAGCTTTTAGAGATATTCTAGGTAAAGGTTAAAAACACTTAATGAATAGTAATTTGGTAAAGCCATCACCACACAAAAAGAGAATGCTGACCAGTAAGTCAGGAAACACCCTTGAAAAAGCTGTTGTCACCTTCAAGTAGTGTTTAGCAGGGAAAACAGTAATGCTGACTGCCAGGTCAGAGAGAACTCTATTTGAAAATATTTTTCCCCATCATATTCAGACAGACCGTAACACATCAGCTCATGTTAACCAGTGTACCTGCAGCTCAACCTCTGTGAACACCCTAAGACCTCTATACCTAGTTGAGCAAGATGAGCTGCTGTTTAAGTTGCTCTGTTACAGCAAACACAATGGGTAGAATTGAAATCCTAATGCCAGCAGAACTGATACTTCTTCCATTTGAGTTAAGTCACACTTGTTATTGGCTATGAGAAGTAGAGGGTTCAGGGCACACGTAAGCAGTGCTGCTGCTGTCCTGTTCACATGCCCTACCCGAGCTACTGGCCAGCACACTGCAGCTGGTACAAACACACCACAGATAATGCTCAGAAATACTCAGATGGTTCAGAGTTTTGTTTAGACCACAGTTAAGGAAAACTGCCAAGCATCCCTCTGTCATCCTGCTCAGTCCCAGATCCCAGTAGGACTATAGGTTCTTTATTCCTGCCCCCTCCTTCAGCCAAGCAGACTAAATGAAGCCTGGCTTCTGATACTGCAGAAGTCCCTTGAGGAGCATGCTGCTGAGTAGTTCATGTTTTCTATTAACTGAAATTACTGTCAATATAAATAAAGATCAGATGCTAACATTCAACATGACCCTACACGCACTGAAACTGACTGAACAGAAGCACACTTCACAGAGCAGGCAAAAAGTTTTCTAATAGCTCAGAAATCCTTGCAAGAATATGCTGCATTTTAAAAGATCCAACTTGAGACTAAGAGCAACTTTCAAGGGTATTTCATACATTAAAAATGAATAGAATGCTTTTCACACAGGGTCCTCTGATACTGCATATTACTGTTTTATGGACTCATAACCTTAATTCCTGCTATCTTCCTTCATCTGATAGCAACTGTTCGTGTGCATTTACTACAGCCTCATTTCAGAAGTGCAAAATTTCCATTAGCAGCAGTGGGAATTAGAAGTGTGTGCTGAAGGAAAAATATGTAATGTTCTAATCTAAGACAAGAGATAAATGACAAGCATGGTGAAGTCACTGAGGTGACAATGTCCCGCGTATAATGAGAATCAATGACAGAGGAAAAACAATCATTCTTGAGATGCAAATGAAGATTGATATATTCATCCTTTACAATGAAAGCCAGAAGGTCACTTCAGTTTGAGAAGAGAATCCAAGACTAGTCTTATGCTGTATGTTTCACACACAACACATGTAAGGCTGAGGGGATTTTAATAGAAGCAACAGTATTAATACGCATTAAACCACTTGATTAAGAAGACTGCTGATAAGAAAAGTCAGAGGCTAACCTTGTTTAACGGCAATAAATACTCTCTCTCTTTGTCCACAGAGATTAATAGCATCTGCAAATTAAAATTAAAGAAAAAAGATCCTTAATTGGATTACACCGTAGCTCCTTCCGGAACAGCACCAGGCAGCCATGCCCTGTACCTCACACATCAAAGACAGCTAAGAAATATTTACAGTATTTTTCTCCACTGCTCGGAATGGTTGCAGGAGAAAAATTCCTTCCTAAGTCTAAAGTCAATTTGTTCCCTGGACCTGGAGGTTTATTTCCTTTTATTTTCATAAACAAAGACTGCATCAGCAAGAGGAAGAGCAAAGTAACATGACAAATTGCTAATATCTTTAATTGGCTTTTTTTTTCCAG
Seq C2 exon
GTCATTGAAGACTGGAAGTATGTTGCCATGGTAGTGGACAGGCTGTTTCTCTGGATATTCGTCCTTGTTTGTGTTCTGGGCACTGTTGGATTATTTCTGCAGCCGCTCTTTCAGAACCACATTGCTGCCACGAACCCTTAGCTCTTATCTAAAATTGCCAATGCCTACATAGATGCTGGGTCTCATCCTGCTCTCAGTTGCCCTCTGCTAAATCCAGAGAGATGTCAAACGAGTTGCTCTCCCATCGGATTTATGGTAGGGATGTGGAAAGCAGCAACATTATTTTGATAGGAAAAAATGTTTAAAAAAGAAAAGGAATCATTTTTCCCAATGGGTTCAGTACTTCTGGTGATCTCATGGCTCTTCTTTCAACTCGTTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003005:ENSGALT00000039804:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.015 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PD(54.4=34.5),PF103294=DUF2417=WD(100=42.2),PF0293211=Neur_chan_memb=PU(86.1=63.1)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(13.0=66.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGACTCCCAGCCTACCTGTTC
R:
CCTGTCCACTACCATGGCAAC
Band lengths:
357-2296
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]