RnoINT0068486 @ rn6
Intron Retention
Gene
ENSRNOG00000054725 | Gtf3c4
Description
general transcription factor IIIC subunit 4 [Source:RGD Symbol;Acc:1592609]
Coordinates
chr3:7404841-7410034:-
Coord C1 exon
chr3:7409946-7410034
Coord A exon
chr3:7409260-7409945
Coord C2 exon
chr3:7404841-7409259
Length
686 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
CCACTGGCTTTCCCTTGCAGATC
3' ss Score
12.44
Exon sequences
Seq C1 exon
GTGCTTTCTAACCTACCAGTCCTGCCAGAGCTTGATCTACAGGCGGTGTTTGCTCCATGACAGCATCGCCAGGCACCCTGTTCCAGAAG
Seq A exon
GTGAGTGCTGGCCTAGCCTTGCGGTAGGGGTGGAGTCAGGCTTGACACCACTTAGTGTCACATCACATTGGTTCAAGCAAAATAAGTGTGCTGTCTGCAGTTACTGTGAAGCCAGAACCAGTTAATGCATGCTGCCTGTTGTGTGTGCTATGTCAGCTGACAGTGGAATGGGGGCTTCAGTCCAGTGTTAGGGCCTGGCTCAAGGGAGTGTGTAGGGCAGTATTTGGCTGGCAGCTCTGCAAGTAATGCTGTGTAGAGAAGCAGCATTGTTGCTGTACTGGTGCAGGCATGGCTCTTCTAGAAGCCGCTGAAGGCTACTTCCTGGCTGGTCTGTGTGCACGTTAGCGTATTGCTGTTTCTGAGAGCACTAGCTAGAGATAAGGTCTTAGGTGTGAGCAAGAGATCAGGCATCTATAGTCCTCAGAATGCCAGTTGTTGGTGTGAGCTTTGCTAATCGTATACTCCAACCAAACAGGCCAGTGAGGCAAGTGTGTAGAATCAAACACAGTAAACAGAAAACAAAAGTATTCTACTTAAAACTCAGTCTGTACTGATTTTTGCTAATTCTCTCAAGGCAGCATGGATTCTGTTTCTGCTTTCAGTTGACCTCAGTTCTCCGTCTGTCATCCATACCTTGTCAACCTTTTCTGAAGCTGATGCTTGGTCCCACTGGCTTTCCCTTGCAG
Seq C2 exon
ATCCTGACTGGATTAAGAGGTTGCTGCAGAGTCCTTGTCCTTTCTGTGATTCTCCTGTCTTCTGAGTTCGGTGAGGAGGATGCGGGAACATGAAGTTGGCTAAAGAGAGTGCCCTGAAGCCTGAAGAGCAGGTGCGCTGGAGAGAGCCTGGCGCTGCTCAGTGGAGAGACACTCTGCTAACTGGAAGGGGGAGGTCATCCTAGGAGCTCATTTCACCAGCACACACACCGTCTTCACGTACTGAAGGCGATCTTGTAAATGACTAGATTCAGAGAGTTGAGTCATGTAAGGGGAGCATTAGCCGTCCCCAGCTCCCCACCTGGTGAGGACCACTTGCTTCCCAAGTGTCTTGCCTAAAGCAGCTTGAGCAGAAGCCTTCTGCTTCTAGAACGCAAAGGTCTCTTCTAGAGAATCTAAGGACCTTCTCGTGAGTTAGGTTTTCGTCCTTGCTTTGTTCTGGGACTGCCTGTAGCTCCAGAGGGCTTACATTGGTTGGTACATGCATGACACTGCGTATGCCAATACACCTTCAAGTGTATGAGGCCAGCTGTTTGTGGCTGGTGTGTGCTCAGCAGACTCATTGCCCATTGACTGGTTTTCACTCATATGGAAGACATTTTCCTAAAACTATATTTTTGAAGCCAAGAATAGAATCATCTTAATGTATCAAATGATCAGGTGACTATTAGAAGTTAATAATTGTCATCTAGTTTTATCTCCTGTGTCATCAGATTTCCTGTCCCGGCTCTTTAGTGTGTAAGAGGAGATTAAGTACCCCGGCCCTCATCACAGCTCCACTTCATGCCCATGTGGTAACCTAGATATTTGTACATACGGGGGAAATGTTGTCTCCTTTTAGTATTAAATCAAAGCTTCAGTATTTCTAACACTGACGTATCCCGACATCTCACTGAGTATTGGGGGAAGGCTGGTCTAGAGACCTCTGGAGAAGGCTGGTCTAGAGAAAGATGGAGAAAGGTGGAGTGGAGGTCCTTGAGCTCTGTGCTACAAGCATGTGCAGCTCAAGTGGAAAGCCTAAGAATTTCCTCTCTTGCCAAAGGCCCTCCATCTTTGGAATACAGGTATTTTTCTGTGGGCTTAAGGAGGAGACACGCACTATCAGTTGGCTGCTAGCTCTTCGCTGAGACCTGAAGCATTCTGGAATGGTGGTCTGGGGTCATCAGAGTAAGTCTCCTAGGATTGGTGCTAATGACTTGGACTGCAGTGCACACATTCTGAAGCTGTGCGGTTGGAGAGTGAGGCGGAAACTAGAGAGCATGAAATGCTTTACTCCTTGATGATCCTTTTTTAATCATTATTATTATTATTATTTTAACATACTTTCCCACTTTGATTTTATATCCTTGGCAAAAGACATTTCGTGGTCCTCACTTCAGAAATGATGTCTTAGTACTTGGGTACCACCACGAGAGACAGACCACATGCCACCCTGCCACACTTCCTGCCCTGAAAAGTAGCTGCACACTGGGCACAGACCCTAAGACGCTTCCAGAAGCTGCTCTGAAATTTCCTATTAAGGTTCTTTCCCTGTGCCATGTGTCTAATGGATTGTTTGTTGGGGTCTTTAATGTCCTGACATAGGGTTGTTTCAAGAACAGCGTCTATCCAGACTTGAGGGGCAGCAAGGACAGAGCCCTGAGTGACCCAGTTTAGACTCTGCATGGCTGCAGCTGAGCCCGCAGCTGTCACTCCTCAGAGGAAGAAGACGGCAGGAGTGGCGATGGTATTGATGGTTGTTCCTTCTGTGTCTACCATGCATGCCAAGCTTCCTTTCTCTTACTCTTGGATCAGTCTCCCTCGGTGTCCTCAGAGACTTCGTGAGAACTTAGAACCTGCGGTTCTTTAACATTTTAACAATTAGAAATTACAAAACAATTTCCAGGGTCTGTACTTGTGTACAGGAAGAAACGTGGCAACTGGAACACAAGTGTTCAGCAAGAGGCCTGTCCCTGCAGCATTCTTAGGACTCTGAAATCTAGCCACAGCCAGTAGGAATCTCTCACACATACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACTGATGTTACTCTTCAGAGCTGGTGAACAAGAGAATTTGTGGTTGATGGTAGCCTCCTGCAAGGGTCTGTATATAGGACCATGGAGGGTTGATGGAGAAAAGTGGGAGTGATCCCAGCGTCTTGTCCCGCTTCCAGCTTGTGCTGCTTGGGGGAGGAGTTGAGGTCTCTTTCAGTTGCAGCTGTAGTAGCTGTTTCAGCAGGGAGAGGAAAAGTAGCCATCAGATTGCTGGCCTGCATTTAGAAGACTAGAGCAGAGATTCCACAGAGACCTTACTGCAGCACTGCTGGGTACCAGGCTCCGTGCCTGGGGCTGTTTGTTACTCTAGGTAGGAATAGGCAGCTTGTTGTGGTTGCCGTTCGTACTGATGTCCTGATATGTTCACCCAGACTCTCTACCTCCTACCAGATCCGCCAGAAGCTGTCATGAGTACCAGTGACGTTTATGGTCAGTCGTAACATTGTTCTGCTTGTCCCTCTGGGGTCTAGCAAGTTTTTAAGAACATGTGTGTGGAAGCATGTAGGCCGAACCTAGCAATAACCTTACCAAGTGAACTAATTAGACTGGGAAAGGTATTCTGTTTGTTCTGTCTGGTTTTTGAGACAGGGTCCCACTATGCTGTAGCTCTGGCTGCCCTGGAACTCTTGTGGACCAGGCTGCCATTGAACTCATATCTGCCTGCCTCTGCCTCCAATATGGGAAAGTTTTAGGGGTTAGTAATTATTAAGTCATTTGATTGGTTATATTGGTATCAGATAAGGTGCAGACCTGGCAGAGGCTAAATAACCTGGGGAGCTGAGCACCTACAGCTCCTGAAATAGCTCAGGTTTACCTTCCCTTCCCCAAGAGGCAGCTCCCAGCATGAGGATGCATTCAGGGCCAGGAAAATAGATAGTGATATAAATTTCTAACGGCCAGGCCATGTGGGTCTTCCTAGAAAACAGCAGTGAGCATCTCGTGGGCAGAGGGCCGCGGAACTCGGGGCTGACTGCAGCTTCATGCCACCACAGTGTCAGTTGTCTGAGCTGAGTGGAGTACAGTCAGTCAGATGCACAGAGTTCTCACACAGCACACCTTGGACTTAGCCACAGCTAGTCACTTATGGTGTGGCAGTCTGCAAAACCTCAGCAGCCTACCTCCCCCTGGAGGATTGGCTTGGAAGGACACCCGGTAGGGTGCAAGGAAACAGATAGTCTGGCTTTACTTATGGAGAAGCCCTAGTGGACGCTGAGGTACACTTTAGAGTATACCTCAGACTGGCGTGGTTAGTTCTTATCTACTCTTTGTTGAAGCTAAGAAGTTCTTGAAGGTAAATCTGCTTAGAGTCTGCTGCTCAACCTGAGTGCTTAGTAGATAAAATGTCCTTAAATGGAGCTAAGCTGCACCCAAGGTAACCTTGCTTCTAGCTGCCAACAGACATGGCAGCTCTGTCCATGGTTCAGGCAGAAGGCAGTGTTCTTGGATCATGTTCTTCAAGGTCATGTTTCTGTCTGGGGAGATGATGCAGTCTGGGATCTAGTCATAAATTTATCTGGAGCCACGTGGGTGTGGCTCACCAACAGGACCTAAGTATTCCTTCCTTGTGATGAAGGAAGCCGCACACATCTGGATTACATTGTAGGCTCACGAACAAAAAACTGGTCCTGGGTTGAGCAGGTCACCTCAGAGTTCTAAATCTCCACTGTATTTTTAAGACTGAAGTTCTTTATCTCAGAGGGGGGAAGAGCGCTTGCTTAGCATTCCTGAGGCCTCAAGTCCATCCTCTGCCTCACTTGGGGCAGGGTCACTGTTTACATCACTACCGTGACATTGTGTTGTTTTCATAGCAAAGAATACTCTAAAATAGATTGGGTGAGGCATGATGGCACACCTATGTTCTAAGCACTCAGGAGCCTTGAGGCAGGAGGATCAAATTGAAGGCCAGGCTGGGCTGTGTGGAGAGAACCTGTCTCAGAGCCAGTGCTCAGATTGGGCAGCATCAGAGGTAGTGATGATGCTGCAACATTTTCAGACCAGGTCTGCATTTTGGCTGACAGACTAGGGTGAGTACTGGTGTTCTCACTCTCTCTATAAGGTACTAATACAAAATCACACACAAGTGTCCATGAACTGTGTCTTTTCCAAGGCTTTGTTTCACATTTGTATTTTGATACGACATGGATGTGAGCATCGCAGTTGTTTAAACAGATGTCTGCTGCGCTTAGTGGTTGAACCTCTGTCTGCCTGATGTCTGTGTAAAGTCTGTGCTTGGCTTTGAATTGTATGTTTACATCTTACTGTTTTTAAATAAAGAGAAAATTTTATGGTTATGCAAAGGGCCTTCTTTTTTAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000054725:ENSRNOT00000088339:4
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:
PF126602=zf-TFIIIC=FE(33.3=100)
A:
NA
C2:
PF126602=zf-TFIIIC=PD(22.2=90.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTGTTTGCTCCATGACAGCA
R:
ACGGCTAATGCTCCCCTTACA
Band lengths:
350-1036
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]