BtaINT0141173 @ bosTau6
Intron Retention
Gene
ENSBTAG00000008676 | SRRM4
Description
serine/arginine repetitive matrix 4 [Source:HGNC Symbol;Acc:HGNC:29389]
Coordinates
chr17:58438110-58440276:-
Coord C1 exon
chr17:58440136-58440276
Coord A exon
chr17:58438390-58440135
Coord C2 exon
chr17:58438110-58438389
Length
1746 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGG
5' ss Score
8.41
3' ss Seq
TCCCCCTCTGATCTCTGCAGTGC
3' ss Score
8.95
Exon sequences
Seq C1 exon
GGAGCGGAACCCCAAGTACATCGAGAAGGATTCGCAGCAACGCGAGCGCGAGCGAGCTCGGCGGAGACGTCGGTCCTACTCGCCCATGCGGAAGCGCCGGAGAGACTCCCCAAGCCATCTGGAGGCGCGGAGGATAACGAG
Seq A exon
GTGAGGCCAGGAAGCTCGGTACCACCTCCACCTCACTTGCACTCCCTTCCCACCCTCCCACCCGCTGGAGCCTCCTTTGGGCTGCATTTCAGGACTGTAGGAGCTCAGGGACCTCCCCAACCGCTGAAATGAGGTTTCAGTTCAAAGCCTGGGGCGAGTCAGCACCCCACCACCCAGAGGGCTTGCCAGAAGGGGGCGGGCGCGGTGGGCGGGGCTAGAATGAGGTGGCAGGCCAAAGGGTGGAGCCGGCCTGAGGAATCGGGTGTGGCCGGAACCTGCGGAAGCTGCCGGGATGCCTCTTGCAGGGCTGGGCCATAGAATGAGGACTGGCCTTGCAATGGGGGACGCAAGCAAGGAACTGAACCAGGACATTGCGTGGGGGTGGAGCCAGGCAGTAGCAACACACCTCTACCTTTAGACTCACGCGCCCAGATGCAAGGCTTGAATACAACCGTAGGTAATTATACCCTGAACCAACTGTAGAGAGGGCCAACAGGATTGTTAGGTACCAGAAGGGGGTGGGGGAGTGGGGTGCGCTATTGGGTAAGGGGAAGACCAGTATTTTGGAGAGGAATCTTGTCTGTGCCACTTTCCGAGTGAGCTGGAAAAGTCTCTTCACCTCCCAGAATCTTAAGTTTTTTCACCCATGAACTGCTGGAGGAAATAACTCCTAAAAGTGTCAAAAGGATAAAATGAAAAGAGGCAAAGAGATATGAATGCAATTTATACACTTAAATGCAGAGCACTAGAACACATTGTGTGCCATTGTGATGGACTGAATGGTCAGACTTGGTAGGTAAAGATTTCTGTAACAGGTAGTCTTAGATGAGAAAAGCCCTAGAAGAGAATCCTGAAGTCTGAGAATCCTCAGGCCTTGAAATGGAGAAAATGGCTGAATGCTGCCCTAAAAATGGCTCTTGAAAATTTGTGGGTCTTCCTTCTGGTCCTCCAAGGGTCAGCTACTCAGTCCAGAGACCCACAAGGAAAGGAGAATCCTGGCTGCCCATGCCTTCTCCCTAGAGATGACCTGAAGGAGAAAAAAGAGCTTGTGCCCCAGACAGTAAGGCAGGGTAATGGTGTCATCTTCTCAGATGTCTCACTGAACAGCCTGCCTTGGCCTAGGACATATTGTGGGAGTCCTACACTCACTGCCTTGACTTTCAGAGGTATCCTTGGAGTGGACTTGGAGGAAGTCTTAAGAAAAAGGCTCTCTGGGTTCTGTACTCAACCCCAAATAATCCACCTGAGTGAATCCATTCAATGTTTCCCAAGCTTCCATCACCCACCACTTTTGCCTTATCTGATTAAGTGTACTGCTTACTTAAATTTCTTTAAATAGATACGCCTTTTTGGGGGGTCCATACATTTATTTCAAAACGAAACTTGATACACTATAATAAATAGAAAAATCAACCTCTTTTGCCATAAATAGAAGGTTCTAGTAAAAATAAAAATAGCAAAACAAAACTGTGATTAAAGCTGAGATGTAGATTCTGTGGCCAGCTGGATGCTCTCTCTGAGCCCAGCCTTGCTATGTTAAAAAAGCGAGATTATCACTTTTCAAAGCATATCAGCATTAGACTGAGACCACCTCCTTGATGTTCTCAGGACTGCAAGGGAAGAGTAACAGGAATTCTTTTTCCCTGCTAAGGAGACGGGACATGTCTCCTGGGACAATGTTTGTGCTCCCGGGATTGCAGCTGGGAGGAGTCCTGCCCTGACGCTTTCCCCCTCTGATCTCTGCAG
Seq C2 exon
TGCCCGGAAACGCCCCATCCCCTACTACCGGCCCAGCCCCTCTTCGTCCAGCGGCCTCAGCAGCACCTCCTCCTGGTACAGCAGCAGCAGCAGCCGCTCAGCCAGCCGAAGCTACTCCCGGAGCCGCAGCCGCAGCCGGAGCAGGACCCTCTCTAGCAGCAGCTGCAGCTCCCGCAGCCCCAGCCTGGGCTCCCGGAGCCGCAGCCGGAGCCGGAGCCGGAGTCGGAGTCGGAGTGGGAGCTACAGCTCAGCAGACAGCTACTCCAGCACGAGGCGCTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000008676:ENSBTAT00000011438:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF152301=SRRM_C=FE(71.2=100)
A:
NA
C2:
PF152301=SRRM_C=PD(16.7=11.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCGAGAAGGATTCGCAGCAAC
R:
CCACTCCGACTCCGACTCC
Band lengths:
358-2104
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development