Sequence
atgc intronic sequence ATGC exonic sequenceCAAATCATAAACGATCCACTGATGAGGAACAGCGCAATTCTTGTGTTTGCAAACAAACAAGACATGgtagtgcccattctgagtagaattgatgctaccgaatgtttatgaaatagatgcatcggtgatgctattccatctactgtcgtcgagttcatatgcttgc...
Basic information
species | Physcomitrella patens |
transcript | PP1S37_304V6.1 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S37_304V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: AT3G03120.1 (Arabidopsis thaliana), 5'ss of exon 5
CAAATCATAAACGATCCACTGATGAGGAACAGCGCAATTCTTGTGTTTGCAAACAAACAAGACATGgtagt-gcccattctgagtagaattgatgctaccgaatgtttatgaaatagatgcatcggtgatgctattccatctactgtcgtcgagttcatatgcttgc
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GATATCATAAGGGACCCATTCATGCTCAACAGTGTCATTCTAGTGTTTGCAAACAAACAAGACATGgtaaaagttcataggctctagctttccttatttcatattttttcgttctc-atttaccaaaattcgtctgaactct----ttatgaatttcag--------
upper sequence: PP1S37_304V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: AT5G17060.1 (Arabidopsis thaliana), 5'ss of exon 5
CAAATCATAAACGATCCACTGATGAGGAACAGCGCAATTCTTGTGTTTGCAAACAAACAAGACATGgtagtgcc-cattctgagtagaattgatgctaccgaatgtttatgaaatagatgcatcggtgatgctattccatctactgtcgtcgagttcatatgcttgc
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GAGATCATAAAAGACCCATTCATGCTAAACAGTATCATTCTGGTGTTTGCAAACAAACAGGACATGgtaattcgatattttcttttggtttttgtttgtttctcgtctgtgcttataattcctcaattcacttctttactctgctggatattag-------------
upper sequence: PP1S37_304V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: EFJ24533 (Selaginella moellendorffii), 5'ss of exon 5
CAAATCATAAACGATCCACTGATGAGGAACAGCGCAATTCTTGTGTTTGCAAACAAACAAGACATGgtagtgcccattctgagtagaattgatgctaccgaatgtttatgaaatagatgcatcggtgatgctattccatctactgtcgtcgagttcatatgcttgc
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GCGATTGTGAACGATCCACTGATGAGAAACAGCGCCATCCTGGTGTTCGCAAACAAGCAAGACATGgtaa--ctctcttcgattttcgtt--tctctccgggag-------agtgaagttttcgctcgtctcttcgtttttgcag---------------------Mapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|162172685|gb|FC348066.1|FC348066EST: CACTGATGAGGAACAGCGCAATTCTTGTGTTTGCAAACAAACAAGACATG AATGGAGCTTTGGGCACTGCAGAGGTCTGTGAAAGATTCGGGCTCTTTGGC
genomic: CACTGATGAGGAACAGCGCAATTCTTGTGTTTGCAAACAAACAAGACATGgtagtgccca ... ttgagcgcagAATGGAGCTTTGGGCACTGCAGAGGTCTGTGAAAGATTCGGGCTCTTTGGC
EST:
gi|18362447|gb|BJ194517.1|BJ194517EST: CACTGATGAGGAACAGCGCAATTCTTGTGTTTGCAAACAAACAAGACATG AATGGAGCTTTGGGCACTGCAGAGGTCTGTGAAAGATTCGGGCTCTTTGGC
genomic: CACTGATGAGGAACAGCGCAATTCTTGTGTTTGCAAACAAACAAGACATGgtagtgccca ... ttgagcgcagAATGGAGCTTTGGGCACTGCAGAGGTCTGTGAAAGATTCGGGCTCTTTGGC
EST:
gi|18365645|gb|BJ197722.1|BJ197722EST: CACTGATGAGGAACAGCGCAATTCTTGTGTTTGCAAACAAACAAGACATG AATGGAGCTTTGGGCACTGCAGAGGTCTGTGAAAGATTCGGGCTCTTTGGC
genomic: CACTGATGAGGAACAGCGCAATTCTTGTGTTTGCAAACAAACAAGACATGgtagtgccca ... ttgagcgcagAATGGAGCTTTGGGCACTGCAGAGGTCTGTGAAAGATTCGGGCTCTTTGGC
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
28 (upstream exon),
34 (downstream exon)
Score:
7CAAATCATAAACGATCCACTGATGAGGAACAGCGCAATTCTTGTGTTTGCAAACAAACAAGACATGgtagtgccca ... ttgagcgcagAATGGAGCTTTGGGCACTGCAGAGGTCTGTGAAAGATTCGGGCTCTTTGGCCTGAAAAATCGAAGATGGCAAATCCAAGGCACTTGTGCTCCCAAAGGTG
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