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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGGGACGGAGTACTGGCAAGATGAAGGCATTGATGAAGAAATGCCAGCCTGCCGCCTTTTACTGAATATTTTTCACCCCTATGATCCAGTAGCATATAGgtaagcaatcttgtcgtgatgtcgaacttgataagaattctgaagagaaactgctcgaccatgtgctgcaagtgtcactcactgtctctacccgtatgattcag

Basic information

species Physcomitrella patens
transcript PP1S74_64V6.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S74_64V6.1 (Physcomitrella patens), 5'ss of exon 13
lower sequence: GLYMA09G36920.1 (Glycine max), 5'ss of exon 16
CAGGGACGGAGTACTGGCAAGATGAAGGCATTGATGAAGAAATGCCAGCCTGCCGCCTTTTACTGAATATTTTTCACCCCTATGATCCAGTAGCATATAGgtaagcaa----tcttgtcgtgatgtcgaacttgataagaattctgaagagaaactgctcgaccatgtgctgcaagtgtcactcactgtctctacccgtatgattcag
 |||    || || ||| |  | |||   ||    || || ||||| || || || |   |  | || |||||||||||||||||||| |||||||| ||||  || |    ||| |     |||  | | |   ||   ||| |||  |||   |  |  ||  | |  |  || |      ||     |  |   ||||  |    
GAGGCCAAGAATATTGGGAGCAGGAAAATATAAGAGAGGAGATGCCGGCTTGTCGGCAGATGTTCAACATTTTTCACCCCTATGATCCCGTAGCATACAGgtttgctacaattctagctccaatgaagta-tcactagtgattatgagtagag--taatgaacattataatttaatttcttgacatcagttg-atttgtatagt----

upper sequence: PP1S74_64V6.1 (Physcomitrella patens), 5'ss of exon 13
lower sequence: AT1G31480.1 (Arabidopsis thaliana), 5'ss of exon 16
CAGGGACGGAGTACTGGCAAGATGAAGGCATTGATGAAGAAATGCCAGCCTGCCGCCTTTTACTGAATATTTTTCACCCCTATGATCCAGTAGCATATAGgtaagcaatcttgtcgtgatgtcgaacttgataagaattctgaagagaaactgctcg----accatgtgctgcaagtgtcactcactgtctctaccc--gtatgattcag
  || |  || |||||| |||| ||      |  |||||| |||||||| || || |   |  | ||||| ||||||||||||||||| || |||||||||| ||   || ||  |  ||     |  |  ||   | | |         |||        ||| | |  |||||||||    | |   ||  ||    || | |  |||
AGGGAAAAGATTACTGGGAAGAGGAGAATGCTATTGAAGAGATGCCAGCTTGTCGTCGAATGTTCAATATATTTCACCCCTATGATCCTGTTGCATATAGgttagtcttcatg--gaaataaaacagcttgtagctagtttatgatatcgctgtctttgttaccttcttttgcaagtgtgtaacgccaactaaacttttgtttcacgcag

upper sequence: PP1S74_64V6.1 (Physcomitrella patens), 5'ss of exon 13
lower sequence: EFJ18894 (Selaginella moellendorffii), 5'ss of exon 14
CAGGGACGGAGTACTGGCAAGATGAAGGCATTGATGAAGAAATGCCAGCCTGCCGCCTTTTACTGAATATTTTTCACCCCTATGATCCAGTAGCATATAGgtaagca-atcttgtcgtgatgtcgaacttgataagaattctgaagagaaactgctcgaccatgtgctgcaagtgtcactcactgtctctacccgtatgattcag
| ||    ||||||||| |||||||||||||||| |||||||||||||| ||| | |   |  |||| || |||||||| |||||||| || || || |||||   | ||  |   ||| |  |    || | |   || ||         || |  ||  |                                           
CGGGTCATGAGTACTGGGAAGATGAAGGCATTGAAGAAGAAATGCCAGCATGCAGGCAAATGATGAACATATTTCACCCGTATGATCCTGTCGCTTACAGgtatcaatatacttctgtgttagcagcgtttacatctatccttt-------cttcgtgattacag----------------------------------------

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|100422161|gb|BY957886.1|BY957886
EST:     TGCCGCCTTTTACTGAATATTTTTCACCCCTATGATCCAGTAGCATATAG                         GCTTGAGCCGCTTGTTTGTAAGGAGTTTGTCGACCAAAAACCTGTATTTAT
genomic: TGCCGCCTTTTACTGAATATTTTTCACCCCTATGATCCAGTAGCATATAGgtaagcaatc ... tatgattcagGCTAGAGCCGCTTGTTTGTAAGGAGTTTGTCGACCAAAAACCTGTATTTAT




















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: 24 (upstream exon), 34 (downstream exon)
Score: 4

CAGGGACGGAGTACTGGCAAGATGAAGGCATTGATGAAGAAATGCCAGCCTGCCGCCTTTTACTGAATATTTTTCACCCCTATGATCCAGTAGCATATAGgtaagcaatc ... tatgattcagGCTAGAGCCGCTTGTTTGTAAGGAGTTTGTCGACCAAAAACCTGTATTTATTCCTTATCATAAAGGAGGGAAACGCATTCATATTGGACTCCAG




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