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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattactttacaatgaaatattgttgttagcatttggagtactcgttgttcattactctgtgcgtccgttgatcatacgattgatctaacgtcaatgcgtttgtttgtcatagGTATCGTGCGCCTGAAGTGCTTCTTCAGTCACCAACTTATTCTCCTGCTATAGATATGTGGGCAGTGGGGGCTATAATGGCTGAACTTTTCACTTTTCGC

Basic information

species Physcomitrella patens
transcript PP1S28_184V6.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S28_184V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA09G34610.1 (Glycine max), 3'ss of exon 7
gtaagattactttacaatgaaatattgttgttagcatttggagtactcgttgttcattactctgtgcgtccgttgatcatacgattgatctaacgtcaatgcgtttgtttgtcatagGTATCGTGCGCCTGAAGTGCTTCTTCAGTCACCAACTTATTCTCCTGCTA-TAGATATGTGGGCAGTGGGGGCTATAATGGCTGAACTTTTCACTTTTCGC--------------------
                                                   ||   |  ||   || | |   || |   |    || |||  |   ||||| ||| |   |    | |   | |  ||  | |      ||   | |  ||||    | ||  ||  |||||||||||||| |||| |||||||||||||| |||||| || ||||                     
---------------------------------------------------gtgagtatctgattgggactaatggtgtcatttatgttctt-cactaatgc-tttctgcattgatgatgatgagtacc--atgctgccatttgtttattaactcccccccccccttctagATATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAG
















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|162172239|gb|FC348804.1|FC348804
EST:     AGGGAAGTTCAGTCGTCTCCACCATACACAGATTATGTCTCCACTCGCTG                         GTATCGTGCGCCTGAAGTGCTTCTTCAGTCACCAACTTATTCTCCTGCTAT
genomic: AGGGAAGTTCAGTCGTCTCCACCATACACAGATTATGTCTCCACTCGCTGgtaagattac ... tttgtcatagGTATCGTGCGCCTGAAGTGCTTCTTCAGTCACCAACTTATTCTCCTGCTAT
EST: gi|100452665|gb|CJ975383.1|CJ975383
EST:     AGGGAAGTTCAGTCGTCTCCACCATACACAGATTATGTCTCCACTCGCTG                         GTATCGTGCGCCTGAAGTGCTTCTTCAGTCACCAACTTATTCTCCTGCTAT
genomic: AGGGAAGTTCAGTCGTCTCCACCATACACAGATTATGTCTCCACTCGCTGgtaagattac ... tttgtcatagGTATCGTGCGCCTGAAGTGCTTCTTCAGTCACCAACTTATTCTCCTGCTAT
EST: gi|162171440|gb|FC346715.1|FC346715
EST:     AGGGAAGTTCAGTCGTCTCCACCATACACAGATTATGTCTCCACTCGCTG                         GTATCGTGCGCCTGAAGTGCTTCTTCAGTCACCAACTTATTCTCCTGCTAT
genomic: AGGGAAGTTCAGTCGTCTCCACCATACACAGATTATGTCTCCACTCGCTGgtaagattac ... tttgtcatagGTATCGTGCGCCTGAAGTGCTTCTTCAGTCACCAACTTATTCTCCTGCTAT
EST: gi|100445020|gb|BY964319.1|BY964319
EST:     AGGGAAGTTCAGTCGTCTCCACCATACACAGATTATGTCTCCACTCGCTG                         GTATCGTGCGCCTGAAGTGCTTCTTCAGTCACCAACTTATTCTCCTGCTAT
genomic: AGGGAAGTTCAGTCGTCTCCACCATACACAGATTATGTCTCCACTCGCTGgtaagattac ... tttgtcatagGTATCGTGCGCCTGAAGTGCTTCTTCAGTCACCAACTTATTCTCCTGCTAT
EST: gi|162169093|gb|FC345983.1|FC345983
EST:     AGGGAAGTTCAGTCGTCTCCACCATACACAGATTATGTCTCCACTCGCTG                         GTATCGTGCGCCTGAAGTGCTTCTTCAGTCACCAACTTATTCTCCTGCTAT
genomic: AGGGAAGTTCAGTCGTCTCCACCATACACAGATTATGTCTCCACTCGCTGgtaagattac ... tttgtcatagGTATCGTGCGCCTGAAGTGCTTCTTCAGTCACCAACTTATTCTCCTGCTAT
EST: gi|100434800|gb|BY960838.1|BY960838
EST:     AGGGAAGTTCAGTCGTCTCCACCATACACAGATTATGTCTCCACTCGCTG                         GTATCGTGCGCCTGAAGTGCTTCTTCAGTCACCAACTTATTCTCCTGCTAT
genomic: AGGGAAGTTCAGTCGTCTCCACCATACACAGATTATGTCTCCACTCGCTGgtaagattac ... tttgtcatagGTATCGTGCGCCTGAAGTGCTTCTTCAGTCACCAACTTATTCTCCTGCTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgcgtccgttgatcatacgattgatctaacgtcaatgcgtttgtttgtcatagGTATCGTGCGCCTGAAGTGCTTCTTCAGTCACCAACTTATTCTCCTGCTATAGATATGTGGGCAGTGGGGGCTATAATGGCTGAACTTTTCACTTTTCGC
                         atctaac  putative branch site (score: 2)
                                         tttgttt  putative PPT
                                         tttgttt  TA-rich tract