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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgcttcttttgcacgaattattcgttgtcaaagacaattgagtatcgttggagttcattcttggcgtactaaatgaggtgccacttctcgggttgcagGCTGAAACTGACAGGGAGCTTGGAACGAACAAGGGGATTTCTGAAAAGCAGATTCGACTGAAAATTTTTTCACCTAATGTTTTGAACATTACGCTTGTGG

Basic information

species Physcomitrella patens
transcript PP1S49_216V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S49_216V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA15G06380.1 (Glycine max), 3'ss of exon 1
-----gttgcttcttttgcacgaattattcgttgtcaaagacaattgagtatcgttggagttcattcttggcgtactaaatgaggtgccacttctcgggttgcagGCTGAAACTGACAGGGAGCTTGGAACGAACAAGGGGATTTCTGAAAAGCAGATTCGACTGAAAATTTTTTCACCTAATGTTTTGAACATTACGCTTGTGG
       | ||  |  ||| ||| || |     ||| |      |       | |   |  ||  | ||| | || || ||       ||||| |     |||||||||||||||| |||||    ||   |||||| ||  | || || ||||||||||||||||| ||||||||||| |||||| |  | || ||  | || |
aatgtaatactcttgatgc-cgatttgtatacggtctacttgtttaatcccccctcctatctctctgttgac-tagtatatcttcactcacttttt---ctgcagGCTGAAACTGATAGGGAAGCAGGTGGGAACAAAGGTGTCTCAGACAAGCAGATTCGACTGAAGATTTTTTCACCAAATGTTCTTGATATCACCTTGGTAG

upper sequence: PP1S49_216V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA04G16340.1 (Glycine max), 3'ss of exon 1
---gttgcttcttttgcacgaattattcgttgtcaaagacaattgagtatcgttggagttc-attcttggcgtactaaatgaggtgccacttctcgggttgcagGCTGAAACTGACAGGGAGCTTGGAACGAACAAGGGGATTTCTGAAAAGCAGATTCGACTGAAAATTTTTTCACCTAATGTTTTGAACATTACGCTTGTGG
   | || ||  |   | |  |  | |   |   |    || || |   |  ||  |  ||   | ||||| |  || |||   |  | ||  |     |||||  ||||||||| |||||    |||  |||||| ||  | ||||| |||||||||||||| || ||||||||||| |||||| |  | || || ||||| |
acggctgtttggtggcctcccaacagtaaatcaaacccgcatttaaaccttttttaatctctgctgttggcttg-tatatgtattctctctcttt---ctgcagATTGAAACTGATAGGGAAGCAGGAGGGAACAAAGGTGTCTCTGACAAGCAGATTCGACTCAAGATTTTTTCACCAAATGTTCTTGATATCACACTTGTTG

upper sequence: PP1S49_216V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA07G30150.1 (Glycine max), 3'ss of exon 1
gttgcttcttttgcacgaattattcgttgtcaaagacaattgagtatcg--ttggagttcattcttggcgtactaaatgaggtgccacttctcgggttgcagGCTGAAACTGACAGGGAGCTTGGAACGAACAAGGGGATTTCTGAAAAGCAGATTCGACTGAAAATTTTTTCACCTAATGTTTTGAACATTACGCTTGTGG
                            || ||   |||| || | |    ||| | || | ||     || | | || |    |   || |   | || ||||||| ||||| |||||   ||||  |||||| ||  | ||||| |||||||||||  |||| |||||||| || |||||| |  |||||||||||||||
----------------------------gtgaatttcaatcgaatttgaatttgaactttactc---aagtgccatatca----ctgtttttgttgatgtagGCTGAGACTGATAGGGAAGCTGGAGGGAACAAAGGTGTGTCTGATAAGCAGATTCGTTTGAAGATTTTTTCGCCCAATGTTCTCGACATTACGCTTGTGG

upper sequence: PP1S49_216V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT4G33650.1 (Arabidopsis thaliana), 3'ss of exon 1
gttgcttcttttgcacgaattattcgttgtcaaagacaattgagtatcgttggagttcattcttggcgtactaaatgaggtgccacttctcgggttgcagGCTGAAACTGACAGGGAGCTTGGAACGAACAAGGGGATTTCTGAAAAGCAGATTCGACTGAAAATTTTTTCACCTAATGTTTTGAACATTACGCTTGTGG
   | || || | | |   ||  | | | |    || | |  | |    ||  |  |   | ||   |||     |||  ||| || |||    ||| ||||||| ||  | ||     |||||  |||||| ||  |  | || |  |||||||| || ||||||| |||||||||||| |||||||| ||||||||||
---gttttttattccc---ttccttgctttatttgatactctattgctcttccaagtttgtattaatgta-----tgaaatgcaacatct----ttgtagGCTGAGACGAATAGATTAGTTGGAGAGAACAAAGGTGTAGCAGATACACAGATTCGTCTTAAAATTTCTTCACCTAATGTATTGAACATCACGCTTGTGG

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|22132080|gb|BQ826970.1|BQ826970
EST:     TCCCTGGCCGGCGCTTTACGGATTTCGAAGCAATCCGTAAAGAGATTCAG                         GCTGAAACTGACAGGGAGCTTGGAACGAACAAGGGGATTTCTGAAAAGCAG
genomic: TCCCTGGCCGGCGTTTTACGGATTTCGAAGCAATCCGTAAAGAGATTCAGgtgaagtttg ... cgggttgcagGCTGAAACTGACAGGGAGCTTGGAACGAACAAGGGGATTTCTGAAAAGCAG
EST: gi|18358344|gb|BJ190403.1|BJ190403
EST:     TCCCTGGCCGGCGTTTTACGGATTTCGAAGCAATCCGTAAAGAGATTCAG                         GCTGAAACTGACAGGGAGCTTGGAACGAACAAGGGGATTTCTGAAAA
genomic: TCCCTGGCCGGCGTTTTACGGATTTCGAAGCAATCCGTAAAGAGATTCAGgtgaagtttg ... cgggttgcagGCTGAAACTGACAGGGAGCTTGGAACGAACAAGGGGATTTCTGAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcgttggagttcattcttggcgtactaaatgaggtgccacttctcgggttgcagGCTGAAACTGACAGGGAGCTTGGAACGAACAAGGGGATTTCTGAAAAGCAGATTCGACTGAAAATTTTTTCACCTAATGTTTTGAACATTACGCTTGTGG
                       tactaaa  putative branch site (score: 1)
                                     ccacttctc  putative PPT
                       tactaaat  TA-rich tract