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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatgatgttgaatgaacatttgcgttgcatcgtttcttgtggatattgtcctctccctttccatgtatgatcattctgatagaagtgagacttttgcagCTATTTTAAAATGCTTGTCAATATGGATATTAGTCTACACTCGATGGAAGTTGTGAATCGCCTTACAACAGCTGTGGATCTTCCTACTGAGTTTGTGCAT

Basic information

species Physcomitrella patens
transcript PP1S82_30V6.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S82_30V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA10G00610.3 (Glycine max), 3'ss of exon 9
ttatg-atgttgaatgaacatttgcgttgcatcgtttcttgtggatattgtcctctccctttccatgtatgatcattctgatagaagtgagacttttgcagCTATTTTAAAATGCTTGTCAATATGGATATTAGTCTACACTCGATGGAAGTTGTGAATCGCCTTACAACAGCTGTGGATCTTCCTACTGAGTTTGTGCAT
 |||| || ||   |  |  | |    |   |  |||  |    | |||| ||| || || |  || |    |  ||||  | |       |    | ||| || || | | | |||||||||||||| || |||||||| || ||||||||||||||  | ||||||||||| || || || ||  || | ||  | || 
gtatgcatttttcctctat-tatattatctgtgctttagtacatacattgccctatcgctatt-attttctttatttctatttgcttatttatggatacagATACTTCACAGTACTTGTCAATATGGACATGAGTCTACATTCAATGGAAGTTGTGAACAGGCTTACAACAGCAGTTGAACTACCGTCTCAATTCATTCAC

upper sequence: PP1S82_30V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA02G00750.2 (Glycine max), 3'ss of exon 9
--ttatgatgttgaatgaacatttgcgttgcatcgtttcttgtggatattgtcctctccctttccatgtatgatcattctgatagaagtgagacttttgcagCTATTTTAAAATGCTTGTCAATATGGATATTAGTCTACACTCGATGGAAGTTGTGAATCGCCTTACAACAGCTGTGGATCTTCCTACTGAGTTTGTGCAT
   |    | ||     |  || |    ||     | |  |    | |||  ||| || || |  || |    |  ||||  | |       |    | ||| || |||| | | |||||||||||||| || |||||||| || ||||||||||||||  | || ||||||||||| || || ||  || | ||  | || 
gtatgcattcttcctctattatattatctgtgc--tctagtacatacattaccctatcgctatt-attttctttatttctatttgcttatttatggatacagATACTTTACAGTACTTGTCAATATGGACATGAGTCTACATTCAATGGAAGTTGTGAACAGGCTGACAACAGCTGTTGAACTACCATCTCAATTCATTCAC
















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|18334747|gb|BJ166764.1|BJ166764
EST:     ATTGCTGTTGAAGTTTTGCTGAAGTTGATGAATTCCAACCAGATTATAGA                         CTATTTTAAAATGCTTGTCAATATGGATATTAGTCTACACTCGATGGAAGT
genomic: ATTGCTGTTGAAGTTTTGCTGAAGTTGATGAATTCCAACCAGATTATAGAgtaagaaacc ... acttttgcagCTATTTTAAAATGCTTGTCAATATGGATATTAGTCTACACTCGATGGAAGT
EST: gi|37822015|gb|BJ580081.1|BJ580081
EST:     ATTGCTGTTGAAGTTTTGCTGAAGTTGATGAATTCCAACCAGATTATAGA                         CTATTTTAAAATGCTTGTCAATATGGATATTAGTCTACACTCGATGGAAGT
genomic: ATTGCTGTTGAAGTTTTGCTGAAGTTGATGAATTCCAACCAGATTATAGAgtaagaaacc ... acttttgcagCTATTTTAAAATGCTTGTCAATATGGATATTAGTCTACACTCGATGGAAGT
EST: gi|162165273|gb|FC341931.1|FC341931
EST:     ATTGCTGTTGAAGTTTTGCTGAAGTTGATGAATTCCAACCAGATTATAGA                         CTATTTTAAAATGCTTGTCAATATGGATATTAGTCTACACTCGATGGAAGT
genomic: ATTGCTGTTGAAGTTTTGCTGAAGTTGATGAATTCCAACCAGATTATAGAgtaagaaacc ... acttttgcagCTATTTTAAAATGCTTGTCAATATGGATATTAGTCTACACTCGATGGAAGT
EST: gi|208360796|gb|DC946492.1|DC946492
EST:     ATTGCTGTTGAAGTTTTGCTGAAGTTGATGAATTCCAACCAGATTATAGA                         CTATTTTAAAATGCTTGTCAATATGGATATTAGTCTACACTCGATGGAAGT
genomic: ATTGCTGTTGAAGTTTTGCTGAAGTTGATGAATTCCAACCAGATTATAGAgtaagaaacc ... acttttgcagCTATTTTAAAATGCTTGTCAATATGGATATTAGTCTACACTCGATGGAAGT
EST: gi|162165272|gb|FC341930.1|FC341930
EST:     ATTGCTGTTGAAGTTTTGCTGAAGTTGATGAATTCCAACCAGATTATAGA                         CTATTTTAAAATGCTTGTCAATATGGATATTAGTCTACACTCGATGGAAGT
genomic: ATTGCTGTTGAAGTTTTGCTGAAGTTGATGAATTCCAACCAGATTATAGAgtaagaaacc ... acttttgcagCTATTTTAAAATGCTTGTCAATATGGATATTAGTCTACACTCGATGGAAGT
EST: gi|162228505|gb|FC404129.1|FC404129
EST:     ATTGCTGTTGAAGTTTTGCTGAAGTTGATGAATTCCAACCAGATTATAGA                         CTATTTTAAAATGCTTGTCAATATGGATATTAGTCTACACTCGATGGAAGT
genomic: ATTGCTGTTGAAGTTTTGCTGAAGTTGATGAATTCCAACCAGATTATAGAgtaagaaacc ... acttttgcagCTATTTTAAAATGCTTGTCAATATGGATATTAGTCTACACTCGATGGAAGT
EST: gi|37822839|gb|BJ580905.1|BJ580905
EST:     ATTGCTGTTGAAGTTTTGCTGAAGTTGATGAATTCCAACCAGATTATAGA                         CTATTTTAAAATGCTTGTCAATATGGATATTAGTCTACACTCGATGGAAGT
genomic: ATTGCTGTTGAAGTTTTGCTGAAGTTGATGAATTCCAACCAGATTATAGAgtaagaaacc ... acttttgcagCTATTTTAAAATGCTTGTCAATATGGATATTAGTCTACACTCGATGGAAGT
EST: gi|18339762|gb|BJ171789.1|BJ171789
EST:     ATTGCTGTTGAAGTTTTGCTGAAGTTGATGAATTCCAACCAGATTATAGA                         CTATTTTAAAATGCTTGTCAATATGGATATTAGTCTACACTCGATGGAAGT
genomic: ATTGCTGTTGAAGTTTTGCTGAAGTTGATGAATTCCAACCAGATTATAGAgtaagaaacc ... acttttgcagCTATTTTAAAATGCTTGTCAATATGGATATTAGTCTACACTCGATGGAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgtcctctccctttccatgtatgatcattctgatagaagtgagacttttgcagCTATTTTAAAATGCTTGTCAATATGGATATTAGTCTACACTCGATGGAAGTTGTGAATCGCCTTACAACAGCTGTGGATCTTCCTACTGAGTTTGTGCAT
                             ttctgat  putative branch site (score: 3)
                                              cttttgc  putative PPT
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatgatgttgaatgaacatttgcgttgcatcgtttcttgtggatattgtcctctccctttccatgtatgatcattctgatagaagtgagacttttgcagCTATTTTAAAATGCTTGTCAATATGGATATTAGTCTACACTCGATGGAAGTTGTGAATCGCCTTACAACAGCTGTGGATCTTCCTACTGAGTTTGTGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - tgttgaa