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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATGTACAGCAAAGATGAACTTAAGTGAGGAAGTTGATCTAGAAGATTATGTTTCTAGGCCTGACAAGATAAGTGCTGCCGAGgtgcgcttcttcacctccataatcggtcttgttctgcgtatgttatatggtcatgttgaattgggatacttgtattcttatcaacagccttttaggttac...

Basic information

species Physcomitrella patens
transcript PP1S243_67V6.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S243_67V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GLYMA11G31470.1 (Glycine max), 5'ss of exon 5
GTATGTACAGCAAAGATGAACTTAAGTGAGGAAGTTGATCTAGAAGATTATGTTTCTAGGCCTGACAAGATAAGTGCTGCCGAGgtgcgcttcttcacctccataatcggtcttgttctgcgta-tgttatatggtcatgttgaattgggatacttgtatt-cttatcaacagccttttaggttac
|| || ||||| ||||||||||| ||||| || || ||||| || |||||||||||| | |||||||| || |||||||| |||||  | |||||      | || |   | |||| |    || | |||| | |  ||| |   |     |    | ||   ||||| | |   ||  | |||  
GTTTGCACAGCCAAGATGAACTTGAGTGATGAGGTAGATCTGGAGGATTATGTTTCTCGCCCTGACAAAATCAGTGCTGCTGAGgtttgtttctttcttgtccta-tgacttttgtgcccaataattttatgtaggaatgcttgttattagtttcaggatcatttatcta-actattggaagtttt

upper sequence: PP1S243_67V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GLYMA18G05730.1 (Glycine max), 5'ss of exon 5
-GTATGTACAGCAAAGATGAACTTAAGTGAGGAAGTTGATCTAGAAGATTATGTTTCTAGGCCTGACAAGATAAGTGCTGCCGAGgtgcgcttcttcacctccataatcggtcttgttctgcgtatgttatatggtcatgttgaattg------ggatacttgtattcttatcaacagccttttaggttac
 || || ||||| || |||||||| ||||| || || || ||||| |||||||||||| | |||||||| || |||||||| |||||  | || |  | ||   |    | | |||| |    ||  |||| | |  ||| | | |||      |   | |||| |   |||    |   ||| | ||   
GGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAGgtttgtttat--atcttattctatgatattgtgcc-tataatttatgtagggatgcttatttgtttcatgatcatttgtctaactataggaattttttgaagt---
















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|15327414|gb|BI488088.1|BI488088
EST:     TTGATCTAGAAGATTATGTTTCTAGGCCTGACAAGATAAGTGCTGCCGAG                         ATTTCTGCCATCTGTCAAGAGGCTGGTATGCATGCAGTCAGAAAGAATCGT
genomic: TTGATCTAGAAGATTATGTTTCTAGGCCTGACAAGATAAGTGCTGCCGAGgtgcgcttct ... catgacgcagATTTCTGCCATCTGTCAGGAGGCTGGTATGCATGCAGTCAGAAAGAATCGT
EST: gi|208371413|gb|DC955749.1|DC955749
EST:     TTGATCTAGAAGATTATGTTTCTAGGCCTGACAAGATAAGTGCTGCCGAG                         ATTTCTGCCATCTGTCAGGAGGCTGGTATGCATGCAGTCAGAAAGAATCGT
genomic: TTGATCTAGAAGATTATGTTTCTAGGCCTGACAAGATAAGTGCTGCCGAGgtgcgcttct ... catgacgcagATTTCTGCCATCTGTCAGGAGGCTGGTATGCATGCAGTCAGAAAGAATCGT
EST: gi|37836792|gb|BJ594800.1|BJ594800
EST:     TTGATCTAGAAGATTATGTTTCTAGGCCTGACAAGATAAGTGCTGCCGAG                         ATTTCTGCCATCTGTCAGGAGGCTGGTATGCATGCAGTCAGAAAGAATCGT
genomic: TTGATCTAGAAGATTATGTTTCTAGGCCTGACAAGATAAGTGCTGCCGAGgtgcgcttct ... catgacgcagATTTCTGCCATCTGTCAGGAGGCTGGTATGCATGCAGTCAGAAAGAATCGT
EST: gi|67693405|gb|BJ953638.1|BJ953638
EST:     CTGACAAGATAAGTGCTGCCGAG                         ATTTCTGCCATCTGTCAGGAGGCTGGTATGCATGCAGTCAGAAAGAATCGT
genomic: CTGACAAGATAAGTGCTGCCGAGgtgcgcttct ... catgacgcagATTTCTGCCATCTGTCAGGAGGCTGGTATGCATGCAGTCAGAAAGAATCGT
EST: gi|37832462|gb|BJ590474.1|BJ590474
EST:     TTGATCTAGAAGATTATGTTTCTAGGCCTGACAAGATAAGTGCTGCCGAG                         ATTTCTGCCATCTGTCAGGAGGCTGGTATGCATGCAGTCAGAAAGAATCGT
genomic: TTGATCTAGAAGATTATGTTTCTAGGCCTGACAAGATAAGTGCTGCCGAGgtgcgcttct ... catgacgcagATTTCTGCCATCTGTCAGGAGGCTGGTATGCATGCAGTCAGAAAGAATCGT
EST: gi|67722444|gb|BJ972703.1|BJ972703
EST:     TGACAAGATAAGTGCTGCCGAG                         ATTTCTGCCATCTGTCAGGAGGCTGGTATGCATGCAGTCAGAAAGAATCGT
genomic: TGACAAGATAAGTGCTGCCGAGgtgcgcttct ... catgacgcagATTTCTGCCATCTGTCAGGAGGCTGGTATGCATGCAGTCAGAAAGAATCGT
EST: gi|37845653|gb|BJ603661.1|BJ603661
EST:     TTGATCTAGAAGATTATGTTTCTAGGCCTGACAAGATAAGTGCTGCCGAG                         ATTTCTGCCATCTGTCAGGAGGCTGGTATGCATGCAGTCAGAAAGAATCGT
genomic: TTGATCTAGAAGATTATGTTTCTAGGCCTGACAAGATAAGTGCTGCCGAGgtgcgcttct ... catgacgcagATTTCTGCCATCTGTCAGGAGGCTGGTATGCATGCAGTCAGAAAGAATCGT
EST: gi|208376580|gb|DC952307.1|DC952307
EST:     TTGATCTAGAAGATTATGTTTCTAGGCCTGACAAGATAAGTGCTGCCGAG                         ATTTCTGCCATCTGTCAGGAGGCTGGTATGCATGCAGTCAGAAAGAATCGT
genomic: TTGATCTAGAAGATTATGTTTCTAGGCCTGACAAGATAAGTGCTGCCGAGgtgcgcttct ... catgacgcagATTTCTGCCATCTGTCAGGAGGCTGGTATGCATGCAGTCAGAAAGAATCGT
EST: gi|208367978|gb|DC951003.1|DC951003
EST:     TTGATCTAGAAGATTATGTTTCTAGGCCTGACAAGATAAGTGCTGCCGAG                         ATTTCTGCCATCTGTCAGGAGGCTGGTATGCATGCAGTCAGAAAGAATCGT
genomic: TTGATCTAGAAGATTATGTTTCTAGGCCTGACAAGATAAGTGCTGCCGAGgtgcgcttct ... catgacgcagATTTCTGCCATCTGTCAGGAGGCTGGTATGCATGCAGTCAGAAAGAATCGT
EST: gi|162164770|gb|FC340492.1|FC340492
EST:     TTGATCTAGAAGATTATGTTTCTAGGCCTGACAAGATAAGTGCTGCCGAG                         ATTTCTGCCATCTGTCAGGAGGCTGGTATGCATGCAGTCAGAAAGAATCGT
genomic: TTGATCTAGAAGATTATGTTTCTAGGCCTGACAAGATAAGTGCTGCCGAGgtgcgcttct ... catgacgcagATTTCTGCCATCTGTCAGGAGGCTGGTATGCATGCAGTCAGAAAGAATCGT
EST: gi|67724576|gb|BJ974835.1|BJ974835
EST:     TTGATCTAGAAGATTATGTTTCTAGGCCTGACAAGATAAGTGCTGCCGAG                         ATTTCTGCCATCTGTCAGGAGGCTGGTATGCATGCAGTCAGAAAGAATCGT
genomic: TTGATCTAGAAGATTATGTTTCTAGGCCTGACAAGATAAGTGCTGCCGAGgtgcgcttct ... catgacgcagATTTCTGCCATCTGTCAGGAGGCTGGTATGCATGCAGTCAGAAAGAATCGT
EST: gi|208398297|gb|DC916436.1|DC916436
EST:     TTGATCTAGAAGATTATGTTTCTAGGCCTGACAAGATAAGTGCTGCCGAG                         ATTTCTGCCATCTGTCAGGAGGCTGGTATGCATGCAGTCAGAAAGAATCGT
genomic: TTGATCTAGAAGATTATGTTTCTAGGCCTGACAAGATAAGTGCTGCCGAGgtgcgcttct ... catgacgcagATTTCTGCCATCTGTCAGGAGGCTGGTATGCATGCAGTCAGAAAGAATCGT
EST: gi|37851697|gb|BJ609705.1|BJ609705
EST:     TTGATCTAGAAGATTATGTTTCTAGGCCTGACAAGATAAGTGCTGCCGAG                         ATTTCTGCCATCTGTCAGGAGGCTGGTATGCATGCAGTCAGAAAGAATCGT
genomic: TTGATCTAGAAGATTATGTTTCTAGGCCTGACAAGATAAGTGCTGCCGAGgtgcgcttct ... catgacgcagATTTCTGCCATCTGTCAGGAGGCTGGTATGCATGCAGTCAGAAAGAATCGT
EST: gi|208387168|gb|DC945467.1|DC945467
EST:     TTGATCTAGAAGATTATGTTTCTAGGCCTGACAAGATAAGTGCTGCCGAG                         ATTTCTGCCATCTGTCAGGAGGCTGGTATGCATGCAGTCAGAAAGAATCGT
genomic: TTGATCTAGAAGATTATGTTTCTAGGCCTGACAAGATAAGTGCTGCCGAGgtgcgcttct ... catgacgcagATTTCTGCCATCTGTCAGGAGGCTGGTATGCATGCAGTCAGAAAGAATCGT
EST: gi|37832812|gb|BJ590824.1|BJ590824
EST:     TTGATCTAGAAGATTATGTTTCTAGGCCTGACAAGATAAGTGCTGCCGAG                         ATTTCTGCCATCTGTCAGGAGGCTGGTATGCATGCAGTCAGAAAGAATCGT
genomic: TTGATCTAGAAGATTATGTTTCTAGGCCTGACAAGATAAGTGCTGCCGAGgtgcgcttct ... catgacgcagATTTCTGCCATCTGTCAGGAGGCTGGTATGCATGCAGTCAGAAAGAATCGT
EST: gi|162186124|gb|FC361328.1|FC361328
EST:     TTGATCTAGAAGATTATGTTTCTAGGCCTGACAAGATAAGTGCTGCCGAG                         ATTTCTGCCATCTGTCAGGAGGCTGGTATGCATGCAGTCAGAAAGAATCGT
genomic: TTGATCTAGAAGATTATGTTTCTAGGCCTGACAAGATAAGTGCTGCCGAGgtgcgcttct ... catgacgcagATTTCTGCCATCTGTCAGGAGGCTGGTATGCATGCAGTCAGAAAGAATCGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATGTACAGCAAAGATGAACTTAAGTGAGGAAGTTGATCTAGAAGATTATGTTTCTAGGCCTGACAAGATAAGTGCTGCCGAGgtgcgcttcttcacctccataatcggtcttgttctgcgtatgttatatggtcatgttgaattgggatacttgtattcttatcaacagccttttaggttac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC