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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtaccagctagcagtttgagtttccgttttttgggtcttgactgtttatgatgacttgtgcataaagttattcaactgacatcaggtgttctgaacgcagATAAGGACACTAAAAGGTCACACCAATGAAAAGAATTTTGTTGGACTTACTGTCAACAGTGAGTATATCGCCTGTGGCAGTGAAACAAACGAGGTGTTTG

Basic information

species Physcomitrella patens
transcript PP1S86_153V6.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S86_153V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GRMZM2G126795_T02 (Zea mays), 3'ss of exon 13
gtaccagctagcagtttgagtttccgttttttgggtcttgactgtttatgatgacttgtgcataa---agttattcaactgacatcaggtgttctgaacgcagATAAGGACACTAAAAGGTCACACCAATGAAAAGAATTTTGTTGGACTTACTGTCAACAGTGAGTATATCGCCTGTGGCAGTGAAACAAACGAGGTGTTTG
  |   | |   |  ||   |  ||  |||       |  |    | |  ||   || || || |   | || ||  |   ||||   ||| | |     ||| || ||||| | | ||| ||||  ||||||||||| || |||||| |  |||| |||| ||||||||| || ||||| ||||||||||| ||||| ||||
-gatttggttcaatattacatgcccagtttgaaataatgcagcaatgaacatacattttggatgaccgatttgttataacaacatt--gtggtttttttccagGTACGGACATTCAGAGGGCACAAAAATGAAAAGAACTTCGTTGGATTGTCTGTGAACAATGAGTATATTGCTTGTGGAAGTGAAACAAATGAGGTTTTTG

upper sequence: PP1S86_153V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 11
gtaccagctagcagtttgagtttccgttttttgggtcttgactgtttatgatgacttgtgcataaagttattcaa-ctgacatcaggtgttctgaacgcagATAAGGACACTAAAAGGTCACACCAATGAAAAGAATTTTGTTGGACTTACTGTCAACAGTGAGTATATCGCCTGTGGCAGTGAAACAAACGAGGTGTTTG
 ||  |  |   | || ||   |    ||||    | |  |   |  |  || | ||    |||||  ||||    || |  |    |    ||    ||| |  | ||  | ||||| ||  | ||||| || || |||||||| ||||| || | |||||| ||||| || ||||||||||||||||| || || ||||
ttaaaatatttaaattggatcatattattttgtactttctaaaataaaatattattta-atataaatatattttttctcattttcattcaaatgtgtacagGTTCGTACTTTCAAAGGCCATGCAAATGAGAAAAACTTTGTTGGTCTTACAGTAAGCAGTGAATATATTGCGTGTGGCAGTGAAACAAATGAAGTCTTTG

upper sequence: PP1S86_153V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: Vv10s0523g00030.t01 (Vitis vinifera), 3'ss of exon 11
----------------------------------------------------------------------gtaccagct-----agcagtttgagtttccgttttttgggtcttgactgtttatgatgacttgtgcata-aagttattcaactgacatcaggtgttctgaa----cgcagATAAGGACACTAAAAGGTCACACCAATGAAAAGAATTTTGTTGGACTTACTGTCAACAGTGAGTATATCGCCTGTGGCAGTGAAACAAACGAGGTGTTTG
                                                                       | |||  |     || |  ||||   ||| |||||      |    ||   || |    | || |  | || | ||||| || |  ||   | |  | |     |  || |  | ||| | | ||| ||  | ||||| ||||||||||| || || || || ||||| || || || ||||||||||||||||||||||| ||||| |
gtaagttattatgtttttattgtttattttgttctatccccgcattataaatccctctgtatggtgatacctgccaatttttttagtacgttgaccatccatttttgcaaaatcttgtggaaattacatatggtacgaacaactaattcatctcaattcctttttcataatttttcttagGTTCGCACATTTAGAGGGCATTCAAATGAGAAGAATTTTGTGGGTCTCACAGTAAACAGCGAATACATTGCCTGTGGCAGTGAAACAAACGAAGTGTTCG

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|100399476|gb|BY972738.1|BY972738
EST:     CATCTACTGATAGTACTTTGTGTCTTTGGGATGTCAAAGAGAACTGCCCG                         ATAAGGACACTAAAAGGTCACACCAATGAAAAGAATTTTGTTGGACTTACT
genomic: CATCTACTGATAGTACTTTGTGTCTTTGGGATGTCAAAGAGAACTGCCCGgtacgctttc ... ctgaacgcagATAAGGACACTAAAAGGTCACACCAATGAAAAGAATTTTGTTGGACTTACT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgatgacttgtgcataaagttattcaactgacatcaggtgttctgaacgcagATAAGGACACTAAAAGGTCACACCAATGAAAAGAATTTTGTTGGACTTACTGTCAACAGTGAGTATATCGCCTGTGGCAGTGAAACAAACGAGGTGTTTG
                            aactgac  putative branch site (score: 2)
                ataaagttattcaa  TA-rich tract