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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattgaattcttctcatcatcagcagtgttgcagagtgtgaagtggtgattttatgcctgcacaggttttgtgctgatagtgctgattttcttatttcagCGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCAACAGAGCCATG

Basic information

species Physcomitrella patens
transcript PP1S79_180V6.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S79_180V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 2
---------------------------------------------------------aattgaattcttctcatc----atcagcagtgttgcagagtgtgaagtg-gtgattttatgcctgcacaggttttgtgctgatagtgctgattttcttatttcagCGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCAACAGAGCCATG
                                                           |||| ||| |  | |     || ||   ||| | | | |  |   || |||| | | |  ||    || |  |    | |  ||| | ||||| || | |||||| || || |||||||| || ||| |||| || ||||||||||| |||||||||||||||||
gtactaattgttttgtgttctgattcaatgttcatttgtttctgattgcggacaaattgttgatttccttgcctgcgagattagatttgtcggaaactaagccttgtgtgaatgtttagctttctagatacttaatttaacgtgtt-atttttttttatcagCGCAAGCTTGCGCAAAGATCAGAGAGAGTGAAATGTGTGGATCTACATCCAACAGAGCCATG

upper sequence: PP1S79_180V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 2
-------------------------------------------------------------aattgaattcttctcatcatcagcagtgttgcagagtgtg--aagtggtgattttatgcctgcacaggttttgtgctgatagtgctgattttcttatt--tcagCGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCAACAGAGCCATG
                                                              |||   ||     |   || ||   ||| | | | |  |   ||||   || || ||| | |       ||   || |  ||| |  |||  || ||  |||||| || || |||||||| || ||| |||| || ||||||||||| |||||||||||||||||
gtactaattgttttttgttctgattcaatgtttatttgtttttggttgccgacaaattgttgatttcgttacctgcgagattagatttgtcggaaactaagcctagtgtgaatgttttgctttctggctacttaatctaac-gtgttattttgatttttgatcagCGCAAGCTTGCGCAAAGATCAGAGAGAGTGAAATGTGTGGATCTGCATCCAACAGAGCCATG

upper sequence: PP1S79_180V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 2
-----------------------------------------------------------------------aattgaattcttctcatcatcagcagtgttgcagagtgtgaagtggtga--ttttatgcctgcacag-gttttgtgctgata-gtgctgattttcttatttcagCGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCAACAGAGCCATG
                                                                        |  ||  | || |  | ||  | | |  |    |        |||     |||||   ||     | |  ||   |||||  ||  |  |  | ||    ||||| || || |||||||| || ||| |||| |||| ||||||||| ||||||||||| |||||
gtactcttcttctggcatttgattcgaggtttattttggtttggttgctgagaattgtttgattagcttttcagcgaccttttat-gtgatttgtatttctctgcaaccaagcatggcagagttttacaactttttggcggcttaaactgatttgttttcgtaatatttgaacagCGAAAGCTTGCGCAAAGATCAGAGAGAGTAAAGTCTGTGGATCTACATCCAACAGAACCATG

upper sequence: PP1S79_180V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 2
-aattgaattcttctcatcatcagcagtgttgcagagtgtgaagtggtgattttatgcctgcacaggttt---tgtgctgatagtgct-----gattttcttatttcagCGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCAACAGAGCCATG
  ||||  |   | ||    | ||   | |||  |  | |    |  ||   ||    |||      |||   |||| ||||| |        | | || ||  ||||| | ||| | ||||||||||||||| ||||||| | ||||||||||||||| ||||| |||||
gtattgtttcgatttccat-ttagtttttttgagggatttctttttatgtcattcgctctgtttttttttcgctgtgttgataatttctttgcgttgtttttggttcagAGAAAATTAGCGCAAAGGTCTGAGAGAGTTAAATCTGTGGATCTTCATCCTACAGAACCATG

upper sequence: PP1S79_180V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 2
-----------------aattgaatt--cttctcatcatcagcagtgttgcagagtgtgaagtggtgattttatgcctgcacaggttttgtgctgatagtgctgattttcttatttcagCGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCAACAGAGCCATG
                   |||||||   ||||    |         |  |    |||  | || | | |   ||   | |  | | |  |  || |  || | | |||   ||  ||| |||||||||||||||| || ||| |||| || | ||||||||| |||||| | ||||||||
gtacgcttgtttattccctttgaattgatttctatgtacagattagatctcgatttgtttaatgtttaatagttgaa-gtattgatgtcattttgcttctggtaaattttggat--cagAGGAAACTCGCGCAAAGATCAGAGAGAGTAAAATCTGTGGATCTGCATCCATCTGAGCCATG

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|18345941|gb|BJ177984.1|BJ177984
EST:     CATGCCTCTTCGCTTAGCGATCAAG                         CGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCA
genomic: CATGCCTCTTCGCTTAGCGATCAAGgtatgattca ... cttatttcagCGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCA
EST: gi|18374691|gb|BJ206269.1|BJ206269
EST:     CATGCCTCTTCGCTTAGCGATCAAG                         CGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCA
genomic: CATGCCTCTTCGCTTAGCGATCAAGgtatgattca ... cttatttcagCGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCA
EST: gi|18366204|gb|BJ198282.1|BJ198282
EST:     CATGCCTCTTCGCTTAGCGATCAAG                         CGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCA
genomic: CATGCCTCTTCGCTTAGCGATCAAGgtatgattca ... cttatttcagCGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgattttatgcctgcacaggttttgtgctgatagtgctgattttcttatttcagCGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCAACAGAGCCATG
                                   tgctgat  putative branch site (score: 3)
                                         ttttcttatttc  CT-rich tract
                                      tgattttcttattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattgaattcttctcatcatcagcagtgttgcagagtgtgaagtggtgattttatgcctgcacaggttttgtgctgatagtgctgattttcttatttcagCGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCAACAGAGCCATG

- - - - - - - - - - - - - tgttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgcaca