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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgccttgacatggtctctaaaacattttctgcacctccatatcttaactgtgaatttacatgaatacaaactgtctgctttctgataattgtaacgcggacaatacattagattccgtcacgtatattacaataaaatcgaggacattttgtttaatgctttcatcctggacacgtgatgcagGTTCAAGTGTGTAGACCTGGATTGTGACGGGATGATTATACTAAATGAGATGCAATATTTTTACGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAG

Basic information

species Physcomitrella patens
transcript PP1S7_163V6.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM2G040094_T01 (Zea mays), 3'ss of exon 8
gtaagtgccttgacatggtctctaaaacattttctgcacctccatatcttaactgtgaatttacatgaatacaaactgtctgctttctgataattgtaacgcggacaatacattagattccgt-cacgtatattacaataaaatcgaggacatttt-gtttaatgctttcatcctggacacgtgatgcagGTTCAAGTGTGTAGACCTGGATTGTGACGGGATGATTATACTAAATGAGATGCAATATTTTTACGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAG
                                                                               ||   | || |   ||   |    ||  || | |||  || |   || |  | | ||   ||||      | ||||| | ||  ||   ||| |            | ||||||||  ||| ||||  ||||| |  | || ||  ||| ||  | ||| || ||||  |||| |||||||||||||||||| |||||||||||||| || 
------------------------------------------------------------------------------actaaatcctaaaggttc--atattgatcattccttatcttacaagcatgcctgtaacttcaaaagttctcatatttttgcttggtgacatcacctc----------ttcagGTTCACATGTATAGATTTGGATGGCAATGGCATACTTACACACATTGAAATACAATTCTTTTTCGAGGAGCAACTTCATCGCATGGAGTGCATGGCCCAA

upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM2G080083_T02 (Zea mays), 3'ss of exon 8
gtaagtgccttgacatggtctctaaaacattttctgcacctccatatcttaactgtgaatttacatgaatacaaactgtctgctttctgataattgtaacgcggacaatacattagattccgtcacgtatattacaataaaatcgaggacattttg----tttaatgctttcatcctggacacgtgatg----cagGTTCAAGTGTGTAGACCTGGATTGTGACGGGATGATTATACTAAATGAGATGCAATATTTTTACGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAG
                                                                                             |   | |    || | |   || | |   |    |||  | |||  ||  |    ||||        | | ||  |||  || |||  ||   ||     ||||||||| ||| ||||  ||||  |  | || ||  ||| ||  | |||  | || |  || |  ||||||||||||||||| |||||||||||||| |||
--------------------------------------------------------------------------------------------gtacaagcttcaactaaatcctaaaatttct----tatcctccaaccaagcctgtaacatccaaaagttctcatatttttttcttggtgacaccatctcttcagGTTCAAATGTATAGATTTGGACGGCAATGGCATACTTACACATATTGAACTACAGTTCTTCTTTGAGGAGCAACTTCATCGCATGGAGTGCATGGCCCAG

upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 9
gtaagtgccttgacatggtctctaaaacattttctgcacctccatatcttaactgtgaatttacatgaatacaaactgtctgctttctgataattgtaacgcggacaatacattagat-tccgtcacgtatattacaataaaatcgaggacattttgtttaatgctttcatcctggacacg--tgatgcagGTTCAAGTGTGTAGACCTGGATTGTGACGGGATGATTATACTAAATGAGATGCAATATTTTTACGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAG
                                                                                          |  |||| |  |    |    |||  || |  |  |   | |||  | ||     |   ||| ||   ||  |  |   ||   ||| ||   |   ||||||| |||||  | || || ||| || | || ||  | |   | ||||| ||||||| ||| |||||||||||| | || || |||||||||||||| || 
-----------------------------------------------------------------------------------------gttgttgtgat-ctattaccttattctatctttgctatacacattgta-tatctcaggttacagttgtatttttattgaaatatgggaaacaactttcgcagGTTTAAGTGCATCGATCTTGATGGTAATGGTATTTTAACTTTCAATGAAATGCAATTTTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAA

upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA20G36530.1 (Glycine max), 3'ss of exon 9
gtaagtgccttgacatggtctctaaaacattttctgcacctccatatcttaactgtgaatttacatgaatacaaactgtctgctttctgataattgtaacgcggacaatacattagattccgtcacgtatattacaataaaatcgaggacattttgtttaatgctttcatcctggacacgtgat--gcagGTTCAAGTGTGTAGACCTGGATTGTGACGGGATGATTATACTAAATGAGATGCAATATTTTTACGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAG
                                                                                       || || |||  |  | |   |||  | | |||  |       | ||    | |  |  | | | |     |    |||     | || | | || |     |||||||||||  ||||  ||||| |  | ||  |  | | |   |||||  |||||| |||||| ||||| ||| | |||||||||||||||||||| || 
--------------------------------------------------------------------------------------atgctatttggtaaacagtggatatttgacattgtggttgacttgttttc-tgatttttaagtcgtcaaagtacgagct---gacttgaaaatgtcactattagGTTCAAGTGCATAGATTTGGATGGAAATGGAGTTCTGACAAGGAATGAACTGCAATTTTTTTATGAGGAACAATTGCATCGGATGGAGTGCATGGCCCAA

upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA10G30930.1 (Glycine max), 3'ss of exon 9
gtaagtgccttgacatggtctctaaaacattttctgcacctccatatcttaactgtgaatttacatgaatacaaactgtctgctttctgataattgtaacgcggacaatacattagattccgtcacgtatattacaataaaatcgaggacattttgtttaatgctttcatcctggacacgtgat--gcagGTTCAAGTGTGTAGACCTGGATTGTGACGGGATGATTATACTAAATGAGATGCAATATTTTTACGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAG
                                                                                       || || |||  |  | |   |||  | | ||   |       | ||    |    |  | | |||     |    |||     | || | | || |     |||||||||||  ||||  ||||| |  | ||  |  | | |   |||||  |||||| |||||| ||||||||| | ||||||||||| |||||||| || 
--------------------------------------------------------------------------------------atgctatttggtaaacagtggatatttgacatcgtggttgacttgttttc-tggtttttaagtcatcaaagtacgagct---gacttgaaaatgtcactattagGTTCAAGTGCATAGATTTGGATGGAAATGGAGTTCTAACAAGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGGATGGAATGCATGGCCCAA

upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 9
gtaagtgccttgacatggtctctaaaacattttctgcacctccatatcttaactgtgaatttacatgaatacaaactgtctgctttctgataattgtaacgcggacaatacattagattccgtcacgtatattacaa-taaaatcgaggacattttgt-ttaatgctttcatcctggacacgtgatg--cagGTTCAAGTGTGTAGACCTGGATTGTGACGGGATGATTATACTAAATGAGATGCAATATTTTTACGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAG
                                                                                             ||   ||   | |     | || | ||     || | |||  || |   |||   |   ||   | |||    |||     | |||  || |||   |||||||||||  | ||  ||||| |  | ||  |  | | ||  |||||  |||||| |||||| ||||||||| | ||||| |||||||||||||| || 
--------------------------------------------------------------------------------------------ttttccaccttgcctcctaagtacactcttaggcgaacattggaagtttgatctttgtggttgactattagctatttgtgatttgacgtgtcatgattagGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA

upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 9
gtaagtgccttgacatggtctctaaaacattttctgcacctccatatcttaactgtgaatttacatgaatacaaactgtctgctttctgataattgtaacgcggacaatacattagattccgtcacgtatattacaataaaatcgaggacattttgtttaatgctttcatcctggacacgtgatgcagGTTCAAGTGTGTAGACCTGGATTGTGACGGGATGATTATACTAAATGAGATGCAATATTTTTACGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAG
                                                                     | ||   || || ||   |    | | | | ||| ||| |  |    | |  | |   | |  |  | |    |     |  | |  ||| |||  |            | ||||  |||||||||||  | ||  ||||| |  | ||  |  | | ||  |||||  |||||| |||||| ||||||||| | ||||| |||||||||||||| || 
---------------------------------------------------------------------tccaccttgcctcctaagtac--actcttaggcgaacattgga----agtttgacctttgtggttgactcttgttagctatttgtgatttgatgtgt------------catgat-tagGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA

upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: EFJ20642 (Selaginella moellendorffii), 3'ss of exon 9
gtaagtgccttgacatggtctctaaaacattttctgcacctccatatcttaactgtgaatttacatgaatacaaactgtctgctttctgataattgtaacgcggacaatacattagattccgtcacgtatattacaataaaatcgaggacattttgtttaatgctttcatc--ctggacacgtgatgcagGTTCAAGTGTGTAGACCTGGATTGTGACGGGATGATTATACTAAATGAGATGCAATATTTTTACGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAG
                                                                                                                                    || |   |  ||  | |  || |||   ||   |  ||   | |  | ||   | ||||||||| ||| | || ||||||||||||||  || | |  | ||| |||||||| || ||||||||||||||| | ||||| ||||||||| | ||||| 
-----------------------------------------------------------------------------------------------------------------------------------gta-agcgacgtcttgaatcttctgtaagatcgatcgattgacagatcgcgacttccagGTTCAAATGTATCGATCTGGATTGTGACGGAGTGGTGACTCCAAACGAGATGCAGTACTTTTACGAGGAGCAATTGCATCGCATGGAGTGCCTAGCTCAA

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|162155853|gb|FC332402.1|FC332402
EST:     TTTATTCTTTCAGAAGAGGACAAGTCTTCCGAACCCAGCTTAGAGTACTG                         GTTCAAGTGTGTAGACCTGGATTGTGACGGGGTGATTATACTAAATGAGAT
genomic: TTTATTCTTTCAGAAGAGGACAAGTCTTCCGAACCCAGCTTAGAGTACTGgtaagtgcct ... cgtgatgcagGTTCAAGTGTGTAGACCTGGATTGTGACGGGATGATTATACTAAATGAGAT
EST: gi|162261177|gb|FC437506.1|FC437506
EST:     TTTATTCTTTCAGAAGAGGACAAGTCTTCCGAACCCAGCTTAGAGTACTG                         GTTCAAGTGTGTAGACCTGGATTGTGACGGGATGATTATACTAAATGAGAT
genomic: TTTATTCTTTCAGAAGAGGACAAGTCTTCCGAACCCAGCTTAGAGTACTGgtaagtgcct ... cgtgatgcagGTTCAAGTGTGTAGACCTGGATTGTGACGGGATGATTATACTAAATGAGAT
EST: gi|18334323|gb|BJ166340.1|BJ166340
EST:     TCCGAACCCAGCTTAGAGTACTG                         GTTCAAGTGTGTAGACCTGGATTGTGACGGGATGATTATACTAAATGAGAT
genomic: TCCGAACCCAGCTTAGAGTACTGgtaagtgcct ... cgtgatgcagGTTCAAGTGTGTAGACCTGGATTGTGACGGGATGATTATACTAAATGAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaataaaatcgaggacattttgtttaatgctttcatcctggacacgtgatgcagGTTCAAGTGTGTAGACCTGGATTGTGACGGGATGATTATACTAAATGAGATGCAATATTTTTACGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAG
                      gtttaat  putative branch site (score: 4)
               acattttgtttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgccttgacatggtctctaaaacattttctgcacctccatatcttaactgtgaatttacatgaatacaaactgtctgctttctgataattgtaacgcggacaatacattagattccgtcacgtatattacaataaaatcgaggacattttgtttaatgctttcatcctggacacgtgatgcagGTTCAAGTGTGTAGACCTGGATTGTGACGGGATGATTATACTAAATGAGATGCAATATTTTTACGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA