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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttctcatcgtaactttttgtatgtactgaatgtagcagtgacgagattagtactattgttgcctacgataacctggtaatcatcacctgtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGAGCAGTTGTCAGCGTGAGACGAGCGCAGGACAAAATAGCTATCTGGACTA

Basic information

species Physcomitrella patens
transcript PP1S39_197V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S39_197V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os10g32970.1 (Oryza sativa), 3'ss of exon 2
-----------------------ctt--tctcatcgtaactttttgtatgtactgaatgtagca---gtgacgagattagtactattgt-tgcctacgataacctggtaatcatcacct-gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGAGCAGTTGTCAGCGTGAGACGAGCGCAGGACAAAATAGCTATCTGGACTA
                       |||  | |  ||| |   | |    ||   || || || ||   ||  |  ||    |  | |    |  |||  ||   ||| | |  | |   | |   |||||| || ||||| ||||||||||||| ||||||||| |||| |||||||||||||  ||||  || ||  | |        |||||  | ||  | |||||||
gtacatttcctctaaaatcattgcttagtttggtcggaggctctgaagtgctttggatataacatctgttgcttgacctatcttctaaagtttctatcatt-tctgctgacaaacttttcgaacatgcagCTGATGGCTCTGATTGGAGAGCAGTTTGATGAAAGTGAGGAAATTTGTGGAGTTGTTGCTAGTGTCCGCCAGAGAGGAGACAAGCTTGCATTGTGGACTA

upper sequence: PP1S39_197V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G002616_T01 (Zea mays), 3'ss of exon 2
ctttctcatcgtaactttttgtatgtactgaatgtagcagtgacgagattagtactattgttgcctacgataacctggtaatcat-cacctgtgg---atgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGAGCAGTTGTCAGCGTGAGACGAGCGCAGGACAAAATAGCTATCTGGACTA
        |    | || |  | | |    ||  || |  ||    |   |   ||  |     |  |    ||||  || || | || ||||      |  || |||||||||||||||| || ||||| ||  | ||||| ||||||||||| ||||||||||| ||| |  |   |||||| | ||| ||||| ||||| |
-------gtaagcaattctattttatcagaaagataactttgttttgcacatctctccttaacacgtcctccaccttatattctttcaactgtcctttgtttagCTGCTGGCTATGATTGGTGAACAATTCGACTATGGTGATGAAATTTGTGGCGCAGTTGTCAGTGTGCGTGGGAAGCAGGAAAGAATTGCTATTTGGACAA

upper sequence: PP1S39_197V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G113096_T01 (Zea mays), 3'ss of exon 2
ctttctcatcgtaactttttgtatgtactgaatgtagcagtgacgagattagtact-attgttgcctacgataacctggtaatcatcacctgtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGAGCAGTTGTCAGCGTGAGACGAGCGCAGGACAAAATAGCTATCTGGACTA
          ||    |||| |  | |  |   ||     |   || ||  || || ||| | |||| |  |   |      |   |||   |   || || || |||||||||| || || ||||| ||  | ||||| ||||||||||||||||| ||||||||| |  |   |||||| | ||||||||||||||| |
---gtaagcagttttattttatcagaaaagggagttttgttcttgacatctgtccttattatagcctccagtcctccacccttacacactgtttcttgtagCTGTTGGCTATGATCGGCGAACAATTCGACTATGGTGATGAAATTTGTGGAGCAGTAGTCAGCGTGCGTAGCAAGCAGGAAAGAATAGCTATCTGGACAA

upper sequence: PP1S39_197V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT5G35620.1 (Arabidopsis thaliana), 3'ss of exon 2
------ctttctcatcgtaactttttgtatgtactgaatgtagcagtgacgagattagtactattgttgcctacgataacctggtaatcatcacctgtgg-atgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGAGCAGTTGTCAGCGTGAGACGAGCG-CAGGACAAAATA-GCTATCTGGACTA
      | |||| | | ||||  |     | ||||        | |||    | |   |  |||   ||  |  | | ||  | |    ||  | | ||  ||| ||||| ||||| ||||||||||||||||||||||||  || || |||||||| |  ||||  || ||  | | |  | |    ||| | | ||| ||       
gtattacattctaaccctaaccctaaccttttact-----cttctgtgttttgttagatgatatg--tggttttggtgactggtt--ctatttcttatgatatgtagTTGATGGCTTTGATTGGAGAGCAATTTGATGAAGCAGATGAGATTTGTGGTGTGGTTGCTAGTGTCCGTCCACAGTCGAAGCAAGACAAGCTCTCCTTGT--

upper sequence: PP1S39_197V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT4G18040.1 (Arabidopsis thaliana), 3'ss of exon 2
ctttctcatcgtaactttttgtatgtactgaat-gtagcagtgacgagattagtactattgttgcctacgataacctggtaatcatcacctg-tggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGAGCAGTTGTCAGCGTGAGACGAGCGCAGGACAAAATAGCTATCTGGACTA
   |    |    | | ||  | | |  ||| | ||| |     ||  || | | | ||||   |  ||       |  |  |  | || || | | |  ||||||| ||  ||||||||||||| |||||| | || || ||||| |||||||||||||||| | | ||| ||  ||| || |  ||| |||| |||||||
--gtacggtttctattcttcttttattttgactcgtaactcctgcgtcatca-tccaattgaatctcac--cggttt--ttctttttacatgcttggtttagTTGCTTGCATTGATTGGAGAGCAGTTTGATCATGGAGATGAAATATGTGGAGCAGTTGTCAACATTAGAGGAAAGCAAGAAAGGATATCTATTTGGACTA

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|208358604|gb|DC949939.1|DC949939
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
EST: gi|67578866|gb|BJ951033.1|BJ951033
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
EST: gi|208369044|gb|DC931290.1|DC931290
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
EST: gi|67578970|gb|BJ951121.1|BJ951121
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
EST: gi|67571986|gb|BJ944810.1|BJ944810
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
EST: gi|208374804|gb|DC932059.1|DC932059
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
EST: gi|162275711|gb|FC451882.1|FC451882
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
EST: gi|208371310|gb|DC944474.1|DC944474
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
EST: gi|67712745|gb|BJ966194.1|BJ966194
EST:     CACCCAGGAGCGGCGGCNAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGA
EST: gi|208370617|gb|DC936133.1|DC936133
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
EST: gi|67695351|gb|BJ955584.1|BJ955584
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
EST: gi|67507600|gb|BJ940481.1|BJ940481
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
EST: gi|208389543|gb|DC945795.1|DC945795
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
EST: gi|162225235|gb|FC402001.1|FC402001
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
EST: gi|162272121|gb|FC447915.1|FC447915
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
EST: gi|19788032|gb|BQ040702.1|BQ040702
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGA
EST: gi|162272120|gb|FC447914.1|FC447914
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
EST: gi|208374770|gb|DC932039.1|DC932039
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
EST: gi|100394449|gb|BY972074.1|BY972074
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
EST: gi|162225236|gb|FC402002.1|FC402002
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
EST: gi|208358581|gb|DC946542.1|DC946542
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
EST: gi|67569897|gb|BJ942721.1|BJ942721
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGA
EST: gi|162275712|gb|FC451883.1|FC451883
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
EST: gi|67700328|gb|BJ960561.1|BJ960561
EST:     CCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
genomic: CCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
EST: gi|208358601|gb|DC946562.1|DC946562
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
EST: gi|67576793|gb|BJ949617.1|BJ949617
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACG
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACG
EST: gi|67698930|gb|BJ959163.1|BJ959163
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
EST: gi|67724457|gb|BJ974716.1|BJ974716
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
EST: gi|67698951|gb|BJ959184.1|BJ959184
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
EST: gi|67507690|gb|BJ940570.1|BJ940570
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
EST: gi|37835847|gb|BJ593859.1|BJ593859
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agattagtactattgttgcctacgataacctggtaatcatcacctgtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGAGCAGTTGTCAGCGTGAGACGAGCGCAGGACAAAATAGCTATCTGGACTA
                      cgataac  putative branch site (score: 3)
       tactatt  TA-rich tract