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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactcttgactcttgaaaccattctggtattcattggctttggcttttctgctgatctgcaagaagttgtatatatgaatcacgtgtgtgctagccgattctttatctccttgtttacatggaatatggatgcagGTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTGCTCCGGCCTGGCCGTTTGGATCGAAAAATTGAAATTCCACTGCCTAATG

Basic information

species Physcomitrella patens
transcript PP1S47_46V6.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: LOC_Os06g40560.1 (Oryza sativa), 3'ss of exon 7
gtactcttgactcttgaaaccattctggtattcattggctttggcttttctgctgatctgcaagaagttgtatatatgaatcacgtgtgtgctagccgattctttatctccttgtttacatggaatatggatgcagGTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTGCTCCGGCCTGGCCGTTTGGATCGAAAAATTGAAATTCCACTGCCTAATG
                               |  ||| |  ||  |  | |  |    ||    ||  ||||| |  || ||  |    |||  |  |||| | | |  |    ||| | |   |  |  || |||||||| ||||| ||||| |||||||| ||||||||| | || |||||  | || || ||||| || |||||  | || ||||||||||||||||| ||||
-----------------------------gatggttgtcactgattcctttaatatgatgtggaaaactgtatgt--gactcctggtattgcatg--gattgtgtgtaacagaattttcct---acttttatacagGTAAAAATGATCATGGCGACTAATCGTCCTGATGTTTTGGACCCTGCACTCCTTCGTCCTGGGCGGTTGGACAGGAAGATTGAAATTCCACTGCCAAATG

upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G171604_T01 (Zea mays), 3'ss of exon 7
gtactcttgactcttgaaaccattctggtattcattggctttggcttttctgctgatctgcaagaagttgtatatatgaatcacgtgtgtgctagccgattctttatctccttg--tttacatgga-atatggat----gcagGTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTGCTCCGGCCTGGCCGTTTGGATCGAAAAATTGAAATTCCACTGCCTAATG
                                      |      ||| | |   || | | |  | |  |  ||| |||   | |||||  |    | |||| |||    ||   || ||| ||| || | ||      |||||||||||||| |||||||| ||||| ||||||||||| || |||||  | || || ||||| ||||| ||  | || ||||||||||| || || || |
--------------------------------------cacaatatttaccgtgcattttctatgattgttgcata-gaacagcttgtgtctt----gtttctgtatgagtttagtttgacaaggatattttgacctgaacagGTAAAGATGATCATGGCCACGAATCGACCTGATGTTCTGGACCCTGCGCTCCTGCGTCCTGGACGTTTAGACAGGAAGATTGAAATTCCGCTACCCAACG

upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G165817_T01 (Zea mays), 3'ss of exon 7
gtactcttgactcttgaaaccattctggtattcattggctttggcttttctgctgatctgcaagaagttgtatatatgaatcacgtgtgtgctagccgattctttatctccttgtttacatggaatatggatgcagGTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTGCTCCGGCCTGGCCGTTTGGATCGAAAAATTGAAATTCCACTGCCTAATG
                     | | || ||||        |    |||| |   | |    | ||  | |||  | ||  ||  ||   | ||  |  | |     |   |  |  ||  | |  | || |  |||||||| ||||| |||||||| ||||| ||||||||||| || || ||  | || || ||||| ||||| ||| | || ||||||||||| || || || |
------------------gtaaatttgttatttggattactcacattttttctaggtaca-acgatatagtagct-tgtgtcttgttgtttctgtctaaattcagtttgacaaggatattttggct-tgaa--cagGTAAAAATGATCATGGCCACAAATCGACCTGATGTTCTGGACCCGGCGCTCCTGCGTCCTGGACGTTTAGATAGGAAGATTGAAATTCCGCTACCCAACG

upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA06G03230.1 (Glycine max), 3'ss of exon 7
gtactcttgactcttgaaaccattctggtattcat-tggctttggcttttctgctgatctgcaagaagttgtatatatgaatcacgtgtgtgctagccgattctttatctccttgtttacatggaatatggatgcagGTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTGCTCCGGCCTGGCCGTTTGGATCGAAAAATTGAAATTCCACTGCCTAATG
                           |||||| | ||| | ||    || |     ||| |||    |||      ||||  |    | |  | |  |||||   ||  | ||  |  | |  | |   | || |||| || ||||||||||| || || || |||||||| ||||| |||||| | || || |||||  | |||||| ||||||| ||||| || ||||||||||
---------------------------gtattcttatggatatgttgattttt----tctacaaatgattgc-----tgaacaaaaaatttaatggtggattcacgatgacattactgtc-tacatttctgttgtagGTTAAAATGATAATGGCAACAAACCGACCTGATGTACTTGACCCTGCTCTCCTGCGTCCTGGGAGATTGGATAGAAAAATAGAAATCCCTCTGCCTAATG

upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA04G03180.1 (Glycine max), 3'ss of exon 7
gtactcttgactcttgaaaccattctggtattcattggctttggcttttctgctgatctgcaagaagttgtatatatgaatcacgtgtgtgctagccgattctttatctccttgtttacatggaatatggatgcagGTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTGCTCCGGCCTGGCCGTTTGGATCGAAAAATTGAAATTCCACTGCCTAATG
                           ||||||      | ||| | || || |  | |  |  ||    |   |    | ||    | |  | |  ||||| | ||  |  |  |  | |  | |   | || |||| || ||||||||||| || || || |||||||| ||||| |||||| | || || |||||  | |||||| ||||||| ||||| || ||||||||||
--------------------------tgtattc-----ttatggatattttgattttttctacaaa----tgactgctgaacaaaaatttaatggtggattcatgatgacactactgtc-tccatttctgctgtagGTTAAAATGATAATGGCAACAAACCGACCTGATGTACTTGACCCTGCTCTCCTGCGTCCTGGGAGATTGGATAGAAAAATAGAAATCCCTCTGCCTAATG

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|18338881|gb|BJ170907.1|BJ170907
EST:     CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAG                         GTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG
genomic: CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtactcttga ... atggatgcagGTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacgtgtgtgctagccgattctttatctccttgtttacatggaatatggatgcagGTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTGCTCCGGCCTGGCCGTTTGGATCGAAAAATTGAAATTCCACTGCCTAATG
                 attctttat  TA-rich tract