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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgctatttcccgattattttataaatgttttagttttatgttcagtgggaacccctgtgtcactaacaatgatacattgcctctgatgtcgatttgcagCTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGGCGCCAGTTGCGAAAGCGGTAGAGGTTTCTGAACCCAAGACGCGCAGGAA

Basic information

species Physcomitrella patens
transcript PP1S97_78V6.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S97_78V6.3 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os09g08430.1 (Oryza sativa), 3'ss of exon 5
gtgctatttcccgattattttataaatgttttagttttatgttcagtgggaacccctgtgtcactaacaatgatacattgcctctgatgtcgatttgcagCTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGGCGCCAGTTGCGAAAGCGGTAGAGGTTTCTGAACCCAAGACGCGCAGGAA
              | | ||| | |||   ||  || |||| ||  ||   |   | |||   ||     ||   |||   |    |||    |||||||||||||||||||| || |||||||||||||| || || || |||||||| |  |||||   ||||| |                                
-------------gtaagtttgtcaataccttt-ttgtatgctctttgtagagttcggtgatgctt----tgtctcatgagca--aatgatactttgcagCTTACATGTCCTCCCCGTGCCACATTGAGCTTATCCTGTCAGAGAAGGAAGAACCAGTGAAGAAAGAG--------------------------------

upper sequence: PP1S97_78V6.3 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G702426_T01 (Zea mays), 3'ss of exon 5
gtgctatttcccgattattttataaatgttttagttttatgttcagtgggaacccctgtgtcactaac-aatgatacattgcctctgatgtcgatttgcagCTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGGCGCCAGTTGCGAAAGCGGTAGAGGTTTCTGAACCCAAGACGCGCAGGAA
                      ||  | |   ||  |  | ||   |       | || | ||||    |||| || |||     || ||  | | |||||||||||||||||| || |||||||||||||| ||||| || |||||||| | ||| ||   ||||| |                                
---------------------gtatgtatcgaaggatggtctttcat------tcttgcgacactgttgaatggtatatt--taatgttgctgttctgcagCTTACATGTCCTCCCCTTGCCACATTGAGCTGATTCTGTCAGAGAAGGAAGAGCCTGTGAAGAAAGAG--------------------------------

upper sequence: PP1S97_78V6.3 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G126594_T02 (Zea mays), 3'ss of exon 5
gtgctatttcccgattattttataaatgttttagttttatgttcagtgggaacccctgtgtcactaacaatgatacattgcctctgatgtcgatttgcagCTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGGCGCCAGTTGCGAAAGCGGTAGAGGTTTCTGAACCCAAGACGCGCAGGAA
            |  ||| | |  || |||  ||||||  | |  | |   | |  |   ||| |   |     |||||   | ||    |    | |||||||||||||||| || |||||||| ||||||||  | || |||||||| |  |||||   ||||| |                                
--------gtaagtctatctaactaaagttgaagtttt--gctatgcgatgaactgttcttcatttggagcttaacattctgtttgcctacctggtccagCTTACATGTCCTCCCCATGCCACATAGAGCTCATCTTGTCGGAGAAGGAAGAACCAGTGAAGAAAGAG--------------------------------

upper sequence: PP1S97_78V6.3 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA18G01110.1 (Glycine max), 3'ss of exon 5
gtgctatttcccgattattttataaatgtt-ttagttttatgttcagtgggaacccc-tgtgtcactaacaatga--tacattgcctctgatgtcgatttgcagCTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGGCGCCAGTTGCGAAAGCGGTAGAGGTTTCTGAACCCAAGACGCGCAGGAA
                         ||||   | ||||| |    |      ||    ||  | ||||  | | |  ||  |||    ||   |   ||||||||||||||||| ||||| |||||||||||||| ||  | ||||||||||| | ||| ||   ||| | |                                
-----------------------gtatgtcgctggttttgttgctatcactgacttaatggattactattacttacttatgttgagagtgtcttttttttgcagCTTACATGTCATCTCCATGCCACATTGAGCTGATATTATCTGAGAAGGAAGAGCCGGTGAAGAAGGAG--------------------------------

upper sequence: PP1S97_78V6.3 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA11G37160.1 (Glycine max), 3'ss of exon 5
gtgctatttcccgattattttataaatgttttagttttatgttcagtgggaacccctgtgtcactaacaatgatacattgcctctgatgtcgatttgcagCTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGGCGCCAGTTGCGAAAGCGGTAGAGGTTTCTGAACCCAAGACGCGCAGGAA
      | |  |  | ||||| |  || || | |  |||     |  |   ||   |   |  ||     ||| | | | | | |  |      |||||||||||||||| ||||| |||||||||||||| ||  | ||||||||||| | ||| ||   ||||| |                                
-----gtatgtcactgattttgttgatattgtcgactta-----atggactactattacat-gcttttgttgagagagtccttttttt------ttgcagCTTACATGTCATCTCCATGCCACATTGAGCTGATATTGTCTGAGAAGGAAGAGCCTGTGAAGAAAGAG--------------------------------

upper sequence: PP1S97_78V6.3 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ26852 (Selaginella moellendorffii), 3'ss of exon 4
gtgctatttcccgattattttataaatgttttagttttatgttcagtgggaacccctgtgtcactaacaatgatacattgcctctgatgt-cgatttgcagCTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGGCGCCAGTTGCGAAAGCGGTA---GAGGTTTCTGAACCCAAGACGCGCAGGAA
                                          | |||||  |   || |  | ||     | | |   |  |   | | |  | || |||||||||||||||||||| |||||||| ||  | || || || ||| |    || |||||   |    |  ||   ||    |||  | |       || ||   
-----------------------------------------gtaagtggtgaattctattcctctttggcttagaggcttacatcgttttgtgcttggcagCTTACATGTCCTCTCCTTGCCACATCGAAGTGATCCTCTCAGAGCACATCGCTCCAGTCAAGGTGACACTACTCGAAACCTCTCGAGCTTTTCTTCGTAG---

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|67695151|gb|BJ955384.1|BJ955384
EST:     GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACC                         CTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
genomic: GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACCgtaagttggc ... cgatttgcagCTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
EST: gi|67696181|gb|BJ956414.1|BJ956414
EST:     GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACC                         CTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
genomic: GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACCgtaagttggc ... cgatttgcagCTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
EST: gi|162259989|gb|FC435292.1|FC435292
EST:     GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACC                         CTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
genomic: GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACCgtaagttggc ... cgatttgcagCTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
EST: gi|67701215|gb|BJ961448.1|BJ961448
EST:     GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACC                         CTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
genomic: GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACCgtaagttggc ... cgatttgcagCTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
EST: gi|67704010|gb|BJ964243.1|BJ964243
EST:     GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACC                         CTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
genomic: GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACCgtaagttggc ... cgatttgcagCTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
EST: gi|67696219|gb|BJ956452.1|BJ956452
EST:     GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACC                         CTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
genomic: GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACCgtaagttggc ... cgatttgcagCTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
EST: gi|162276588|gb|FC451971.1|FC451971
EST:     GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACC                         CTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
genomic: GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACCgtaagttggc ... cgatttgcagCTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
EST: gi|67701414|gb|BJ961647.1|BJ961647
EST:     GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACC                         CTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
genomic: GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACCgtaagttggc ... cgatttgcagCTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
EST: gi|162252890|gb|FC429263.1|FC429263
EST:     GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACC                         CTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
genomic: GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACCgtaagttggc ... cgatttgcagCTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
EST: gi|162259990|gb|FC435293.1|FC435293
EST:     GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACC                         CTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
genomic: GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACCgtaagttggc ... cgatttgcagCTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgggaacccctgtgtcactaacaatgatacattgcctctgatgtcgatttgcagCTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGGCGCCAGTTGCGAAAGCGGTAGAGGTTTCTGAACCCAAGACGCGCAGGAA
                   taacaat  TA-rich tract