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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttgtagacagcttagtacttttctgtatgatataacatctgttgaactgcactttgtaatacgaagattatctgctttggaaacaatctcaattacttccagtttgatggacttgccagtgtcgtggtttccttagGTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATTGGATGCATGGTGAATGGAGCGGGGCTTGCAATGGCTACAATGGATATCA

Basic information

species Physcomitrella patens
transcript PP1S9_103V6.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S9_103V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 8
gtttgttgtagacagcttagtacttttctgtatgatataacatctgttgaactgcactttgtaatacga-agattatctgctttggaaacaatctcaattacttccagtttgatggacttgccagtgtcgtggtttccttagGTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATTGGATGCATGGTGAATGGAGCGGGGCTTGCAATGGCTACAATGGATATCA
                                      |  ||   ||||  |||   | |    | |  | |   | || | |    | |||   || |      | ||  |||   ||  |  |       || |   |||| |||||||  || |  ||| |||| ||||| ||  | ||||| |||||||| ||||||||||| || || ||  | ||||||||||||||||| ||||
-------------------------------------gaggatggcttgacttgcctctggagggatgttacagcttttgttgttctgagaatggaaactgaagatattt--atgagtttatctctaatacctttac---agGTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATTGGCTGCATGGTGAACGGTGCAGGATTGGCAATGGCTACAATGGACATCA

upper sequence: PP1S9_103V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 8
gtttgttgtagacagcttagtacttttctgtatgatataacatctgttgaactgcactttgtaatacgaagattatctgctttggaaacaatctcaattacttccagtttgatggacttgccagtgtcgtggtttcct---tagGTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATTGGATGCATGGTGAATGGAGCGGGGCTTGCAATGGCTACAATGGATATCA
                                      |  |||||||    ||  |||  | ||       |||| | |||    |||  |||   ||  | |   ||   |    |||   ||| | |   |   |    ||||  |||||| |||||  ||  | ||||| || || || ||||| |||||||| ||||||||||||||||| ||| | |||||||| ||||||||||| |
-------------------------------------catgatctgtt----tgtgcttgattattaagcccttatatcctt---gaaccttctttctttttactgtttgtgtaacattgtatgtgccttttatctttgaacagGTGACTGCTGCAAAGGCAGATTTAAATTATATTGGGTTAGATGGAGAAATTGGCTGCATGGTGAATGGAGCAGGGTTAGCAATGGCCACAATGGATATAA

upper sequence: PP1S9_103V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA13G18730.1 (Glycine max), 3'ss of exon 8
gtttgttgtagacagcttagtacttttctgtatgatataacatctgttgaactgcactttgtaatacgaagattatctgctttggaaacaatctcaattacttccagtttgatggact-tgccagtgtcgtgg-tttccttagGTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATTGGATGCATGGTGAATGGAGCGGGGCTTGCAATGGCTACAATGGATATCA
                                         |||||||    ||  |||  | ||       |||| | |||         | |   |||||    || ||    | | ||   |  |  |   |||    ||||  |||||| |||||  ||| | ||||| || || || ||||| ||||| || ||||||||||||||||| ||| | |||||||| ||||||||||| |
---------------------------------------ttatctgtt----tgtgcttgattattaagcccttatatccttgaatcttctttttttttactgggtgtgtgtaacattatgtgtgccttttaactttgaacagGTGACTGCTGCAAAGGCAGACTTAAATTATATTGGGTTAGATGGAGAAATAGGCTGCATGGTGAATGGAGCAGGGTTAGCAATGGCCACAATGGATATAA

upper sequence: PP1S9_103V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv07s0005g03790.t01 (Vitis vinifera), 3'ss of exon 8
--------gtttgttgtagacagcttagtacttttctgtatgatataacatctgttgaactgcactt---tgtaatacgaagattatctgctt-tggaaacaatctcaa---ttacttccagtttgatggact-tgccagtgtcgtggtttcctt-------agGTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATTGGATGCATGGTGAATGGAGCGGGGCTTGCAATGGCTACAATGGATATCA
          || || || |   |||    || || | | ||  ||   |  ||   |   |||| |     ||  |  |||   |||  | | |    ||||   |||     |  |  ||    ||      ||      | ||||||||  |       |||| |||||||  || |  ||  |||| ||||| || || ||||| |||||||| |||||||||||||| || ||  | ||||||||||| |||||||| |
gttgggttacttctttta-atttcttgaccctgttttatctgtgatg-taagtggaaagtagcacatgtacataccataaaggcaatccccctctcttcacaactacaaggtaaaactaaagaacaatatgtaatgttctatttgtggtttcactgtacaatagGTGGCTGCTGCCAAAGCAGATTTGAACTACATCGGCTTAGATGGAGAAATTGGTTGCATGGTGAATGGTGCTGGCTTAGCAATGGCTACCATGGATATAA

upper sequence: PP1S9_103V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: EFJ13492 (Selaginella moellendorffii), 3'ss of exon 8
gtttgttgtagacagcttagtacttttctgtatgatataacatctgttgaactgcactttgtaatacgaagattatctgctttggaaacaatctcaattacttccagtttgatggacttgccagtgtcgtggtttccttagGTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATTGGATGCATGGTGAATGGAGCGGGGCTTGCAATGGCTACAATGGATATCA
                                                                                 || || ||  | |  ||   |||  |||| |      |||| || |||          |||| |||||||     |  ||  |||| ||||| ||||||||||| || ||||| ||||||||||||||||| || || || ||||| || ||||||||||
--------------------------------------------------------------------------------gtttgagaccttgttcatagtttcacgttttaa-----tgcctgt-tcgaaaaac----agGTCGCTGCTGCTGCCGCCGATTTGAACTACATTGGATTGGATGGCGAGATTGGCTGCATGGTGAATGGAGCAGGACTCGCGATGGCAACCATGGATATCA

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|18338652|gb|BJ170676.1|BJ170676
EST:     AAAAGGAAATCTTTGCCATGCGAGACACAACACAGGAAGACCCTCGTGAG                         GTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATT
genomic: AAAAGGAAATCTTTGCCATGCGAGACACAACACAGGAAGACCCTCGTGAGgtttgttgta ... gtttccttagGTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATT
EST: gi|208365272|gb|DC946817.1|DC946817
EST:     AAAAGGAAATCTTTGCCATGCGAGACACAACACAGGAAGACCCTCGTGAG                         GTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATT
genomic: AAAAGGAAATCTTTGCCATGCGAGACACAACACAGGAAGACCCTCGTGAGgtttgttgta ... gtttccttagGTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATT
EST: gi|208352527|gb|DC918236.1|DC918236
EST:     AAAAGGAAATCTTTGCCATGCGAGACACAACACAGGAAGACCCTCGTGAG                         GTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATT
genomic: AAAAGGAAATCTTTGCCATGCGAGACACAACACAGGAAGACCCTCGTGAGgtttgttgta ... gtttccttagGTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATT
EST: gi|67724647|gb|BJ974906.1|BJ974906
EST:     AAAAGGAAATCTTTGCCATGCGAGACACAACACAGGAAGACCCTCGTGAG                         GTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATT
genomic: AAAAGGAAATCTTTGCCATGCGAGACACAACACAGGAAGACCCTCGTGAGgtttgttgta ... gtttccttagGTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATT
EST: gi|67727713|gb|BJ977972.1|BJ977972
EST:     AAAGGAAATCTTTTGCCATGCGAGACACAACACAGGAAGACCCTCGTGAG                         GTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATT
genomic: AAAGGAAATC-TTTGCCATGCGAGACACAACACAGGAAGACCCTCGTGAGgtttgttgta ... gtttccttagGTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATT
EST: gi|208397427|gb|DC916353.1|DC916353
EST:     AAAAGGAAATCTTTGCCATGCGAGACACAACACAGGAAGACCCTCGTGAG                         GTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGNTGAAATT
genomic: AAAAGGAAATCTTTGCCATGCGAGACACAACACAGGAAGACCCTCGTGAGgtttgttgta ... gtttccttagGTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATT
EST: gi|37829801|gb|BJ587813.1|BJ587813
EST:     AAAAGGAAATCTTTGCCATGCGAGACACAACACAGGAAGACCCTCGTGAG                         GTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATT
genomic: AAAAGGAAATCTTTGCCATGCGAGACACAACACAGGAAGACCCTCGTGAGgtttgttgta ... gtttccttagGTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacaatctcaattacttccagtttgatggacttgccagtgtcgtggtttccttagGTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATTGGATGCATGGTGAATGGAGCGGGGCTTGCAATGGCTACAATGGATATCA
                    gtttgat  putative branch site (score: 5)
                                              tttcctt  putative PPT
         aattactt  TA-rich tract