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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCGGGGTCTAAAGAAGCATTTGAAGCGACTGAATGCCCCTAGGCATTGGATGCTCGACAAGTTGGGTGGTGCATTCgtaagttttgcattatgaccaatctcttcgtcttgttgtttcccacttttctgactgttaaaatgggtgcatcagaaacctcaccagaattatggttttcattggcatgggaattagatgatgtattggtttgaatgtgacacccttcaaagggagaataccgtcaccacattgatccaggaattatatcatgattctag

Basic information

species Physcomitrella patens
transcript PP1S39_422V6.3
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S39_422V6.3 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os05g30530.1 (Oryza sativa), 5'ss of exon 2
GCTCGGGGTCTAAAGAAGCATTTGAAGCGACTGAATGCCCCTAGGCATTGGATGCTCGACAAGTTGGGTGGTGCATTCgtaagt--tttgcattatgaccaatctcttcgtcttgttgtttcccacttttctgactgttaaaatgggtgcatcagaaacctcaccagaattatggttttcattggcatgggaattagatgatgtattggtttgaatgtgacacccttcaaagggagaataccgtcaccacattgatccaggaattatatcatgattctag
||  ||||| | ||||||||| ||||| | || |||||||| || ||||||||||| |||||| | ||||| ||||| ||||||   ||| ||     | | |    ||     |||      || | |    | || |||  | | ||  |   |||    |   | |  ||| ||| |                                                                                                    
GCGAGGGGTTTGAAGAAGCATCTGAAGAGGCTCAATGCCCCCAGCCATTGGATGCTTGACAAGCTTGGTGGAGCATTTgtaagtacattgtatagccgcaagttatatcacgcagttcaaatgcattctgtataatgctaatgtag-tgtttggcaaatgggaaagggaa-atgatttcc----------------------------------------------------------------------------------------------------

upper sequence: PP1S39_422V6.3 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os02g01560.1 (Oryza sativa), 5'ss of exon 2
GCTCGGGGTCTAAAGAAGCATTTGAAGCGACTGAATGCCCCTAGGCATTGGATGCTCGACAAGTTGGGTGGTGCATTCgtaagttttgcattatgaccaatctcttcgtcttgttgtttcccacttttctgactgttaaaatgggtgcatcagaaacctcaccagaattatggttttcattggcatgggaattagatgatgtattggtttgaatgtgacacccttcaaagggagaataccgtcaccacattgatccaggaattatatcatgattctag
||  ||||| | ||||||||| ||||| | || ||||| || | ||||||||||||||||||| | ||||| || || ||||||||  |||| |     |    |   |     || ||    ||| |||   | ||    |  ||  | | || | || |      | ||    ||  ||  ||| |                                                                                          
GCAAGGGGTTTGAAGAAGCATCTGAAGAGGCTCAATGCGCCCAAGCATTGGATGCTCGACAAGCTTGGTGGAGCTTTTgtaagtttgtcattcttgtttacacttaactacacatgcttgaagcttatcttttttttt---tctgt-tacctgatagcttatatttctaattacctt--ttaccatag------------------------------------------------------------------------------------------

upper sequence: PP1S39_422V6.3 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G125271_T01 (Zea mays), 5'ss of exon 2
GCTCGGGGTCTAAAGAAGCATTTGAAGCGACTGAATGCCCCTAGGCATTGGATGCTCGACAAGTTGGGTGGTGCATTCgtaagttttgcattatgaccaatctcttcgtcttgttgttt--cccacttttctgactgttaaaatgggtgcatcagaaacctcaccagaattatggttttcattggcatgggaattagatgatgtattggtttgaatgtgacacccttcaaagggagaataccgtcaccacattgatccaggaattatatcatgattctag
||| | ||  | ||||||||||||||| | || |||||||| | |||||||||||| |||||| | || || || || ||||||   | | | |      ||| |   | || || | |   ||| || ||| |   ||    | |||   | |   |                                                                                                                          
GCTAGAGGATTGAAGAAGCATTTGAAGAGGCTCAATGCCCCCAAGCATTGGATGCTGGACAAGCTTGGCGGAGCTTTTgtaagtaaagaaattttgtagctctgtcactttttttttctactccatttgtctaatgtttctgtttggtcttttatgtag-------------------------------------------------------------------------------------------------------------------------

upper sequence: PP1S39_422V6.3 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA02G05370.1 (Glycine max), 5'ss of exon 2
GCTCGGGGTCTAAAGAAGCATTTGAAGCGACTGAATGCCCCTAGGCATTGGATGCTCGACAAGTTGGGTGGTGCATTCgtaagttttgcattatgaccaatctcttcgtcttgttgtttcccacttttctgactgttaaa-atgggtgcatcagaaacctcaccagaattatggttttcattggcatgggaattagatgatgtattggtttgaatgtgacacccttcaaagggagaataccgtcaccacattgatccaggaattatatcatgattctag
||  | ||  | ||||||||||||||| | || |||||||| | |||||||||||| |||||  ||||||||||||| ||||||   | |   ||    |||| ||   |  ||| |          | | | | | ||| |  | |  ||      |||    ||                                                                                                                 
GCGAGAGGATTGAAGAAGCATTTGAAGAGGCTTAATGCCCCAAAGCATTGGATGCTTGACAAACTGGGTGGTGCATTTgtaagt---gaaagttgctttatctttttaaca-gttttcaggtgtgcatttcattttaaaagactgatatatatttttcctgtttag-----------------------------------------------------------------------------------------------------------------

upper sequence: PP1S39_422V6.3 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA14G06170.1 (Glycine max), 5'ss of exon 2
GCTCGGGGTCTAAAGAAGCATTTGAAGCGACTGAATGCCCCTAGGCATTGGATGCTCGACAAGTTGGGTGGTGCATTCgtaagttttgcattatgaccaatctcttcgtcttgttgtttcccacttttctgactgttaaaatgggtgcatcagaaacctcaccagaattatggttttcattggcatgggaattagatgatgtattggtttgaatgtgacacccttcaaagggagaataccgtcaccacattgatccaggaattatatcatgattctag
||| |||| |||||||||||||||||  | || ||||| |||| |||||||||||| |||||  ||||||||||||| ||||||     | | | | || | | |      | |||      | | || |||    | |  ||    | |    | |||    ||                                                                                                                 
GCTAGGGGACTAAAGAAGCATTTGAAAAGGCTCAATGCTCCTAAGCATTGGATGCTTGACAAACTGGGTGGTGCATTTgtaagtg--aaaatttaatcattttgtaaccagttttgaagggtattattttgaagactgatgtgaac-ctttttcatcctgtatag-----------------------------------------------------------------------------------------------------------------

upper sequence: PP1S39_422V6.3 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA16G23730.1 (Glycine max), 5'ss of exon 2
GCTCGGGGTCTAAAGAAGCATTTGAAGCGACTGAATGCCCCTAGGCATTGGATGCTCGACAAGTTGGGTGGTGCATTCgtaagttttgcattatgaccaatctcttcgtcttgttgtttcccacttttctgactgttaaaatgggtgcatcagaaacctcaccagaattatggttttcattggcatgggaattagatgatgtattggtttgaatgtgacacccttcaaagggagaataccgtcaccacattgatccaggaattatatcatgattctag
||  | ||  ||||||||||| ||||| | || |||||||| | |||||||||||| |||||  ||||||||||||| ||||||              ||| ||||  ||||             ||    | | || ||    |    ||| | |  |     || || |  || |  ||                                                                                                 
GCGAGAGGATTAAAGAAGCATCTGAAGAGGCTTAATGCCCCAAAGCATTGGATGCTTGACAAACTGGGTGGTGCATTTgtaagt-----------gaaaatttctttatctt-------------ttgaaaagttttcaaggatgcatttcaaagatttatgtggacttttttttcttgtttag----------------------------------------------------------------------------------------------

upper sequence: PP1S39_422V6.3 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA02G43080.2 (Glycine max), 5'ss of exon 2
GCTCGGGGTCTAAAGAAGCATTTGAAGCGACTGAATGCCCCTAGGCATTGGATGCTCGACAAGTTGGGTGGTGCATTCgtaagttttgcattatgaccaatctcttcgtcttgttgtttcccacttttctgactgttaaaatgggtgcatcagaaacctcaccagaattatggttttcattggcatgggaattagatgatgtattggtttgaatgtgacacccttcaaagggagaataccgtcaccacattgatccaggaattatatcatgattctag
||| ||||  | ||||||||| | ||| | || ||||| |||| |||||||||||| |||||  ||||||||||||| ||||||     | | | | || |||        | |||      | | || | |    | |  ||    |||    | |||   |||                                                                                                                 
GCTAGGGGATTGAAGAAGCATCTCAAGAGGCTCAATGCTCCTAAGCATTGGATGCTTGACAAACTGGGTGGTGCATTTgtaagtg--aaactttcatcattcttggtccagttttgaagtgtattattttaaagactgatgtgaa-acattttcatcctgtacag-----------------------------------------------------------------------------------------------------------------

upper sequence: PP1S39_422V6.3 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv08s0058g00390.t01 (Vitis vinifera), 5'ss of exon 3
GCTCGGGGTCTAAAGAAGCATTTGAAGCGACTGAATGCCCCTAGGCATTGGATGCTCGACAAGTTGGGTGGTGCATTCgtaagttt-tgcattatgaccaatctcttcgtcttgttg--tttcccacttttctgactgttaaaatgggtgcatcagaaacctcaccagaattatggttttcattggcatgggaattagatgatgtattggtttgaatgtgacacccttcaaagggagaataccgtcaccacattgatccaggaattatatcatgattctag
||| | ||  | ||||| ||||||||| | || |||||||||| |||||||||||| |||||| | || |||||||| ||||||   || |  || |  || |     | ||  |||  ||||| |   |  |  |   | |  | | || |   |     | |       |||  ||||  | ||    |                                                                                          
GCTAGAGGGTTGAAGAAACATTTGAAGAGGCTCAATGCCCCTAAGCATTGGATGCTTGACAAGCTTGGAGGTGCATTTgtaagtcaatgaaaaataataaaccatgaagcctgattggttttcctatgctgttttcctgttatctagttgta---gtgtttttattttt-ctattattttt-tgggtgcag------------------------------------------------------------------------------------------

upper sequence: PP1S39_422V6.3 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv13s0067g01820.t01 (Vitis vinifera), 5'ss of exon 1
GCTCGGGGTCTAAAGAAGCATTTGAAGCGACTGAATGCCCCTAGGCATTGGATGCTCGACAAGTTGGGTGGTGCATTCgtaagttttgcattatgaccaatctcttcgtcttgttgtttcccacttttctgactgttaaaatgggtgcatcagaaacctcaccagaattatggttttcattggcatgggaattagatgatgtattggtttgaatgtgacacccttcaaagggagaataccgtcaccacattgatccaggaattatatcatgattctag
      ||  | ||||||||||||||| | || ||||| || | |||||||||||| |||||| | || |||||||| ||||||     ||     ||    || |  | || |     | || ||  |  ||  |||       | ||  |  |       |  |   ||  |  | ||| | || |                                                                                          
-----AGGGTTGAAGAAGCATTTGAAGAGGCTCAATGCACCGAAGCATTGGATGCTAGACAAGCTTGGAGGTGCATTTgtaagtcaaaaatctgttcctgattcatatttttctatcgactcatttcac--acccttatctcacatccaaaatcattgatggctcatccataatcct-atttgtatag------------------------------------------------------------------------------------------

upper sequence: PP1S39_422V6.3 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv06s0004g07150.t01 (Vitis vinifera), 5'ss of exon 2
GCTCGGGGTCTAAAGAAGCATTTGAAGCGACTGAATGCCCCTAGGCATTGGATGCTCGACAAGTTGGGTGGTGCATTCgtaagttttgcattatgaccaatctcttcgtcttgttgtttcccacttttctgactgttaaaatgg-gtgcatcagaaacctcaccagaat-tatggttttcattggcatgggaattagatgatgtattggtttgaatgtgacacccttcaaagggagaataccgtcaccacattgatccaggaattatatcatgattctag
|| || ||  ||||||| ||||||||| | || |||||||| | |||||||||||| |||||  | || |||||||| ||||||  |           || || |||    ||| ||||||     ||   | ||||| |     | |  | |    | |  |   ||| | |  |  ||  |   |  |                                                                                          
GCACGAGGGTTAAAGAAACATTTGAAGAGGCTTAATGCCCCAAAGCATTGGATGCTTGACAAACTTGGGGGTGCATTTgtaagtgat-----------aagcttttctcagtgt-gtttccattacttaataatgttagaccctcgggttttacttgctttgctttaatgtcttataatctgtcatacag------------------------------------------------------------------------------------------

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|67704660|gb|BJ964893.1|BJ964893
EST:     GACTGAATGCCCCTAGGCATTGGATGCTCGACAAGTTGGGTGGTGCATTC                         GTGTAGATTACCTTGGAGTTTGGTTTACGAGCCAGATGTAAGATGCAGGCA
genomic: GACTGAATGCCCCTAGGCATTGGATGCTCGACAAGTTGGGTGGTGCATTCgtaagttttg ... atgattctagGTGTAGATTACCTTGGAGTTTGGTTTACGAGCCAGATGTAAGATGCAGGCA