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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTGCAATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACCAGgtatacttgttccattgagccagccattggtttcctagatgctaaacccaccagacggtcagtcaccctttgattagcgtttagttggtgtggacaataa...

Basic information

species Zea mays
transcript GRMZM2G012501_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G012501_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g12590.1 (Oryza sativa), 5'ss of exon 6
AAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTGCAATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACCAGgtatacttgttccattgagccagccattggtttcctagatgctaaacccaccagacggtcagtcaccctttgattagcgtttagttggtgtggacaataa-----
||| |||||||| ||||||||||||||||||||||| ||||||||||| |||||||||  | ||||||| || ||||||||||| ||||||||||||||||| |   | ||   ||    |   || ||     ||| |   || ||  |    |  |  |     |   |  | | | |  || ||   | ||  ||||     
AAATCCAGAAATCGTGAAAAGATGGAGCAACGAAGTGCAGGAAGCTGTTCAATCAAGATTTGCACTTGTGCAATTTCATGGCCTAGCTCTTCTTCACCAGgtttg--tattttgtttcatcgatcaatgcccaactaaac-ttagactaatagcaaagcaaa--gacaggtattgaacatgaaggtgagatagattataatgcct

upper sequence: GRMZM2G012501_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA12G04820.1 (Glycine max), 5'ss of exon 6
AAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTGCAATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACCAGgtatact-tgttccattga--gccagccattg-gtttcctagatgctaaacccaccagacggtc--agtcaccctttgattagcgtttagttggtgtggacaataa--
||| || || ||||| ||||||||||| || || |||||||||||||| |||||||| ||  | ||||| || ||||||| ||| ||| | || || |||||||  |  ||| |||  |  |   |   |||   || || ||   ||     |||| | | ||  | |||    | | || ||   || ||  | || |  || |  
AAATCCCGAGATTGTAAAAAGATGGAGTAATGAGGTTCAGGAAGCTGTTCAATCAAGGGCAGCTCTTGTGCAATTTCATGCCCTGGCTTTGCTGCATCAGgtatgttgcgttgcatgaatggtttgatgttgtagtttcttgacaata---ttaccaaatgatccaaatcatgaatcgtttggc---taatt--tttgaatcatgaat

upper sequence: GRMZM2G012501_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA04G01470.1 (Glycine max), 5'ss of exon 6
AAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTGCAATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACCAGgtatacttgt----tccattgagccagccattggtttcctagatgctaaacccaccagacggtcagtcaccctttgattagcgtttagttggtgtggacaataa
||| || |||||||| |||||||||||||| || |||||||||||||| |||||||||||  | ||||| || |||||||  || | | | || || ||||||| |||      |   |||   | |     |||||      |  |||| |  |   |   |  |||| | ||  |    | ||||||  || |  |   |  
AAATCCTGAAATTGTAAAAAGATGGAGCAATGAGGTTCAGGAAGCTGTTCAATCAAGAGCAGCCCTTGTACAATTTCATGCACTGGGTTTGCTGCATCAGgtatgcttccaaaattatttggttctgtacagggtttttggtgtattaaagcacctcaaaactttgtcatcattctagggtcatttagt--gtatcaaagtt--

upper sequence: GRMZM2G012501_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA06G01520.1 (Glycine max), 5'ss of exon 6
AAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTGCAATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACCAGgtatacttgtt---ccattgagccagccattggtttcctag-atgctaaacccaccagacggtcagtcaccctttgattagcgtttagttggtgtggacaataa
 || || |||||||| |||||||||||||| ||||||||||||||||| |||||||||||  | ||||| || |||||||  || | | | || || ||||||| |||        |||  ||     |  || ||  | |  |  |||| |  |   |   |  |||  | ||  |    | |||||   || |  | | |  
GAATCCTGAAATTGTAAAAAGATGGAGCAATGAAGTTCAGGAAGCTGTTCAATCAAGAGCAGCCCTTGTACAATTTCATGCACTGGGTTTGCTACATCAGgtatgcttccaaaattatttggctctgtacagggtttttggtgtattaaagcacctcaaaacttggtcttcattctagggtcatttag--agtatcaa-agtg-

upper sequence: GRMZM2G012501_T01 (Zea mays), 5'ss of exon 6
lower sequence: AT4G34450.1 (Arabidopsis thaliana), 5'ss of exon 5
AAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTGCAATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACCAGgtatacttgttccattgagccagccattggtttcctagatgctaaacccaccagacggtcagtcaccctttgattagcgtttagttggtgtggacaataa--
||||||||||||||| |||||||||||||| |||||||| |||| | | ||||| ||| |  | ||||| ||||| |||| ||| ||| | || || |||||    ||||| ||||       ||    ||    | |    |    | ||     | | | | |  |    | | | |   |  |     ||| ||| |  
AAACCCAGAAATTGTTAAAAGATGGAGCAATGAAGTTCAAGAAGGTATTCAATCCAGATCAGCCCTTGTTCAGTTCCATGCCCTAGCTTTGCTCCATCAGgttagtttgttgcattattatcaccga-agtcgattggtctatgtttctactctttgtttaattaaacagccact-gagaagaagtatctcggaaaatgaga

upper sequence: GRMZM2G012501_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv03s0063g02450.t01 (Vitis vinifera), 5'ss of exon 6
AAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTGCAATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACCAGgtatacttgttccattgagccagccattggtttcctagatgctaaacccaccagacggtcagtcaccctttgattagcgtttagttggtgtggacaataa-
||||||||| || |||| ||| ||||| || ||||| ||||||||||| |||||||| ||  ||||||| || ||||||| ||| ||||| || || |||||||  | | |   |||   |     ||   ||   |      | ||  |  ||   || ||  |     |   | |   ||  | |  ||  |   |   
AAACCCAGAGATAGTGAGAAGGTGGAGTAATGAAGTACAGGAAGCTGTTCAATCAAGGGCAGCACTTGTGCAATTTCATGCCCTAGCTCTCCTGCATCAGgtatgttggattttttggttccatgtttaagtttaaattcagaatacagagtagcttgttagaaagatagttcct-gaacttcatagaggtaaaattttgc

upper sequence: GRMZM2G012501_T01 (Zea mays), 5'ss of exon 6
lower sequence: PP1S276_96V6.1 (Physcomitrella patens), 5'ss of exon 6
AAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTGCAATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACCAGgtatacttgttccattgagccagccattggtttcctagatgctaaacccaccagacggtcagtcaccctttgattagcgtttagttggtgtggacaataa---------
 ||||| |||||||||||  | |||||||| ||||||||||||||||| || || | ||| || || || ||||| || ||  | ||  | ||||| ||||| |  ||   ||| |   ||  || ||  ||  ||   |||| || |  ||     |  | | ||||| ||| |      |     |  |  |    |          
CAACCCCGAAATTGTGAAGCGCTGGAGCAATGAAGTTCAGGAAGCTGTCCAGTCTAAAGCACCTCTCGTTCAGTTCCACGGTTTGGCATTGCTTCATCAGgtttcttttaaccact---ccgtccttt--ttctct---tgctgaatcatccttgaagg-atttaccctgtgaatgatacatgagaagactctatggcatgtttatgag

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|211106006|gb|FK992441.1|FK992441
EST:     AATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACCAG                         ATTAGACAGAATGATCGTTTAGCTGTAAGCAAACTAGTTTCAAGTTTGACA
genomic: AATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACCAGgtatacttgt ... caacttgcagATTAGACAGAATGATCGTTTAGCTGTAAGCAAACTAGTTTCAAGTTTGACA
EST: gi|148973647|gb|EE024760.2|EE024760
EST:     AATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACCAG                         ATTAGACAGAATGATCGTTTAGCTGTAAGCAAACTAGTTTCAAGTTTGACA
genomic: AATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACCAGgtatacttgt ... caacttgcagATTAGACAGAATGATCGTTTAGCTGTAAGCAAACTAGTTTCAAGTTTGACA
EST: gi|76917670|gb|DV166948.1|DV166948
EST:     AATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACCAG                         ATTAGACAGAATGATCGTTTAGCTGTAAAGCAA-CTAGTTTCAAGTTTGAC
genomic: AATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACCAGgtatacttgt ... caacttgcagATTAGACAGAATGATCGTTTAGCTGTAA-GCAAACTAGTTTCAAGTTTGAC
EST: gi|211106005|gb|FK992440.1|FK992440
EST:     AATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACCAG                         ATTAGACAGAATGATCGTTTAGCTGTAAGCAAACTAGTTTCAAGTTTGACA
genomic: AATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACCAGgtatacttgt ... caacttgcagATTAGACAGAATGATCGTTTAGCTGTAAGCAAACTAGTTTCAAGTTTGACA
EST: gi|67016076|gb|CO444825.1|CO444825
EST:     AATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACCAG                         ATTAGACAGAATGATCGTTTAGCTGTAAGCAAACTAGTTTCAAGTTTGACA
genomic: AATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACCAGgtatacttgt ... caacttgcagATTAGACAGAATGATCGTTTAGCTGTAAGCAAACTAGTTTCAAGTTTGACA
EST: gi|148970762|gb|EE021504.2|EE021504
EST:     AATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACCAG                         ATTAGACAGAATGATCGTTTAGCTGTAAGCAAACTAGTTTCAAGTTTGACA
genomic: AATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACCAGgtatacttgt ... caacttgcagATTAGACAGAATGATCGTTTAGCTGTAAGCAAACTAGTTTCAAGTTTGACA
EST: gi|148967121|gb|EE018293.2|EE018293
EST:     AATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACCAG                         ATTAGACAGAATGATCGTTTAGCTGTAAGCAAACTAGTTTCAAGTTTGACA
genomic: AATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACCAGgtatacttgt ... caacttgcagATTAGACAGAATGATCGTTTAGCTGTAAGCAAACTAGTTTCAAGTTTGACA
EST: gi|148946070|gb|EC891366.2|EC891366
EST:     AATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACCAG                         ATTAGACAGAATGATCGTTTAGCTGTAAGCAAACTAGTTTCAAGTTTGACA
genomic: AATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACCAGgtatacttgt ... caacttgcagATTAGACAGAATGATCGTTTAGCTGTAAGCAAACTAGTTTCAAGTTTGACA

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTGCAATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACCAGgtatacttgttccattgagccagccattggtttcctagatgctaaacccaccagacggtcagtcaccctttgattagcgtttagttggtgtggacaataa

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT