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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAAATATTTGAAGGGCATTCTCACTATGTGATGCAAGTTACATTTAACCCAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAGgtttgtgttatctccgctttaaaaattctggttggccacaatgttgcattatttggtaccgacaggcgacagctttttcatagcttgatggtgatatcctattttttgtcaatatcag

Basic information

species Zea mays
transcript GRMZM2G124886_T03
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124886_T04 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 6
TCAAATATTTGAAGGGCATTCTCACTATGTGATGCAAGTTACATTTAACCCAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAGgtttgtgttatctccgctttaaaaattctggttggccacaatgttgcattatttggtaccgacaggcgacagctttttcatagcttgatggtgatatcctattttttgtcaatatcag
|||||| || || ||||||||||||||||| |||||||| ||||||||||| |||||||| || || |||||||||||||| || ||||||||| |||||||||| | | | |   | ||| |   | || |||||     | ||||||| | |   |              |||  ||     ||||  ||| |  |||  |||     ||| ||||
TCAAATCTTCGAGGGGCATTCTCACTATGTTATGCAAGTCACATTTAACCCGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAGgtttgcgat-tttgttccttaca---tttgcttggcatagtttttgcatt-tctaacattt-----------cttggtctggatttgaatgtggtgcccttattt-----aatttcag

upper sequence: GRMZM2G124886_T04 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA07G03890.1 (Glycine max), 5'ss of exon 6
TCAAATATTTGAAGGGCATTCTCACTATGTGATGCAAGTTACATTTAACCCAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAGgtttgtgttatctccgctttaaaaattctggttggccacaatgttgcattatttggtaccgacaggcgacagctttttcatagcttgatggtgatatcctattttttgtcaatatcag
 || |||||||| || |||||||| ||||| |||||||| |||||||| || ||||| |||||||||||||| ||||| || || |||||||| |||||||| |   |  | | |   ||   | || ||    || |   | ||   ||||||   | | ||    || |    ||  | ||     |  | || |  | |||| |  ||       
CCAGATATTTGAGGGACATTCTCATTATGTCATGCAAGTGACATTTAATCCTAAAGACACAAACACCTTTGCCAGTGCATCTCTTGATCGCACCATAAAGgtatacat-gtgttcttcttgctagttgtgtcctgc-attttctttgtttatttccaaac-acctatgataaaaattaaaaagtaatgtattaatgttatcttttcttgcag------

upper sequence: GRMZM2G124886_T04 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 6
TCAAATATTTGAAGGGCATTCTCACTATGTGATGCAAGTTACATTTAACCCAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAGgtttgtgttatctccgctttaaaaattctggttggccacaatgttgcattatttggtaccgacaggcgacagctttttcatagcttgatggtgatatcctattttttgtcaatatcag
 || ||||||||||| |||||||| ||||| |||||||| |||||||| || ||||| |||||||||||||||||||| || || ||||| |||||||||||  |  |||| | |   ||       |||||||    | ||| |  | |   |     |  | |  | |  || |||   ||                                   
CCAGATATTTGAAGGCCATTCTCATTATGTCATGCAAGTAACATTTAATCCCAAAGACACAAACACCTTTGCTAGTGCATCTCTTGATCGGACAATAAAGgta-gaattatgttcttgtt------cctggttgtttcctatgatataatgcattaatgcacctgttgtcttctctttt-cag-----------------------------------

upper sequence: GRMZM2G124886_T04 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 6
TCAAATATTTGAAGGGCATTCTCACTATGTGATGCAAGTTACATTTAACCCAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAGgtttgtgttatctccgctttaaaaattctggttggccacaatgttgcattatttggtaccgacaggcgacagctttttcatagcttgatggtgatatc-ctattttttgtcaatatcag
 || ||||||||||| |||||||| ||||| |||||||| |||||||| || ||||| |||||||||||||| ||||| || || ||||| ||||||||||| |   |    ||   ||     ||  |  ||    | ||      |  | |    |  || |  | |      | | |||   ||    ||||    || || |       | ||||
CCAGATATTTGAAGGTCATTCTCATTATGTCATGCAAGTAACATTTAATCCCAAAGACACAAACACCTTTGCAAGTGCATCTCTTGATCGGACAATAAAGgtgtaattatgttcttgttcctggatgtttcttttttaaaaaaaaaaaaaagtaaaaa--gaaaaactatgatcctatgatataatg-cattgatgcaactgttatcatctcttttcag

upper sequence: GRMZM2G124886_T04 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 6
TCAAATATTTGAAGGGCATTCTCACTATGTGATGCAAGTTACATTTAACCCAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAGgtttgtgt-tatctccgctttaaaaattctggttggccacaatgttgcattatttggtaccgacaggcgacagctttttcatagcttgatggtgatatcctattttt--tgtcaatatcag
 || |||||||| || |||||||| ||||| |||||||| |||||||| || ||||| |||||||||||||| ||||| || || |||||||| |||||||| | |   | | | |   |    | || ||      |   |  || | || |||  | ||      | |        | | |  || |  || || |  || | ||    |||||  |||
CCAGATATTTGAGGGACATTCTCATTATGTCATGCAAGTGACATTTAATCCTAAAGACACAAACACCTTTGCCAGTGCATCTCTTGATCGCACCATAAAGgtatatacatgtgttcttctcgctagttgtg-----tcctgaattttctttgtttatttccatacatctatga-----taaaaatttaaaagtaatgtattaatgttatcttcaattgcag

upper sequence: GRMZM2G124886_T04 (Zea mays), 5'ss of exon 6
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 5'ss of exon 6
TCAAATATTTGAAGGGCATTCTCACTATGTGATGCAAGTTACATTTAACCCAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAGgt-ttgtgttatctccgctttaaaa----attctggtt--ggccacaatgttgcattatttggtaccgacaggcgacagctttttcatagcttgatggtgatatcctattttttgtcaatatcag
||| ||||| || || || || ||||||||||||||||| |||||||| |||||||| || ||||| ||||| ||||| ||||| ||||| || ||||||||  ||   |       | || |||    ||| |||||  | || |   ||    | |||        ||| ||     | | ||||                                      
TCAGATATTCGAGGGACACTCACACTATGTGATGCAAGTCACATTTAATCCAAAAGACACCAACACTTTTGCCAGTGCATCCCTTGATCGTACCATAAAGgtgctgaaatggtctaacattgaaacatcattatggtttagtccgcttagtccgctcattctacgtttacatgcatgttcatcttcag-------------------------------------

upper sequence: GRMZM2G124886_T04 (Zea mays), 5'ss of exon 6
lower sequence: AT3G15980.3 (Arabidopsis thaliana), 5'ss of exon 6
TCAAATATTTGAAGGGCATTCTCACTATGTGATGCAAGTTACATTTAACCCAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAGgtttgtgttatctccgctttaaaaattctggttggccacaatgttgcattatttggtaccgacaggcgacagctttttcatagcttgatggtgatatcctattttttgtcaatatcag
||| |||||||| || ||||| |||||||||||||||||   |||||| ||||||||||| ||||| ||||| |||||||| || ||||| || |||||||| |||   |  |||        |  | |  | |   |    |||  |  |   |||||    |    | ||  ||||| |||  | ||  | ||  | | ||  |  |||       
TCAGATATTTGAGGGACATTCGCACTATGTGATGCAAGTGGTATTTAATCCAAAAGATACCAACACTTTTGCCAGTGCTTCGCTTGATCGTACCATAAAGgtgtgtaagaggtccaagcactgagcttttatggctta----gtt--agcacgaggtactttta----aaagggttttcttagactaattttcatg-cttgttcatattcag------

upper sequence: GRMZM2G124886_T04 (Zea mays), 5'ss of exon 6
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 6
TCAAATATTTGAAGGGCATTCTCACTATGTGATGCAAGTTACATTTAACCCAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAGgtttgtgttatctccgctttaaaaattctggttggccacaatgttgcatta-tttggtaccgacaggcgacagctttttcatagcttgatggtgatatcctattttttgtcaatatcag
||| || ||||| || || ||||| |||||||||||||| |||||||| ||||||||||| ||||| ||||||||||| || ||||||||||| || ||||| ||   |   |   || |    |   || ||  |  || | ||  |  | ||| |   |  || |    ||  |  |  |       || |||||||   ||||             
TCAGATCTTTGAGGGCCACTCTCATTATGTGATGCAAGTGACATTTAATCCAAAAGATACCAACACTTTTGCTAGTGCATCTCTGGATCGCACCATTAAGgtatgatctggattttctgttggcaacttg-ttaactgcatttttttaccaattttgcttcatcaagtatgagtgtgctatttatgctctgatgatatctccttttccag---------

upper sequence: GRMZM2G124886_T04 (Zea mays), 5'ss of exon 6
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 6
TCAAATATTTGAAGGGCATTCTCACTATGTGATGCAAGTTACATTTAACCCAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAGgtttgtgttatctccgctttaaaaattctggt-tggccacaatgttgcattatttggtaccgacaggcgacagctttttcatagcttgatggtgatatcctattttttgtcaatatcag
||| || |||||||||||||||||||| ||||||||||| |||||||| |||||||| || ||||||||||| ||||| ||||| |||||||| |||||||| || ||         | |  | |  ||| | ||  |   | | ||  ||  |   |  |  |    |       || ||||| |||||  |  |     ||| | ||          
TCAGATTTTTGAAGGGCATTCTCACTACGTGATGCAAGTGACATTTAATCCAAAAGACACCAACACCTTTGCAAGTGCCTCCCTCGATCGCACTATAAAGgtgtgagtggaaatgtttcttgataacctgttgtgaacttgaagatgtgtt--tcaatgtc--ctaatgttgatccttccatag-ttgattttattg----attgtgtg----------

upper sequence: GRMZM2G124886_T04 (Zea mays), 5'ss of exon 6
lower sequence: PP1S79_180V6.2 (Physcomitrella patens), 5'ss of exon 6
TCAAATATTTGAAGGGCATTCTCACTATGTGATGCAAGTTACATTTAACCCAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAGgt--------------ttgtgttatctccgctttaaaaattctggttggcc-acaatgttgca---ttatttggtaccgacaggcgacagcttt--ttcatagcttgatggtgatatcctattttt-tgtcaatatcag------------------------------------------------------
|||||| || |||||||| ||||| ||||| |||||||| || ||||| || ||||| |  ||||||||||| ||||||||  ||||||| ||  | |||||              ||  ||  | |    ||    | |  | | || |    ||| || ||   | ||  ||| ||    |   | ||||||    ||||          ||  | | | |  | |   | | ||                                                        
TCAAATTTTCGAAGGGCACTCTCATTATGTCATGCAAGTAACGTTTAATCCCAAAGACAGCAACACCTTTGCAAGTGCTTCTTTGGATCGAACTGTGAAGgtgaggtaccagttggttccgtcgtttatttttctgcagtattagctgtcttgaaatattacaaaatcatagggttccttatgctaatagctttaccccatattcaagcaacgaagttcaactgatgtaagattgtcttccaagacaatagaacaaaacgatggcttaattgtatggactgtctttttaacag

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|78107583|gb|DV526001.1|DV526001
EST:     CAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAG                         ATATGGAGTCTTGGTTCTCCTGACCCAAATTTCACACTAGATGGCCATTCC
genomic: CAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAGgtttgtgtta ... tcaatatcagATATGGAGTCTTGGTTCTCCTGACCCAAATTTCACACTAGATGGCCATTCC
EST: gi|50325003|gb|CO520129.1|CO520129
EST:     CAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAG                         ATATGGAGTCTTGGTTCTCCTGACCCAAATTTCACACTAGATGGCCATTCC
genomic: CAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAGgtttgtgtta ... tcaatatcagATATGGAGTCTTGGTTCTCCTGACCCAAATTTCACACTAGATGGCCATTCC