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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagttcagtctggtgatcagtgtatgacatcatttcagtcgtagttaattgcattagagctgtactattctagtctaacgattttgctaaatggttgcagTCGTTGATGATTGCTGCAATCCCAAATATCATCGGTTGGCTTGCGATCTCCTTTGCAAAAGTATTCAACAA

Basic information

species Zea mays
transcript GRMZM2G160504_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G160504_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g49270.1 (Oryza sativa), 3'ss of exon 2
aagttcagtctggtgatcagtgtatgacatcatttcagtcgt-agttaattgcattagagctgtactattctagtctaacgattttgctaaatgg---ttgcagTCGTTGATGATTGCTGCAATCCCAAATATCATCGGTTGGCTTGCGATCTCCTTTGCAAAAGTATTCAACAA
   ||   | |  ||  | || | || |||  || |||| || ||||   | | | |  | | |||| || ||  |||||    ||| |   ||    || ||||| ||||||||||||||||| ||||| ||||| ||||||||||| |||||||||||||||           
--attttatttaatgtcctgtttttggcatggttgcagtagtcagttg--tacttcaatggtctactcttttaagctaactgaattgtttggtgaattttccagTCATTGATGATTGCTGCAATTCCAAACATCATTGGTTGGCTTGCCATCTCCTTTGCAAAA-----------

upper sequence: GRMZM2G160504_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g49260.1 (Oryza sativa), 3'ss of exon 2
aagttcagtctggtgatcagtgtatgacatcatttcagtcgtagttaattgcattagagctgtactattctagtctaacgattttgctaaatgg--ttgcagTCGTTGATGATTGCTGCAATCCCAAATATCATCGGTTGGCTTGCGATCTCCTTTGCAAAAGTATTCAACAA
    |  |  |  |  |   |  || || | ||   |   |||||||| | || |  |||| || |||| || ||||| | | ||||| | ||    | ||||||||||| ||||| ||  | || || ||||| ||||||||||| |||||||||||||||           
-ttctttggttcatacttcata-atcacttaatcagatcagtagttaactacagtgaagctctattattttactctaatggtcttgctgattgaatctccagTCGTTGATAATTGCGGCGGTTCCTAACATCATTGGTTGGCTTGCCATCTCCTTTGCAAAA-----------

upper sequence: GRMZM2G160504_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA16G25310.1 (Glycine max), 3'ss of exon 3
---------aagttcagtc--tggtgatcagtgtat-gacatca---tttcagtcgtagttaattgcattagagctgt-actattctagtctaacgattttgctaaatggttgcagTCGTTGATGATTGCTGCAATCCCAAATATCATCGGTTGGCTTGCGATCTCCTTTGCAAAAGTATTCAACAA
            || | ||  | ||  |   ||| | ||  |||   |||||   | |  |   || ||  ||   || | |  |    | |  ||  |||  | |||| |||||||| |||||||||||||| ||||| ||||| || || |||||||| || || ||||| |||           
gtattttatttatttattcatttgtagtgcatgttttgaagtcagtctttcaaaggaaaatttatgaatgtgaagagtgattgatgatttttggcgtgttttttgaatg-ttgcagTCATTGATGATTGCTGCGATCCCCAATATAATAGGGTGGCTTGCTATTTCTTTTGCCAAA-----------

upper sequence: GRMZM2G160504_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA18G16220.1 (Glycine max), 3'ss of exon 5
---------aagttcagtc--tggtgatcagtgtat-gacatca---tttcagtcgtagttaattgcattagagctgt-actattctagtctaacgattttgctaaatggttgcagTCGTTGATGATTGCTGCAATCCCAAATATCATCGGTTGGCTTGCGATCTCCTTTGCAAAAGTATTCAACAA
            || | ||  | ||  |   ||| | ||  |||   |||||   | |  |   || ||  ||   || | |  |    | |  ||  |||  |  |  ||||||||| |||||||||||||| ||||| ||||| || || |||||||| || || ||||| |||           
gtattttattgatttattcatttgtagtgcatgttttgaagtcaatctttcaaaggaaaatctatgaatgtgaagagtgattggtgatttttggcgtgttttttttaatgttgcagTCATTGATGATTGCTGCGATCCCCAATATAATAGGGTGGCTTGCTATTTCTTTTGCCAAA-----------

upper sequence: GRMZM2G160504_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA14G08070.1 (Glycine max), 3'ss of exon 3
------------aagttcagtctggtgatca-gtgtatgacatcatttcagtcgtagttaattgcattagagctgta---ctattctagtc---taacg------attttgctaaatgg--ttgcagTCGTTGATGATTGCTGCAATCCCAAATATCATCGGTTGGCTTGCGATCTCCTTTGCAAAAGTATTCAACAA
               ||   ||  ||| | | |||||||   |   || | |   | | | |||  || |||   |    ||| |  | |     ||||      | |||  |   ||   |||||||| |||||||||||  | || |||||||| || |||||||| || ||||| |||||||||           
gtacccttttttctcttttttcgtgtgtttatgtgtatgcttttcctttaatttcaat-atttgagtttgagggatgaggctaattcaattggtcaacgggttacaatttcttgtctgaaattgcagTCTTTGATGATTGCATCCATTCCAAATATTATTGGTTGGCTGGCTATCTCATTTGCAAAA-----------

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|148959411|gb|EC905439.2|EC905439
EST:     TCGGGGCGATCGCCAGCGGGCAGATGGCCGAGTACATTGGCCGTAAAGGG                         TCGTTGATGATTGCTGCAATCCCAAATATCATCGGTTGGCTTGCGATCTCC
genomic: TCGGGGCGATCGCCAGCGGGCAGATGGCCGAGTACATTGGCCGTAAAGGGgtgagaaatt ... atggttgcagTCGTTGATGATTGCTGCAATCCCAAATATCATCGGTTGGCTTGCGATCTCC
EST: gi|78120837|gb|DV539221.1|DV539221
EST:     TCGGGGCGATCGCCAGCGGGCAGATGGCCGAGTACATTGGCCGTAAAGGG                         TCGTTGATGATTGCTGCAATCCCAAATATCATCGGTTGGCTTGCGATCTCC
genomic: TCGGGGCGATCGCCAGCGGGCAGATGGCCGAGTACATTGGCCGTAAAGGGgtgagaaatt ... atggttgcagTCGTTGATGATTGCTGCAATCCCAAATATCATCGGTTGGCTTGCGATCTCC
EST: gi|149102783|gb|EE288131.2|EE288131
EST:     TCGGGGCGATCGCCAGCGGGCAGATGGCCGAGTACATTGGCCGTAAAGGG                         TCGTTGATGATTGCTGCAATCCCAAATATCATCGGTTGGCTTGCGATCTCC
genomic: TCGGGGCGATCGCCAGCGGGCAGATGGCCGAGTACATTGGCCGTAAAGGGgtgagaaatt ... atggttgcagTCGTTGATGATTGCTGCAATCCCAAATATCATCGGTTGGCTTGCGATCTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taattgcattagagctgtactattctagtctaacgattttgctaaatggttgcagTCGTTGATGATTGCTGCAATCCCAAATATCATCGGTTGGCTTGCGATCTCCTTTGCAAAAGTATTCAACAA
                                       tgctaaa  putative branch site (score: 2)
                 tactatt  TA-rich tract