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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtattcagtgtttacagtgttcgtactgataccaattgtaccaatatgacttgattattctctgaccctatcagGAATCCTTGAGGAGAATTTTAATTATATTTTCAAAATTGAACCCCAGTATAAGATATGTGCAAGGGATGAATGAAGTTTTGGCACCTTTATTTTATGTAT

Basic information

species Zea mays
transcript GRMZM2G122935_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G122935_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os11g28990.1 (Oryza sativa), 3'ss of exon 5
gtttgtattcagtgtttacagtgttcgtactgataccaattgtaccaata----tgacttg-atta---ttctctgac-cctatcagGAATCCTTGAGGAGAATTTTAATTATATTTTCAAAATTGAACCCCAGTATAAGATATGTGCAAGGGATGAATGAAGTTTTGGCACCTTTATTTTATGTAT
||||   |||||||  |      | | || |   |   |   ||| | ||    | | ||| | ||   || ||  || | | |||||||||  | ||| |  || | ||||| || |||||||| || || |  ||||||||||||||||||||||||||||||||||||||| | |||||||| |
gtttcacttcagtgccttggaattccttatttccatttaaactacaagtaattgtcatttggactaaatttttcaaacacatttcagGAATCTCTAAGGCGTGTTCTCATTATCTTCTCAAAATTAAATCCTACCATAAGATATGTGCAAGGGATGAATGAAGTTTTGGCACCTCTTTTTTATGTGT

upper sequence: GRMZM2G122935_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA18G00430.2 (Glycine max), 3'ss of exon 5
gtttgtattcagtgt-ttacagtgttcgtactgataccaattg------------taccaatatgacttgattattctctgaccctatcagGAATCCTTGAGGAGAATTTTAATTATATTTTCAAAATTGAACCCCAGTATAAGATATGTGCAAGGGATGAATGAAGTTTTGGCACCTTTATTTTATGTAT
|||  |  ||  | | ||    | |||| | | || |||| |             | ||| | ||||||     || || |    |  |||||  | || | ||  || |||||| | ||| |||| |||||| |  ||||||||||| | ||||||||||||||||| ||||| ||| | || ||||| |
gttcttcctctatttatttttattttcgaattcatgccaactcggtcctttttcttgccattttgactttcaacttttccggattttgcagGAGGCTTTAAAGACCATATTAATTGTTTTTGCAAAGTTGAACTCGGGTATAAGATATTTTCAAGGGATGAATGAAGTATTGGCTCCTCTCTTCTATGTGT

upper sequence: GRMZM2G122935_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA11G36520.1 (Glycine max), 3'ss of exon 5
-------------gtttgtattcagtgtttacagt-gttcgtactgataccaattg--taccaatatgacttgattattctctgaccctatcagGAATCCTTGAGGAGAATTTTAATTATATTTTCAAAATTGAACCCCAGTATAAGATATGTGCAAGGGATGAATGAAGTTTTGGCACCTTTATTTTATGTAT
              |||  |||   | || | | |  | |  ||| |  ||  ||   | ||| | ||||||     || || |    | ||||||  | || | ||  || |||||||| ||| |||| |||||| |  ||||||||||||| ||||||||||||||||| ||||| ||| | || ||||| |
gttcttcctctattttttaattttattttcaaattcataccaactcaatcctttttcttgccattttgactttcaacttttccggatttttcagGAGGCTTTAAAGACCATATTAATTATTTTTGCAAAGTTGAACTCAGGTATAAGATATGTTCAAGGGATGAATGAAGTATTGGCTCCTCTCTTCTATGTGT

upper sequence: GRMZM2G122935_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT1G04830.2 (Arabidopsis thaliana), 3'ss of exon 5
-------gtttgtattcagtgtttacagtgttcgtactgataccaattgtaccaatatgacttgattattctctgaccctatcagGAATCCTTGAGGAGAATTTTAATTATATTTTCAAAATTGAACCCCAGTATAAGATATGTGCAAGGGATGAATGAAGTTTTGGCACCTTTATTTTATGTAT
        ||||| |||    |   ||   ||    ||  |    |||   | ||  | | |    | |    | ||      |||||||  ||| ||  || ||| || ||||| | || || ||||   | || |||||||| ||||||||||| ||| |||| |||||| | ||||||||||
gtaacctttttgtgttct-catcagcaaattttcacctatttttgattaatcaaagctcagtgacatttcgatttacatgtctagGAATCTATGAAGAATATATTACTTGTATTTGCGAAGTTAAACCAAGGCATCAGATATGTTCAAGGGATGAACGAAATTTTAGCACCTATCTTTTATGTAT

upper sequence: GRMZM2G122935_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv05s0029g01350.t01 (Vitis vinifera), 3'ss of exon 5
gtttgtattcagtgtttacagtgttcgtactgataccaattgtaccaatatgacttgattattctctgaccctat--cagGAATCCTTGAGGAGAATTTTAATTATATTTTCAAAATTGAACCCCAGTATAAGATATGTGCAAGGGATGAATGAAGTTTTGGCACCTTTATTTTATGTAT
|| ||| ||   |  ||   |  |  |   |||||| ||    ||| || ||||   ||||        |  |||  |||||  | |||||||  || || ||| | ||| |||| ||||| ||  ||||||||||||||||||||||||||||| ||||||| ||| |||| |||||||
gtatgtgtt-gttacttgaggcatgagacttgatacaaacatcacccatttgaccaaattaaatggatcctgtatttcagGATGCTTTGAGGAACATATTGATTGTGTTTGCAAAGTTGAATCCGGGTATAAGATATGTGCAAGGGATGAATGAAATTTTGGCGCCTCTATTCTATGTAT

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|78110295|gb|DV528710.1|DV528710
EST:     TAAAGCGAACACATCCTGATATTTCATTTTTCTCATCAAAGTCTAACCAG                         GAATCCTTGAGGAGAATTTTAATTATATTTTCAAAATTGAACCCCAGTATA
genomic: TAAAGCGAACACATCCTGATATTTCATTTTTCTCATCAAAGTCTAACCAGgtttgtattc ... accctatcagGAATCCTTGAGGAGAATTTTAATTATATTTTCAAAATTGAACCCCAGTATA
EST: gi|76011673|gb|DT938843.1|DT938843
EST:     TAAAGCGAACACATCCTGATATTTCATTTTTCTCATCAAAGTCTAACCAG                         GAATCCTTGAGGAGAATTTTAATTATATTTTCAAAATTGAACCCCAGTATA
genomic: TAAAGCGAACACATCCTGATATTTCATTTTTCTCATCAAAGTCTAACCAGgtttgtattc ... accctatcagGAATCCTTGAGGAGAATTTTAATTATATTTTCAAAATTGAACCCCAGTATA
EST: gi|76017397|gb|DT944567.1|DT944567
EST:     TAAAGCGAACACATCCTGATATTTCATTTTTCTCATCAAAGTCTAACCAG                         GAATCCTTGAGGAGAATTTTAATTATATTTTCAAAATTGAACCCCAGTATA
genomic: TAAAGCGAACACATCCTGATATTTCATTTTTCTCATCAAAGTCTAACCAGgtttgtattc ... accctatcagGAATCCTTGAGGAGAATTTTAATTATATTTTCAAAATTGAACCCCAGTATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcgtactgataccaattgtaccaatatgacttgattattctctgaccctatcagGAATCCTTGAGGAGAATTTTAATTATATTTTCAAAATTGAACCCCAGTATAAGATATGTGCAAGGGATGAATGAAGTTTTGGCACCTTTATTTTATGTAT
                                              ccctatc  CT-rich tract
                               ttgattatt  TA-rich tract