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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattgttttaatctttatcctttctgctggattacttatttgtaatgtgattgccagatatatgttgtctgcattctgatgcatctgtgtgacttttcagATTGAAGTTGAAAACCCTTGTGTAATTATGAGTCAAGACAAAAGCAGAGAGTTTTTACATTCAGGAAATGACAAGGATAAGTTCAAG

Basic information

species Zea mays
transcript GRMZM2G025340_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G025340_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA09G36430.1 (Glycine max), 3'ss of exon 4
aattgttttaatctttatcctttctgctggattacttatttgtaatgtgattgccagatatatgttgtctgca--ttctgatgcatctgtgtgacttttcagATTGAAGTTGAAAACCCTTGTGTAATTATGAGTCAAGACAAAAGCAGAGAGTTTTTACATTCAGGAAATGACAAGGATAAGTTCAAG
 |||   |||||    |     ||| | | | | | | | | |  | |  ||      | ||| ||   | ||  || |  || |||| | | | ||| |||||||| || || || || |||||||||||||||||||||||||||||||| ||||| ||||| || ||| |||||||||| || |||
-attcacttaataacaaataaatcttcagcaatgcctttatttcctttttttagagattttatttttcttacaacttttcttgaatctat-tcattttgcagATTGACGTGGAGAATCCATGTGTAATTATGAGTCAAGACAAAAGCAGAGAATTTTTGCATTCTGGGAATAACAAGGATAAATTTAAG

upper sequence: GRMZM2G025340_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT5G61460.1 (Arabidopsis thaliana), 3'ss of exon 4
aattgttttaatc-tttatcctttctgctggattacttatttgtaatgtgat-tgccagatatatgttgt-ctgcattctgatgcatctgtgtgacttttcagATTGAAGTTGAAAACCCTTGTGTAATTATGAGTCAAGACAAAAGCAGAGAGTTTTTACATTCAGGAAATGACAAGGATAAGTTCAAG
    |||||   | || || |    |  | ||  | |  |  || || | |  | |  |  |||    || ||| ||||| ||  || | | |   | |  ||||||| |||||||| || |||||  | |||||||||||||||||||| ||||| |||||||| ||||||||||| ||||| ||||||
gtgagttttggccgttcattcaaaattttagaa-agtattaagtgatatcagatacttggcatactcagtactgtattcttat-tatat-tttacatgtgtagATTGATGTTGAAAATCCGTGTGTGGTAATGAGTCAAGACAAAAGCAGGGAGTTCTTACATTCTGGAAATGACAAAGATAAATTCAAG

upper sequence: GRMZM2G025340_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT5G07660.1 (Arabidopsis thaliana), 3'ss of exon 4
------aattgttttaatctttatcctttctgctggattacttatttgtaatgtgattgcca-gatatatgttgtctgcattctgatgcatctgtgtgacttttc--------agATTGAAGTTGAAAACCCTTGTGTAATTATGAGTCAAGACAAAAGCAGAGAGTTTTTACATTCAGGAAATGACAAGGATAAGTTCAAG
        || | ||    || |   |    |   ||| | |||| |   ||  ||||  |  | ||| ||| || | ||||    || |||||| | |   ||         ||||||| ||||| || || ||||| || |||||||||||||| ||||| ||||| |||||||| || || ||||| ||||| ||||||
gtgagcttttctcttcgatttaagattaaaagtatgatcatttatgttatatcagattttcgtgttatttgtggtattcattgct-tggatctgtattatgctttcgttgactagATTGATGTTGAGAATCCCTGTGTGATAATGAGTCAAGACAAGAGCAGGGAGTTCTTACATTCTGGTAACGACAAAGATAAATTCAAG

upper sequence: GRMZM2G025340_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv16s0013g00490.t01 (Vitis vinifera), 3'ss of exon 4
-----aattgttttaatctttatcctttct--gctggattacttatttgtaatgtgattgccagatatatgttgtctgcattctgatgcatctgtgtgacttttcagATTGAAGTTGAAAACCCTTGTGTAATTATGAGTCAAGACAAAAGCAGAGAGTTTTTACATTCAGGAAATGACAAGGATAAGTTCAAG
     ||   || ||    || ||||| |     | | ||| |||||     |   |   || | |   |  |||     ||  ||||  |||   |   || ||||||||| |||||||| || ||||| || ||||||||||||||||||||||| ||||| |||||||| |||||||| ||||| ||||||
taatgaaggattctataaattctccttccccaattagtttatttattcaactttaaacatcctgctcagtaatgt-----tttagatgtgtcttact--tttctcagATTGATGTTGAAAATCCATGTGTGATAATGAGTCAAGACAAAAGCAGAGAATTTTTGCATTCAGGGAATGACAAAGATAAATTCAAG

upper sequence: GRMZM2G025340_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ36741 (Selaginella moellendorffii), 3'ss of exon 4
aattgttttaatctttatcctttctgctggattacttatttgtaatgtgattgccagatatatgttgtctgcattctgatgcatctgtgtgacttttcagATTGAAGTTGAAAACCCTTGTGTAATTATGAGTCAAGACAAAAGCAGAGAGTTTTTACATTCAGGAAATGACAAGGATAAGTTCAAG
                                             || |  | ||  | |||| ||  |||  | ||||      ||  ||   ||  |||| || || ||||| |||||||| || ||||| |||||||| ||| | |||||  | ||||| |||||||||||||| ||||| |||
--------------------------------------------gtgagtcttccgta-atatttttcctgtttactgac----ttggatg--cttatagATAGATGTCGAAAATCCTTGTGTGATCATGAGCCAAGACAAGAGCCGCGAGTTCCTGCATTCCGGAAATGACAAGGAAAAGTTTAAG

upper sequence: GRMZM2G025340_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ27923 (Selaginella moellendorffii), 3'ss of exon 4
aattgttttaatctttatcctttctgctggattacttatttgtaatgtgattgccagatatatgttgtctgcattctgatgcatctgtgtgacttttcagATTGAAGTTGAAAACCCTTGTGTAATTATGAGTCAAGACAAAAGCAGAGAGTTTTTACATTCAGGAAATGACAAGGATAAGTTCAAG
                                             || |  | ||  | |||| ||  |||  | ||||      ||  ||   ||  |||| || || ||||| |||||||| || ||||| |||||||| ||| | |||||  | ||||| |||||||||||||| |||||||||
--------------------------------------------gtgagtcttccgta-atattttacctgtttactgac----ttggatg--cttatagATAGATGTCGAAAATCCTTGTGTGATCATGAGCCAAGACAAGAGCCGCGAGTTCCTGCATTCCGGAAATGACAAGGAAAAGTTCAAG

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|93012303|gb|EB637823.1|EB637823
EST:     AGGTGGCACATCGCAAGGATGACCTAAATGAAATAATTGAACATTTTAAC                         ATTGAAGTTGAAAACCCTTGTGTAATTATGAGTCAAGACAAAAGCAGAGAG
genomic: AGGTGGCACATCGCAAGGATGACCTAAATGAAATAATTGAACATTTTAACgtaagttgct ... gacttttcagATTGAAGTTGAAAACCCTTGTGTAATTATGAGTCAAGACAAAAGCAGAGAG
EST: gi|6021095|gb|AW066023.1|AW066023
EST:     AGGTGGCACATCGCAAGGATGACCTAAATGAAATAATTGAACATTTTAAC                         ATTGAAGTTGAAAACCCTTGNGTAATTATGAGTCAAGACAAAAGCAGAGAG
genomic: AGGTGGCACATCGCAAGGATGACCTAAATGAAATAATTGAACATTTTAACgtaagttgct ... gacttttcagATTGAAGTTGAAAACCCTTGTGTAATTATGAGTCAAGACAAAAGCAGAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgattgccagatatatgttgtctgcattctgatgcatctgtgtgacttttcagATTGAAGTTGAAAACCCTTGTGTAATTATGAGTCAAGACAAAAGCAGAGAGTTTTTACATTCAGGAAATGACAAGGATAAGTTCAAG
                            ttctgat  putative branch site (score: 3)
                                               cttttc  putative PPT
            atatatgtt  TA-rich tract