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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactaaactattcttccattttgtccttacccttaccttttactcaccccttgtctgttttgccatggttgcagGTATAGCAAACACAATGGATCTTCCAGAAAAGTTATTGCCTCGTATATCAAGTCGGATGGGTATCCAACGACTGTGTTTTGGTCCATACAATTATAGACA

Basic information

species Zea mays
transcript GRMZM2G168249_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168249_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os06g08790.1 (Oryza sativa), 3'ss of exon 9
gtaactaaactattcttccattttgtccttaccctta-----ccttttactcaccccttgtctgttttgccatggttgcagGTATAGCAAACACAATGGATCTTCCAGAAAAGTTATTGCCTCGTATATCAAGTCGGATGGGTATCCAACGACTGTGTTTTGGTCCATACAATTATAGACA
||| ||| ||| || ||   ||||     |    |||     ||||||| | || | ||| |||||      ||   ||||||||||| ||||||||||||||||| |||||||||||||||||||| ||||||||||||||||||||||||||||||||||| ||||| |||||| | ||
gtacctatacttttgttt-gttttacgtgtgattttagatggccttttaattactctttggctgttac----tgaacgcagGTATAGCGAACACAATGGATCTTCCTGAAAAGTTATTGCCTCGTATTTCAAGTCGGATGGGTATCCAACGACTGTGTTTTGGCCCATATAATTATCGGCA

upper sequence: GRMZM2G168249_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA13G41490.1 (Glycine max), 3'ss of exon 9
-----------------------------------------------------------------------------------gtaactaaactattcttccattttg---tccttacccttaccttttactcaccccttgtctgttttgccatggttgcagGTATAGCAAACACAATGGATCTTCCAGAAAAGTTATTGCCTCGTATATCAAGTCGGATGGGTATCCAACGACTGTGTTTTGGTCCATACAATTATAGACA
                                                                                   | | | | |  ||| |  ||  |||    | ||   | |  |    ||| |    |      |  ||  |    | |||| |||||||| || |||||||||||||| |||||| | |||||||||||||| || ||||| || ||  | || || ||||| ||||| ||||||   ||
gtaagataatgcacttttcaattattttttcagtattatgatctcccagtttgcagaagtaatttaaaatagtgggaaaacaagaatccatatgattataacaacttgatgcctttgtgcattgcaaaaacttatttttcagtactaatgtaaccaattcagGGATAGCAAATACTATGGATCTTCCAGAGAAGTTACTTCCTCGTATATCAAGCCGAATGGGCATACAGAGGCTTTGCTTTGGCCCATATAATTATCAGCA

upper sequence: GRMZM2G168249_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA15G03900.1 (Glycine max), 3'ss of exon 11
-----------------------------------------------------------------------------------gtaactaaactattcttccattttgtccttacccttaccttttactcaccccttgtctgttttgccatggttgcagGTATAGCAAACACAATGGATCTTCCAGAAAAGTTATTGCCTCGTATATCAAGTCGGATGGGTATCCAACGACTGTGTTTTGGTCCATACAATTATAGACA
                                                                                   | | | | |  ||| |  || ||||    | || ||     || |  |  | |  |||    | | ||   | |||| |||||||| || |||||||||||||| |||||| | |||||||||||||| || ||||| || ||  | || || ||||| ||||| ||||||   ||
gtaagataatgcatttttcaattattttttcagtattatgatctcccagttttctgaagtaatttaaaatagttggaaaacaagaatccatatgattataacaatttga---tgcctttgtgcattgcaaaaacttattcttcagtactatcaattcagGGATAGCAAATACTATGGATCTTCCAGAGAAGTTACTTCCTCGTATATCAAGCCGAATGGGCATACAGAGGCTTTGCTTTGGCCCATATAATTATCAGCA

upper sequence: GRMZM2G168249_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv06s0004g00530.t01 (Vitis vinifera), 3'ss of exon 9
---------------------------------------------------------------------------------------------gtaactaaactattcttccattttgtccttacccttaccttttactcaccccttgt-ctgttttgcca---tggttgcagGTATAGCAAACACAATGGATCTTCCAGAAAAGTTATTGCCTCGTATATCAAGTCGGATGGGTATCCAACGACTGTGTTTTGGTCCATACAATTATAGACA
                                                                                             ||  |  |  |  |       |    |   | |  |     | |  ||    |  | |||| ||   |   |   | |||| |||||||| || |||||||||||||| |||||  | || ||||| ||||| || |||||||| ||| | || |||||||| || || ||||||  |||
gtaggacttttatttttttaacaaggtttatcttctcttgtgacaaatatagccatgtaatgttgtttccttttatagaataaggtattgtgagtggcacaggtgataaattgctacaacaaaagcagttgtagtaatacaattataatgctgtgttataaatctaaattcagGGATAGCAAATACCATGGATCTTCCAGAGAAGTTGCTTCCCCGTATTTCAAGCCGAATGGGTATTCAAAGGCTTTGTTTTGGGCCCTATAATTATCAACA

upper sequence: GRMZM2G168249_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv06s0004g02050.t01 (Vitis vinifera), 3'ss of exon 10
--------------------------------------------------------------------------------------------gtaactaaactattcttccattttgtccttacccttaccttttactcaccccttgt-ctgttttgcca---tggttgcagGTATAGCAAACACAATGGATCTTCCAGAAAAGTTATTGCCTCGTATATCAAGTCGGATGGGTATCCAACGACTGTGTTTTGGTCCATACAATTATAGACA
                                                                                            ||  |  |  |  |       |    |   | |  |     | |  ||    |  | |||| ||   |   |   | |||| |||||||| || |||||||||||||| |||||  | || ||||| ||||| || |||||||| ||| | || |||||||| || || ||||||  |||
gtaggactttatttttttaacgaggtttatcttctcttgtgacaaatatagccatgtaatgttgtttcctttaatagaataaggtattgtgagtggcacaggtgataaattgctgcaacaaaagcagttgtagtaatacaattataatgctgtgttataaatctaaattcagGGATAGCAAATACCATGGATCTTCCAGAGAAGTTGCTTCCCCGTATTTCAAGCCGAATGGGTATTCAAAGGCTTTGTTTTGGGCCCTATAATTATCAACA

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|32931679|gb|CF036491.1|CF036491
EST:     TAACATTCTTGACTGGCCTACCAAACCAAATTCAAATCTAGTTGTTATAG                         GTATAGCAAACACAATGGATCTTCCAGAAAAGTTATTGCCTCGTATATCAA
genomic: TAACATTCTTGACTGGCCTACCAAACCAAATTCAAATCTAGTTGTTATAGgtaactaaac ... atggttgcagGTATAGCAAACACAATGGATCTTCCAGAAAAGTTATTGCCTCGTATATCAA
EST: gi|15209030|gb|BI430914.1|BI430914
EST:     TGGCCTACCAAACCAAATTCAAATCTAGTTGTTATAG                         GTATAGCAAACACAATGGATCTTCCAGAAAAGTTATTGCCTCGTATATCAA
genomic: TGGCCTACCAAACCAAATTCAAATCTAGTTGTTATAGgtaactaaac ... atggttgcagGTATAGCAAACACAATGGATCTTCCAGAAAAGTTATTGCCTCGTATATCAA
EST: gi|15209031|gb|BI430915.1|BI430915
EST:     TGGCCTACCAAACCAAATTCAAATCTAGTTGTTATAG                         GTATAGCAAACACAATGGATCTTCCAGAAAAGTTATTGCCTCGTATATCAA
genomic: TGGCCTACCAAACCAAATTCAAATCTAGTTGTTATAGgtaactaaac ... atggttgcagGTATAGCAAACACAATGGATCTTCCAGAAAAGTTATTGCCTCGTATATCAA
EST: gi|60348765|gb|DN215738.1|DN215738
EST:     TAACATTCTTGACTGGCCTACCAAACCAAATTCAAATCTAGTTGTTATAG                         GTATAGCAAACACAATGGATCTTCCAGAAAAGTTATTGCCTCGTATATCAA
genomic: TAACATTCTTGACTGGCCTACCAAACCAAATTCAAATCTAGTTGTTATAGgtaactaaac ... atggttgcagGTATAGCAAACACAATGGATCTTCCAGAAAAGTTATTGCCTCGTATATCAA
EST: gi|211040609|gb|FL332006.1|FL332006
EST:     TAACATTCTTGACTGGCCTACCAAACCAAATTCAAATCTAGTTGTTATAG                         GTATAGCAAACACAATGGATCTTCCAGAWAAGTTATTGCCTCGTATATCAA
genomic: TAACATTCTTGACTGGCCTACCAAACCAAATTCAAATCTAGTTGTTATAGgtaactaaac ... atggttgcagGTATAGCAAACACAATGGATCTTCCAGAAAAGTTATTGCCTCGTATATCAA
EST: gi|60344624|gb|DN211597.1|DN211597
EST:     TAACATTCTTGACTGGCCTACCAAACCAAATTCAAATCTAGTTGTTATAG                         GTATAGCAAACACAATGGATCTTCCAGAAAAGTTATTGCCTCGTATATCAA
genomic: TAACATTCTTGACTGGCCTACCAAACCAAATTCAAATCTAGTTGTTATAGgtaactaaac ... atggttgcagGTATAGCAAACACAATGGATCTTCCAGAAAAGTTATTGCCTCGTATATCAA
EST: gi|31354612|gb|CD438969.1|CD438969
EST:     TAACATTCTTGACTGGCCTACCAAACCAAATTCAAATCTAGTTGTTATAG                         GTATAGCAAACACAATGGATCTTCCAGAAAAGTTATTGCCTCGTATATCAA
genomic: TAACATTCTTGACTGGCCTACCAAACCAAATTCAAATCTAGTTGTTATAGgtaactaaac ... atggttgcagGTATAGCAAACACAATGGATCTTCCAGAAAAGTTATTGCCTCGTATATCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtccttacccttaccttttactcaccccttgtctgttttgccatggttgcagGTATAGCAAACACAATGGATCTTCCAGAAAAGTTATTGCCTCGTATATCAAGTCGGATGGGTATCCAACGACTGTGTTTTGGTCCATACAATTATAGACA
                     tactcac  putative branch site (score: 1)
                  ttttact  TA-rich tract