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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttaacttttatgctccatgtttgcatttgtttgacgattcatagggtgcttctttatctcaactttttaagacttggttgtatgatccagaagctcaaacaatcactggtatgttttggaatattaaacaggattttgctttgactcaatgcagCGGATGCCGAGCAGATGCAAATGAAGCCGCTGTTATACTTCTTCCTTCAAATATCACTGTTTTCACACTTGACTTTTCTGGGTCAGGTCTATCCGGCGGG

Basic information

species Zea mays
transcript GRMZM2G081642_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081642_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g10440.1 (Oryza sativa), 3'ss of exon 3
gtatttaacttttatgctccatgtttgcatttgtttgacgattcatagggtgcttctttatctcaactttttaagacttggttg-tatgatccagaagctcaaacaatcactggtatgttttggaatattaaacaggattttgctttgactcaatgcagCGGATGCCGAGCAGATGCAAATGAAGCCGCTGTTATACTTCTTCCTTCAAATATCACTGTTTTCACACTTGACTTTTCTGGGTCAGGTCTATCCGGCGGG
                                                        | |     | | |||     |||   || |  ||| ||    ||||| ||||||| | ||| ||||||||| || |||||| ||||||||||||||||||||| |||||||| ||||||||||||||||| ||||||||||| |||||| |||||||||||||||| |||||||| ||||| |||||||||||||| || || 
------------------------------------------------------gttatgagctagcatttcct--cttaactgatgagattcat---ctcaagcaatcaccgatatcttttggaatctttaacaggcttttgctttgactcaatgcagTGGATGCCGGGCAGATGCAAATGAAGCTGCTGTTATACTGCTTCCTGCAAATATCACTGTTTTTACACTTGATTTTTCCGGGTCAGGTCTATCAGGTGGA

upper sequence: GRMZM2G081642_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA17G00770.1 (Glycine max), 3'ss of exon 4
gtatttaacttttatgctccatgtttgcatttgtttgacgattcatagggtgcttctttatctcaactttttaagacttggt---tgtatgatccagaagctcaaacaatcactggtatgttttggaatattaaacaggattttgctttgactcaatgcagCGGATGCCGAGCAGATGCAAATGAAGCCGCTGTTATACTTCTTCCTTCAAATATCACTGTTTTCACACTTGACTTTTCTGGGTCAGGTCTATCCGGCGGG
                                   |     ||  ||   ||  ||||    | |   |||||| |  | ||   || ||||||    || |     |   | |    | || |    | | | |   |    | | |  | |  |||||| |||||  | |||||||| |||||||| ||||| || ||||||||||||||||| |||||||| || |||||||| || ||||||||  |||| |  || 
----------------------------------gtacttgttattaaaatgactcttgtcttgatgcttttaaaaaattgtatatgcatgatcatagagttttt-tagctattctattcttctcccttgtgatatgtgtgcatacatacaat-gatgcagTGGATGTAGGGCAGATGCCAATGAAGCTGCTGTAATTCTTCTTCCTTCAAATATTACTGTTTTTACCCTTGACTTCTCGGGGTCAGGCTTATCTGATGGA

upper sequence: GRMZM2G081642_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA09G02050.1 (Glycine max), 3'ss of exon 4
gtatttaa-cttttatgctccatgtttgcatttgtttgacgattcatagggtgcttctttatctcaacttttt---aagacttggttgtatgatccagaagctcaaacaatcactggtatgttttggaatattaaacaggattttgctttgactcaatgcagCGGATGCCGAGCAGATGCAAATGAAGCCGCTGTTATACTTCTTCCTTCAAATATCACTGTTTTCACACTTGACTTTTCTGGGTCAGGTCTATCCGGCGGG
|||   ||  |||||||     || |  || | |   ||   |  ||| |||      | ||    ||  |||   || | |   || | |  | |||||  | | ||| ||| |      || |    | || |   | || |   | |      |||||| |||||  | |||||||| |||||||| |||||||| |||||||| |||||||| ||||| || || ||||||||||| ||||||||  | || |  || 
gtaagcaaatttttatggatactgctatcact-gcaagagattctatacggtttacagtcataaagaccctttttgaacattcttttctttttttcagaa--tgacacactcattc---cattcttctcttttcatatgtatgtacatgtacaatgatgcagTGGATGTAGGGCAGATGCCAATGAAGCTGCTGTTATTCTTCTTCCATCAAATATTACTGTCTTTACTCTTGACTTTTCGGGGTCAGGCTTGTCTGATGGA

upper sequence: GRMZM2G081642_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G40050.1 (Glycine max), 3'ss of exon 4
gtatttaacttttatgctccatgtttgcatttgtttgacgattcatagggtgcttctttatctcaactttttaagacttggtt--gtatgatccagaagctcaaacaatcactggtatgttttggaatattaaacaggattttgctttgactcaatgcagCGGATGCCGAGCAGATGCAAATGAAGCCGCTGTTATACTTCTTCCTTCAAATATCACTGTTTTCACACTTGACTTTTCTGGGTCAGGTCTATCCGGCGGG
                          | |||||||     ||| | | |||  || | |   |   ||||| || | |||  |  || |||||   |   |  | | ||  ||  | |  |      |  ||     |  |  |   |      |||||| |||||  | |||||||| |||||||| ||||| || ||||||||||||||||| |||||||| || |||||||| || ||||||||  |||| |  || 
--------------------------gtatttgtt-----attaaaatggttattgtcttgat--gcttttaaaaaattgtatatgtgtgatcattattttttagctatt-ctattcttctcccttgtgatatgtgtgcatacg---tacaatgatgcagTGGATGTAGGGCAGATGCCAATGAAGCTGCTGTAATTCTTCTTCCTTCAAATATTACTGTTTTTACCCTTGACTTCTCGGGGTCAGGCTTATCTGATGGA

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|211317674|gb|FL189179.1|FL189179
EST:     ATCCCAGAGAATACTGCCCTCCCATGTGTGGTCTATTGCCATGGAAATAG                         CGGATGCCGAGCAGATGCAAATGAAGCCGCTGTTATACTTCTTCCTTCAA-
genomic: ATCCCAGAGAATACTGCCCTCCCATGTGTGGTCTATTGCCATGGAAATAGgtatttaact ... ctcaatgcagCGGATGCCGAGCAGATGCAAATGAAGCCGCTGTTATACTTCTTCCTTCAAA
EST: gi|26455576|gb|CA827159.1|CA827159
EST:     ATCCCAGAGAATACTGCCCTCCCATGTGTGGTCTATTGCCATGGAAATAG                         CGGATGCCGAGCAGATGCAAATGAAGCCGCTGTTATACTTCTTCCTTCAAA
genomic: ATCCCAGAGAATACTGCCCTCCCATGTGTGGTCTATTGCCATGGAAATAGgtatttaact ... ctcaatgcagCGGATGCCGAGCAGATGCAAATGAAGCCGCTGTTATACTTCTTCCTTCAAA
EST: gi|21481543|gb|BQ578226.1|BQ578226
EST:     ATCCCAGAGAATACTGCCCTCCCATGTGTGGTCTATTGCCATGGAAATAG                         CGGATGCCGAGCAGATGCAAATGAAGCCGCTGTTATACTTCTTCCTTCAAA
genomic: ATCCCAGAGAATACTGCCCTCCCATGTGTGGTCTATTGCCATGGAAATAGgtatttaact ... ctcaatgcagCGGATGCCGAGCAGATGCAAATGAAGCCGCTGTTATACTTCTTCCTTCAAA
EST: gi|148941968|gb|EC886955.2|EC886955
EST:     ATCCCAGAGAATACTGCCCTCCCATGTGTGGTCTATTGCCATGGAAATAG                         CGGATGCCGAGCAGATGCAAATGAAGCCGCTGTTATACTTCTTCCTTCAAA
genomic: ATCCCAGAGAATACTGCCCTCCCATGTGTGGTCTATTGCCATGGAAATAGgtatttaact ... ctcaatgcagCGGATGCCGAGCAGATGCAAATGAAGCCGCTGTTATACTTCTTCCTTCAAA
EST: gi|149069709|gb|EE158095.2|EE158095
EST:     ATCCCAGAGAATACTGCCCTCCCATGTGTGGTCTATTGCCATGGAAATAG                         CGGATGCCGAGCAGATGCAAATGAAGCCGCTGTTATACTTCTTCCTTCAAA
genomic: ATCCCAGAGAATACTGCCCTCCCATGTGTGGTCTATTGCCATGGAAATAGgtatttaact ... ctcaatgcagCGGATGCCGAGCAGATGCAAATGAAGCCGCTGTTATACTTCTTCCTTCAAA
EST: gi|101394355|gb|EB819112.1|EB819112
EST:     ATCCCAGAGAATACTGCCCTCCCATGTGTGGTCTATTGCCATGGAAATAG                         CGGATGCCGAGCAGATGCAAATGAAGCCGCTGTTATACTTCTTCCTTCAAA
genomic: ATCCCAGAGAATACTGCCCTCCCATGTGTGGTCTATTGCCATGGAAATAGgtatttaact ... ctcaatgcagCGGATGCCGAGCAGATGCAAATGAAGCCGCTGTTATACTTCTTCCTTCAAA
EST: gi|149041290|gb|EE046926.2|EE046926
EST:     ATCCCAGAGAATACTGCCCTCCCATGTGTGGTCTATTGCCATGGAAATAG                         CGGATGCCGAGCAGATGCAAATGAAGCCGCTGTTATACTTCTTCCTTCAAA
genomic: ATCCCAGAGAATACTGCCCTCCCATGTGTGGTCTATTGCCATGGAAATAGgtatttaact ... ctcaatgcagCGGATGCCGAGCAGATGCAAATGAAGCCGCTGTTATACTTCTTCCTTCAAA
EST: gi|213187018|gb|FM194143.1|FM194143
EST:     TCCCAGAGAAATACTGCCCTCCCATGTGTGGTCTATTGCCATGGAAATAG                         CGGATGCCGAGCAGATGCAAATGAAGCCGCTGTTATACTTCTTCCTTCAAA
genomic: TCCCAGAG-AATACTGCCCTCCCATGTGTGGTCTATTGCCATGGAAATAGgtatttaact ... ctcaatgcagCGGATGCCGAGCAGATGCAAATGAAGCCGCTGTTATACTTCTTCCTTCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatcactggtatgttttggaatattaaacaggattttgctttgactcaatgcagCGGATGCCGAGCAGATGCAAATGAAGCCGCTGTTATACTTCTTCCTTCAAATATCACTGTTTTCACACTTGACTTTTCTGGGTCAGGTCTATCCGGCGGG
                                       ctttgac  putative branch site (score: 4)
              ttttggaatattaaa  TA-rich tract