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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcggtaacctttgcattgttttggctgatctcttctctttaatctctgtgttaaaccaatatcgtattttctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG

Basic information

species Zea mays
transcript GRMZM2G057576_T01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 17
gtcggtaacctttgcattgttttggctga--tctcttctctttaatctctgtgttaaaccaatatcgtattttctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG
||| ||| |||||   ||||||||| | |  | | || |  ||   || | |||| ||  || ||  |||| |  ||||||||||||  |||| || || ||||||||||||||||| || ||||| |||||||||||||| |||
gtcagta-cctttttgttgttttggtttacttttttttttctttgcctgtctgtttaattaacattatattgt--gatgcagCATTACACAGAATTACCAGATATCAAGCGTGTCATGGTGAATACCCATGCCATTGAGCCACAG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 17
gtcggtaacctttgcattgttttggctga-tctcttctctttaatctctgtgttaaaccaatatcgtattttctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG
||| ||| |||||   ||||||||| | | | | || |  ||   || | |||| ||  || ||  |||| |  ||||||||||||  |||| || || ||||||||||||||||| || ||||| |||||||||||||| |||
gtcagta-cctttttgttgttttggtttactttttttttctttgcctgtctgtttaattaacattatattgt--gatgcagCATTACACAGAATTACCAGATATCAAGCGTGTCATGGTGAATACCCATGCCATTGAGCCACAG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 17
-gtcggtaacctttgcattgttttggc----tgatctcttctctttaatctctgtgttaaaccaatatcgtattttctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG
  ||  |     ||   || |  || |    | ||    |||  |||   | | | || ||||      |||| ||    ||||||||||| | ||||||||||| ||||| ||||||||||| ||||| |||||||||||||| |||
gttctttgcttcttaagttctgatgacagtataatgatctcttgttagaatatttcttgaaccgtgtctgtatatt---gtgcagCATTATACTGAGTTGCCTGACATCAAACGTGTCATTGTGAATACACATGCCATTGAGCCACAG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 16
------gtcggtaacctttgcattgttttggctgatctcttctcttta------atctctgtgttaaaccaatatcgtattttctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG
             |  | ||  || || |  ||| | |  |   || |      | |  | | ||  ||  ||  |    ||| || ||||||||||  |||||||||| ||||| || ||||| ||||||||||| ||||| |||||||| |||
gtaatgactcaccaaatgtgttttattattactggttttcttatttaacccaaaagccttctcttttactgattacactatttttggtgcagCATTACACAGAGTTGCCAGATATAAAACGTGTGATTGTAAATACACATGCAATTGAGCCACAG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 17
-gtcggtaacctttgcattgttttggctg----atctcttctctttaatctctgtgttaaaccaatatcgtattttctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG
  ||  |     ||   || |  || |||    || |  ||| ||||   | | | || ||||      || | ||    ||||||||||| | ||||||||||| ||||| ||||||||||| ||||| |||||||||||||| |||
gttctttgcttcttaagttctgatgactgtataatgttctctttttagaatatttcttgaaccttgtctgtgtatt---gtgcagCATTATACTGAGTTGCCTGACATCAAACGTGTCATTGTGAATACACATGCCATTGAGCCACAG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 15
gtcggtaacctttgcattgtt--ttggctgatctcttctctttaatctctgtgttaaaccaatatcgtatttt-ctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG
||   |  | | |    |  |   || ||| | | |  | |   |    | | || ||||  | | || | || ||  ||||||||||||| ||||||||||| ||||| ||||||||||| ||||| |||||||| || || |||
gttctttgcttctattcttatgactgactgttatttcttgtcagaataatttcttgaacct-tcttgtgtgttgcttgtgcagCATTATTCCGAGTTGCCTGACATCAAACGTGTCATTGTGAATACACATGCCATCGAACCGCAG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 16
------gtcggtaacctttgcattgttttggctgatctcttctctttaatc------tctgtgttaaaccaatatcgtattttctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG
             |  | ||  || || |  ||| | |  |   || |  |        | | ||  |   ||  | |  ||| || ||||||||||  |||||||||| ||||| || ||||| ||||||||||| ||||| |||||||| |||
gtaatgactcaccaaatgtgttttattcttactggttttcttatttaacccaaaggccttctcttttattgattacattatttttggtgcagCATTACACAGAGTTGCCAGATATAAAACGTGTAATTGTAAATACACATGCAATTGAGCCACAG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 17
gtcggtaacctttgcattgttttggctgatc----tcttctctttaatctctgtgttaaaccaatatcgtatttt-ctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG
||   |  | |||  ||| || || ||||      | |  | |   |    | | || ||||  | | || | || || |||||||||||||| || |||||||| ||||| ||||||||||| ||||| |||||||| || || |||
gttctttgctttt--attcttatgactgactgtaatttcttgtcagaataatttcttgaacct-tcttgtgtgttgcttatgcagCATTATTCCGAATTGCCTGACATCAAACGTGTCATTGTGAATACACATGCCATCGAACCACAG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 15
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 17
-------gtcggtaacctttgcattgttttgg--ctgatctcttctctttaatctctgtgttaaaccaatatcgtattttctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG
        ||  |  | | |  | | || | |  || ||   |    |||  | ||     |||     | || | ||   |  |||||||||| |||||||| ||||||||||| ||||| ||||| || || ||||| |||||||| |||
gtttttgctcaatgtcttctttaatattcttggcctaatagatgtatttttttttcccctctaacttcgtttccttttgctttgtgcagCATTACTCAGAGTTACCTGATATCAAACGTGTAATTGTGAACACACATGCTATTGAGCCACAG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 15
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 17
--gtcggtaacctttgca--ttgttttggctgatctctt--ctctttaatctctgtgttaaaccaatatcgtatttt-----------------ctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG
  |    |     |||||  |  ||||   | || | ||  || ||| ||   |   | |||  |||      | ||                  |  ||||||||||| | |||||||| ||||| || || |||||||| ||||| ||||| |||||||| |||
gtgaaattggttcttgcaattcattttattttattttttaccttttttattgttacatgaaattaattatacgtcttggttaaaacacttatattttgtgcagCATTATACTGAGTTGCCAGATATAAAACGCGTCATTGTGAATACACATGCAATTGAGCCACAG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 15
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 17
--------gtcggtaacctttgcattgttttggctgatctcttc--tctttaatctctgtgttaaaccaatatcgtattttctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG
        ||   | ||  |   |||| |     | || ||      |||| ||   | | ||  |  ||     |  | ||| |||||||||||| | || ||||| |||||||| ||||||||||| || || |||||||||||||| |||
gtataatggtttctcactatctgattgatgaactttatttcacagacctttgattgtt-tcttggattaaatgattcatctcttatgcagCATTATACTGAATTGCCCGATATCAAACGTGTCATTGTGAACACACATGCCATTGAGCCACAG

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|16137384|gb|BI894249.1|BI894249
EST:     GTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAG                         CATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
genomic: GTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgtcggtaacc ... tctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
EST: gi|18384990|gb|BM418189.1|BM418189
EST:     GTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAG                         CATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
genomic: GTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgtcggtaacc ... tctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
EST: gi|15188223|gb|BI417200.1|BI417200
EST:     GTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAG                         CATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
genomic: GTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgtcggtaacc ... tctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
EST: gi|18385023|gb|BM418222.1|BM418222
EST:     GTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCACCAG                         CATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
genomic: GTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgtcggtaacc ... tctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
EST: gi|22489541|gb|BU049464.1|BU049464
EST:     GGCTGGATTATACTTGCGTGCCCTCCAG                         CATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
genomic: GGCTGGATTATACTTGCGTGCCCTCCAGgtcggtaacc ... tctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
EST: gi|18053133|gb|BM318791.1|BM318791
EST:     GTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAG                         CATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTTATGCC
genomic: GTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgtcggtaacc ... tctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
EST: gi|15313673|gb|BI478897.1|BI478897
EST:     GTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAG                         CATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
genomic: GTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgtcggtaacc ... tctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
EST: gi|15313671|gb|BI478896.1|BI478896
EST:     GTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAG                         CATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
genomic: GTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgtcggtaacc ... tctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
EST: gi|15177612|gb|BI398551.1|BI398551
EST:     GTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAG                         CATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
genomic: GTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgtcggtaacc ... tctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
EST: gi|88758497|gb|DY542866.1|DY542866
EST:     GTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAG                         CATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
genomic: GTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgtcggtaacc ... tctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
EST: gi|32929052|gb|CF033864.1|CF033864
EST:     CGTGCCCTCCAG                         CATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
genomic: CGTGCCCTCCAGgtcggtaacc ... tctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgatctcttctctttaatctctgtgttaaaccaatatcgtattttctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG
                                            ttctgat  putative branch site (score: 3)
                                        tattttct  CT-rich tract
           tctttaat  TA-rich tract