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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgtcggtaacctttgcattgttttggctgatctcttctctttaatctctgtgttaaaccaatatcgtattttctgatgcag

Basic information

species Zea mays
transcript GRMZM2G057576_T01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 17
TGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgtcggtaacctttgcattgttttggctga--tctcttctctttaatctctgtgttaaaccaatatcgtattttctgatgcag
||| |||||||| ||||| ||||||||||||||||||||||| || |||||| |||||||||| |||||||||||||| || |||||||| || ||||||||| ||| |||||   ||||||||| | |  | | || |  ||   || | |||| ||  || ||  |||| |  |||||||
TGCTGATGCCATCCTTGCTAATGGTATGTTCAGTCATTATGATCGCCCTCGTGTTGCTCAGCTTTGTGAAAAGGCTGGCTTGTACTTGCGAGCTCTCCAGgtcagta-cctttttgttgttttggtttacttttttttttctttgcctgtctgtttaattaacattatattgt--gatgcag

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 17
TGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgtcggtaacctttgcattgttttggctga-tctcttctctttaatctctgtgttaaaccaatatcgtattttctgatgcag
||| |||||||| ||||| ||||||||||||||||||||||| || |||||| |||||||||| |||||||||||||| || |||||||| || ||||||||| ||| |||||   ||||||||| | | | | || |  ||   || | |||| ||  || ||  |||| |  |||||||
TGCTGATGCCATCCTTGCTAATGGTATGTTCAGTCATTATGATCGCCCTCGTGTTGCTCAGCTTTGTGAAAAGGCTGGCTTGTACTTGCGAGCTCTCCAGgtcagta-cctttttgttgttttggtttactttttttttctttgcctgtctgtttaattaacattatattgt--gatgcag

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA14G37510.1 (Glycine max), 5'ss of exon 15
TGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgtcggtaacctttgcattgtt--ttggctgatctcttctctttaatctctgtgttaaaccaatatcgtatttt-ctgatgcag
||| ||||| ||  | || ||||| ||||| ||||||||||||||||| || ||||||||||| ||||||||||| ||  | | | | || || || |||||   |  | | |    |  |   || ||| | | |  | |   |    | | || ||||  | | || | || ||  |||||
TGCTGATGCTATATTGGCCAATGGCATGTTTAGTCATTATGACCGTCCACGGATTGCTCAGCTTTGTGAAAAGGCCGGCCTTTTCATTCGGGCTCTTCAGgttctttgcttctattcttatgactgactgttatttcttgtcagaataatttcttgaacct-tcttgtgtgttgcttgtgcag

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA11G35460.1 (Glycine max), 5'ss of exon 16
TGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgtcggtaacc------tttgcattgttttggctgatctcttctctttaatc------tctgtgttaaaccaatatcgtattttctgatgcag
||| ||||| ||| | || ||||| |||||||| |||||||||||||||||||||||||| || |||||||| |||||  | ||  ||||  |  | || ||    |  |      | ||  || || |  ||| | |  |   || |  |        | | ||  |   ||  | |  ||| || |||||
TGCTGATGCAATTTTGGCTAATGGAATGTTCAGCCATTATGACCGTCCTCGTATTGCTCAACTTTGTGAAAAAGCTGGTCTTTATGTGCGATCTTTGCAAgtaatgactcaccaaatgtgttttattcttactggttttcttatttaacccaaaggccttctcttttattgattacattatttttggtgcag

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 17
TGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgtcggtaacctttgcat-tgttttgg-ctgatctcttctct---ttaatctctgtgttaaaccaat-----atcgtatt--ttctgatgcag
||| ||||| ||  | || ||||| |||||||| ||||||||||||||||||||||| ||||| || ||||| || ||  | ||  |||| ||  | || ||  | |  ||    || ||||||   ||      ||||||   ||| |||    || |||||  |     || | |||  |  || |||||
TGCTGATGCAATATTGGCTAATGGCATGTTCAGCCATTATGACCGTCCTCGTATTGCCCAGCTTTGCGAAAAAGCGGGCCTTTATGTGCGAGCTTTGCAAgtaaggactctccaaatgtgttttattctcgcactttctctatgttagtcttaaagtcaaaccctttgttgattgcattattcttggtgcag

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA18G02960.1 (Glycine max), 5'ss of exon 16
TGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgtcggtaacc------tttgcattgttttggctgatctcttctcttta------atctctgtgttaaaccaatatcgtattttctgatgcag
||| ||||| ||| | || ||||| |||||||| |||||||||||||||||||||||||| || |||||||| |||||  | ||  |||| ||  | || ||    |  |      | ||  || || |  ||| | |  |   || |      | |  | | ||  ||  ||  |    ||| || |||||
TGCTGATGCAATTTTGGCTAATGGAATGTTCAGCCATTATGACCGTCCTCGTATTGCTCAACTTTGTGAAAAAGCTGGTCTTTATGTGCGAGCTTTGCAAgtaatgactcaccaaatgtgttttattattactggttttcttatttaacccaaaagccttctcttttactgattacactatttttggtgcag

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA14G06340.2 (Glycine max), 5'ss of exon 17
TGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgtcggtaacctttgcat-tgttttgg-ctgatctcttctct---ttaatctctgtgttaaacc---aat--atcgtatt--ttctgatgcag
||| ||||| ||  | || ||||| |||||||| ||||||||||||||||||||||| || || |||||||| |||||  | ||  |||| ||  | || ||  | |  ||    || ||||||   ||      ||||||   |||||||     | |||||   |||  || | |||  |  || |||||
TGCTGATGCAATATTGGCTAATGGCATGTTCAGCCATTATGACCGTCCTCGTATTGCCCAACTTTGTGAAAAAGCTGGCCTTTATGTGCGAGCTTTGCAAgtaaggactctccaaatgtgttttattcttgcactttctctatgttaatcttaaaatcaaacccttaattgattgcattattcttggtgcag

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA01G38580.1 (Glycine max), 5'ss of exon 17
TGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgtcggtaacct-ttgcattgttttggc----tgatctcttctctttaatctctgtgttaaaccaatatcgtattttctgatgcag
||| ||||| ||  | || ||||| ||||||||||||||||| || || |||||||  || || ||||||||||||||  | | | | || || || |||||   |  | | ||   || |  || |    | ||    |||  |||   | | | || ||||      |||| || ||  |   
TGCTGATGCTATATTGGCCAATGGCATGTTCAGTCATTATGATCGCCCACGTATTGGACAACTATGTGAAAAGGCTGGCCTGTTCATACGGGCTCTTCAGgttctttgcttcttaagttctgatgacagtataatgatctcttgttagaatatttcttgaaccgtgtctgtatattgtgcag---

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 17
TGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgtcggtaacctttgcattgttttggctgatc----tcttctctttaatctctgtgttaaaccaatatcgtatttt-ctgatgcag
||| ||||| ||  | || ||||| ||||| ||||||||||||||||| || ||||||||||| ||||||||||||||  | | | | || || || |||||   |  | |||  ||| || || ||||      | |  | |   |    | | || ||||  | | || | || || ||||||
TGCTGATGCTATATTGGCCAATGGCATGTTTAGTCATTATGACCGTCCACGGATTGCTCAGCTTTGTGAAAAGGCTGGCCTTTTCATTCGGGCTCTTCAGgttctttgctttt--attcttatgactgactgtaatttcttgtcagaataatttcttgaacct-tcttgtgtgttgcttatgcag

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 15
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 17
TGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgtcggtaacc--tttgcattgttttggctgatctcttctcttta--atctctgtgttaaaccaatatcgtattttctgat----gcag
 || |||||  |  | || ||||| |||||||  || |||||||| ||||| |||||||| || ||||||||||||||| | ||  | |   || |  |||| ||||     |||  |   ||||  | |  |   |   ||||  ||||          | | |    |   || ||||    ||||
GGCTGATGCGGTATTAGCAAATGGGATGTTCACCCACTATGACCGGCCTCGCATTGCTCAACTTTGTGAAAAGGCTGGACTTTATATCCAATCCTTGAAGgttggtacatgttttttaccatttttaccggccaaatagatttatcatcttctcaccttccaacttcttttccttttgatttgtgcag

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 15
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 17
TGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgt-------cggtaacctttgcattgttttgg--ctgatctcttctctttaatctctgtgttaaaccaatatcgtattttctgatgcag
 || ||||| ||  | || ||||| |||||||| ||||||||||| |||||| |||||||||| ||||||||||||||| | ||| | |   |  |  ||||       |  |  | | |  | | || | |  || ||   |    |||  | ||     |||     | || | ||   |  |||||
GGCTGATGCAATCTTAGCAAATGGGATGTTCAGCCATTATGACCGGCCTCGTGTTGCTCAGCTTTGTGAAAAGGCTGGACTTTACATCCAATCTTTAAAGgtttttgctcaatgtcttctttaatattcttggcctaatagatgtatttttttttcccctctaacttcgtttccttttgctttgtgcag

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 15
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 17
TGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgtcggtaacctttgcattgttt---tggctgatctcttctctttaatctctg------tgttaaaccaatatcgtattttctgatgcag
 |||||||| ||  | || ||||||||||| ||||| ||||| || || |||||||| |||||||||||||| |||||  | ||  |||| ||||| |||||        ||  || | | |   ||    |  |  | ||    | || ||      | ||  |  ||     |  | ||| ||||||
CGCAGATGCTATATTAGCTAATGGTATGTTTAGTCACTATGATCGCCCACGTATTGCACAGCTCTGTGAAAAAGCTGGTCTTTATGTGCGAGCCCTTCAGgtataatggtttctcactatctgattgatgaactttatttcacagacctttgattgtttcttggattaaatgattcatctcttatgcag

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 15
lower sequence: PP1S270_53V6.1 (Physcomitrella patens), 5'ss of exon 17
TGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgtc-ggtaacctttgcattgttttggctgatctcttctctttaatctctgt--gtta-aaccaatatcgtattttctgatgcag----------------------------------------------------
 |||||||| ||| |  | ||||| || ||||  ||||||||||||||||| ||||||||||| ||||| ||||||||  | ||  |||||||  | |||||   | ||         |  | |        | |   |  || | | | |  | |  ||| |  | | |  | |   ||  ||                                                    
CGCAGATGCGATTTTGACTAATGGCATCTTCAAACATTATGACCGTCCTCGAATTGCTCAGCTTTGTGAGAAGGCTGGCGTGTATATGCGTGCTATGCAGgtttagaaattcgcttgctagtgtaatgacattttataccatactttttatccgctgcaactataaacctcgtctagaattgagcataactactttacacgacttaaatcgccgcgttgatgttttatcacttcag

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

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgtcggtaacctttgcattgttttggctgatctcttctctttaatctctgtgttaaaccaatatcgtattttctgatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA