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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttctgtcagttgaaagtatccgtttctctgtcaattgttgataggctcttgatagttatttttcttaatattatcagcttttctgatactgttgtttatgaactgcatctgccttcagCTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTATGGTGACATTATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCC

Basic information

species Zea mays
transcript GRMZM2G120857_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120857_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g16900.3 (Oryza sativa), 3'ss of exon 6
--------------------------------------------------------gtatgttctgtcagt-tgaaagtatccg-tttctctgtcaattgttgat-aggctcttgata-----gttatttttcttaatattat---cagct--tttctgatactgttg-tttatgaactgcatctgccttcagCTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTATGGTGACATTATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCC
                                                         |   |       || |||   | || | |    |||  || ||   || |  || ||  ||     |  | || | ||  | |  |   ||| |  ||  ||| ||  ||| ||| |||||    ||  | | ||||||||||||||||||||||||||||| ||| | |||||||||||||| |||||||| |||||||||||||| ||||||||| |||| || ||||||||| 
gtatgttgttctgctgataccaaaacctgtgctttgtttggtgttaatgttgaagcattcttcacactggtctgatgatctctgatcgacctgagaaatgcaaattatcctatttgtattctagccacttctattgctgtcctggacagttaattaatgacaccattgatttgtgaacattgtccccttgcagCTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTATGGTGATATTATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCT

upper sequence: GRMZM2G120857_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA13G20790.1 (Glycine max), 3'ss of exon 4
gtatgttctgtcagttgaaagtatccgtttctctgtcaattgttgataggctcttgatagttatttttcttaatattatcagcttttctgatactgttgtttatgaactgcatctgccttcagCTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTATGGTGACATTATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCC
                   | |||  ||     ||     ||   | |     ||   |  ||     |||| ||||   |  ||     ||  | ||| ||||       | || ||  |||||||||||||||||||  ||||| || ||| |||||||||| || || |||||||| ||||||||||| || |||||||| ||| | ||||| |||||  
-----------------gtaatattggtgaacttgatgtatgagaaaactgcatttggaaata-----cttagtatttggaaatt----aatgatattggttatttttctgaccttccg-cagCTTGTGAAGAATCCTGCACTTTTCGATGTACTAGTGATGCCTAACCTTTATGGTGATATTATTAGTGACCTTTGTGCTGGCTTGGTTGGGGGATTGGGTT

upper sequence: GRMZM2G120857_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA10G06590.2 (Glycine max), 3'ss of exon 4
gtatgttctgtcagttgaaagtatccgtttctctgtcaattgttgatag-gctcttgatagttatttttcttaatattatcagcttttctgatactgttgtttatgaactgcatctgccttcagCTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTATGGTGACATTATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCC
                   | |||  ||     ||     ||   | |  ||  |||  | |        ||| ||| |  |  ||   ||| |||| |  | ||   ||| | || ||| |||||||||||||||||||  ||||| || ||| |||||||||| || || |||||||| ||||| ||||| || |||||||| ||||| || || |||||| 
-----------------gtaatattggtgaaattgatgtatgagaaaactgcatttggaaatag------ttagtatcaggaaattaa-tgacactgct--taattttctg-accttcct-cagCTTGTGAAGAATCCTGCACTTTTCGATGTACTAGTGATGCCTAACCTTTATGGTGATATTATCAGTGACCTTTGTGCTGGCTTGATTGGAGGATTGGGCT

upper sequence: GRMZM2G120857_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT3G09810.1 (Arabidopsis thaliana), 3'ss of exon 4
---------------------------------------------------------------gtatgttctgtcagt---tgaaagtatccgtttctctgtcaattgttgataggctcttgatagttatttt--tcttaatattatcagcttttctgatactgttgtttatgaactgca-tctgccttc----agCTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTATGGTGACATTATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCC
                                                               ||   ||  || |||   ||  |  |||   ||   | | ||   | |||   |     |    || ||   |||   | |    |  ||| || ||       | |  ||     | |||   |||    |||||||||| || || |  |||||||| || || |||||||||||||||||||| || ||||| || ||| | ||||||||  |  | |||||  | || |
gtaagctataacatgatatccaccctatcttttgttccaaattatgtaaaggtcaatctcattgttaattaagttagtatttgggataatcttgttgattttgaaggttagatttcccagcaacccatacttgggtctgcttttcgctaattttacttatggaacaatgtgggattgataatcttaattctgacagCTTGTGAAAAACCCAGCACTTTTTGATGTCTTGGTGATGCCAAATCTCTATGGAGATATTATCAGCGATTTGTGTGCTGGACTTGTTGGGGGACTAGGAC

upper sequence: GRMZM2G120857_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT5G03290.1 (Arabidopsis thaliana), 3'ss of exon 4
--------------------------------gtatgttctgtcagttgaaagtatccg---tttctctgtcaattgttga---taggctcttgatagtt---atttttcttaatattatcagcttttctgatac--------tgttgtttatgaactgcatctgccttcagCTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTATGGTGACATTATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCC
                                ||   ||  || ||| |   | |  ||   |  |  |||  |||    |   | |  ||||   |  |   ||||   ||    || ||  || || | | |         ||    | || | ||  |  | ||| ||||||||||| || || |  |||||||| || || ||||||||||| || || |||||||||||||| ||||| ||||| || ||| | || ||  | ||  
gtaagctatgacaccgaatctactattttttcgttaattaagttagtggtcgggactcgggatcaccttgtagatttagaagtttggtttcttagcaacttgtatttgagttctgcttttccactgtttttacatgtggaatatgcgactgataatcttgagatacctgcagCTTGTGAAAAACCCAGCACTTTTTGATGTCTTGGTGATGCCAAACCTGTACGGTGACATTATTAGCGATCTGTGTGCCGGATTGGTTGGAGGACTAGGAT

upper sequence: GRMZM2G120857_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv08s0040g01700.t01 (Vitis vinifera), 3'ss of exon 4
gtatgttctgtcagttgaaagtatccgtttctctgtcaattgttgataggctcttgatagttatttttcttaatattatcagcttttctgatactgttgtttatgaactgcatctgccttcagCTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTATGGTGACATTATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCC
| |   | ||| ||   || |    | || ||  |   ||  |  | |    |   |   |          || | ||  | |   ||| |     || | | |  | |  |        |||||||||||||||||||  |||||||| || || |||||||| || |||||||||||||||||||||||||| |||||||| ||||| |||||  | ||| 
gcaaaatatgtaagaaaaacgagatcatt-ctaggcatatgatacagaaatgcactaggat----------aaaactaggaaccactctaac----ttctctcttgaataaa--------cagCTTGTGAAGAATCCTGCGCTTTTTGATGTGTTGGTGATGCCTAACCTCTATGGTGACATTATTAGTGATCTCTGTGCTGGCTTGATTGGGGGACTAGGCT

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|37380928|gb|CF627310.1|CF627310
EST:     ATCATTGACAATTGCTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTAT
genomic: ATCATTGACAATTGCTGTATGACGgtatgttctg ... ctgccttcagCTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTAT
EST: gi|76019790|gb|DT946960.1|DT946960
EST:     ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTAT
genomic: ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACGgtatgttctg ... ctgccttcagCTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTAT
EST: gi|110194437|gb|EC876335.1|EC876335
EST:     ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTAT
genomic: ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACGgtatgttctg ... ctgccttcagCTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTAT
EST: gi|31250098|gb|CD219122.1|CD219122
EST:     ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTAT
genomic: ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACGgtatgttctg ... ctgccttcagCTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTAT
EST: gi|74239665|gb|DT647579.1|DT647579
EST:     ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTAT
genomic: ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACGgtatgttctg ... ctgccttcagCTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTAT
EST: gi|23199568|gb|BU582133.1|BU582133
EST:     ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTAT
genomic: ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACGgtatgttctg ... ctgccttcagCTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTAT
EST: gi|87155757|gb|DY400546.1|DY400546
EST:     ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTAT
genomic: ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACGgtatgttctg ... ctgccttcagCTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTAT
EST: gi|29544695|gb|CB605075.1|CB605075
EST:     ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTAT
genomic: ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACGgtatgttctg ... ctgccttcagCTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTAT
EST: gi|32915735|gb|CF020547.1|CF020547
EST:     ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTAT
genomic: ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACGgtatgttctg ... ctgccttcagCTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTAT
EST: gi|33103704|gb|CF063664.1|CF063664
EST:     ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTAT
genomic: ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACGgtatgttctg ... ctgccttcagCTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTAT
EST: gi|29167895|gb|CB411155.1|CB411155
EST:     ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTAT
genomic: ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACGgtatgttctg ... ctgccttcagCTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTAT
EST: gi|211333614|gb|FL125152.1|FL125152
EST:     ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCC
genomic: ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACGgtatgttctg ... ctgccttcagCTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCC
EST: gi|9731686|gb|BE510438.1|BE510438
EST:     ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTAT
genomic: ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACGgtatgttctg ... ctgccttcagCTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTAT
EST: gi|211333619|gb|FL125157.1|FL125157
EST:     ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTAT
genomic: ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACGgtatgttctg ... ctgccttcagCTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTAT
EST: gi|37381420|gb|CF627593.1|CF627593
EST:     ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTAT
genomic: ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACGgtatgttctg ... ctgccttcagCTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTAT
EST: gi|37384800|gb|CF629499.1|CF629499
EST:     ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTAT
genomic: ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACGgtatgttctg ... ctgccttcagCTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTAT
EST: gi|31250137|gb|CD219161.1|CD219161
EST:     ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTAT
genomic: ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACGgtatgttctg ... ctgccttcagCTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaatattatcagcttttctgatactgttgtttatgaactgcatctgccttcagCTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTATGGTGACATTATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCC
                 ttctgat  putative branch site (score: 3)
                                            tctgccttc  putative PPT
     tattatca  TA-rich tract