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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGCCGTGAAGTGTCTGAAAAGTACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACGgtatgttctgtcagttgaaagtatccgtttctctgtcaattgttgataggctcttgatagttatttttcttaatattatcagcttttctgatactgttgtttatgaactgcatctgccttcag

Basic information

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

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120857_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g16900.3 (Oryza sativa), 5'ss of exon 6
TGTTGCCGTGAAGTGTCTGAAAAGTACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACGgtatgtt------ctgtcagttgaaagtatccgtttctctgt-caattgttgataggctcttgatagttatttttcttaatattatcagcttttctgatac----tgttgtttatgaactgcatctgccttcag-----------------------------------------------------------
|| || ||||||||| |||| |||||||||||||||  ||||||||||||||||||||||||||| ||||||||||||||||      |||  |    ||  | | | ||  |  ||   | ||||||     |||| | | |  | |       | | |||  | |     || |    | |  | | || | |  | |  | |  |                                                            
TGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACGgtatgttgttctgctgataccaaaacctgtgctttgtttggtgttaatgttgaagcattcttcacactggtctgatgatctctgatcgacctgagaaatgcaaattatcctatttgtattctagccacttctattgctgtcctggacagttaattaatgacaccattgatttgtgaacattgtccccttgcag

upper sequence: GRMZM2G120857_T02 (Zea mays), 5'ss of exon 5
lower sequence: PP1S83_44V6.1 (Physcomitrella patens), 5'ss of exon 4
TGTTGCCGTGAAGTGTCTGAAAAGTACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACGgtatgttctgtcagttgaaagtatccgtttctctgtcaattgttgataggctcttgatagttatttttcttaatattatcagcttttctgatactgttgtttatgaactgcatctgccttcag
|||||| | ||| |  |||   ||||||| || |||   || || ||||||||||||||||||||||| |||| |||| |||   |||          | |   ||  |    | ||| |||  |   |||| ||  |    || || |      |  |||     |||  ||  ||  ||   |             
TGTTGCAGGGAAATAGCTGCTGAGTACCCAGACATTGTGTATGAAGAGGTCATCATTGACAATTGCTGCATGATGgtaagtttcatcaacc-------ttctaatcgttagagaatgtggattcgaatttga-aggaaccagtcctagt-----taaatttatgcgtacatttagtttggactagtga----------
















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

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTGCCGTGAAGTGTCTGAAAAGTACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACGgtatgttctgtcagttgaaagtatccgtttctctgtcaattgttgataggctcttgatagttatttttcttaatattatcagcttttctgatactgttgtttatgaactgcatctgccttcag

- - - - - - - - - - - - - - - - - - - - - GAGGAG