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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAATGGTGGCGCGTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAGgtgagatcacattacatgtacagttataggtgcaccaagccatttcttgctgtatctagtaaagaacgctgtgtaaaaatgcaaccaagcagcagcataatataaattgtgactgttttacttttttttcag

Basic information

species Zea mays
transcript GRMZM2G033526_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G033526_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os10g42100.1 (Oryza sativa), 5'ss of exon 7
GCAATGGTGGCGCGTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAGgtgagatcacatt-acatgtacagttataggtgcaccaagccatttcttg-------------------------ctgtatctagtaa--agaacgct----gtgtaaaaatgcaaccaagcagcagcataatataaattgtgactgttttacttttttttcag
|| ||||||||  | || || ||||||||||||||||| |||||||| ||||||||||| ||||| || | | |||   |  ||   |||   |||||  ||  ||| | ||                           | ||| |  | |  || ||||      || || ||   ||  |||||  | ||  || |||||      |||||||||| |       
GCGATGGTGGCAAGAGGGGATCTTGGTGCTGAACTTCCAATTGAGGAAGTTCCTTTGCTGCAGgttagtttaaatttgtagataattttactagtgcaagaaaacatgtgtttgttcccccctcactctctacatcccttttatttgtttattagcacgcctaaaatgcaacaaatgaataaagcactaacaacatttaaatcacatgtgttttacttctccag---

upper sequence: GRMZM2G033526_T02 (Zea mays), 5'ss of exon 7
lower sequence: AT1G32440.1 (Arabidopsis thaliana), 5'ss of exon 7
GCAATGGTGGCGCGTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAGgtgagatcacattacatgtacagttataggtgcaccaagccatttcttgctg-tatcta-gtaaagaacgctgtgtaaaaatgcaaccaagcagcagcataatataaattgtgactgttttacttttttttcag
|||||||| || |||||||| ||||| ||||||||||| ||||| || || || ||| ||||||| |   ||      |      |||   |   ||  |    |     || || ||| || | |        |||||   |||   |                                                
GCAATGGTTGCTCGTGGAGATCTTGGAGCTGAACTTCCCATTGAAGAGGTCCCGTTGTTACAGgtaaatcca------agacttggtttctgaaacattactttagactctgttggtatttatgcatttgctattgtgtcttaattttag-----------------------------------------------
















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|22133857|gb|BQ833942.1|BQ833942
EST:     TGGAGACCTTGNG-GCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAG                         GCAGAGATTGTCCAAACATGTCGAAGCATGGAGAAACCAGTCATTGTCGCT
genomic: TGGAGACCTTG-GTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAGgtgagatcac ... tttttttcagGCAGAGATTGTCCAAACATGTCGAAGTATGGAGAAACCAGTCATTGTCGCT
EST: gi|32858382|gb|CD998063.1|CD998063
EST:     GTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAG                         GCAGAGATTGTCCAAACATGTCGAAGCATGGAGAAACCAGTCATTGGCGCT
genomic: GTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAGgtgagatcac ... tttttttcagGCAGAGATTGTCCAAACATGTCGAAGTATGGAGAAACCAGTCATTGTCGCT
EST: gi|22542067|gb|BU092505.1|BU092505
EST:     G-GGAGACCTTGG-GCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAG                         GCAGAGATTGTCCAAACATGTCGAAGCATGGAGAAACCAGTCATTGTCGCT
genomic: GTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAGgtgagatcac ... tttttttcagGCAGAGATTGTCCAAACATGTCGAAGTATGGAGAAACCAGTCATTGTCGCT
EST: gi|87155458|gb|DY400247.1|DY400247
EST:     GTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAG                         GCAGAGATTGTCCAAACATGTCGAAGCATGGAGAAACCAGTCATTGTCGCT
genomic: GTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAGgtgagatcac ... tttttttcagGCAGAGATTGTCCAAACATGTCGAAGTATGGAGAAACCAGTCATTGTCGCT
EST: gi|60341691|gb|DN208664.1|DN208664
EST:     GTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAG                         GCAGAGATTGTCCAAACATGTCGAAGTATGGAGAAACCAGTCATTGTCGCT
genomic: GTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAGgtgagatcac ... tttttttcagGCAGAGATTGTCCAAACATGTCGAAGTATGGAGAAACCAGTCATTGTCGCT
EST: gi|67016939|gb|CO445688.1|CO445688
EST:     GTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAG                         GCAGAGATTGTCCAAACATGTCGAAGCATGGAGAAACCAGTCATTGTCGCT
genomic: GTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAGgtgagatcac ... tttttttcagGCAGAGATTGTCCAAACATGTCGAAGTATGGAGAAACCAGTCATTGTCGCT
EST: gi|20208070|gb|BQ134159.1|BQ134159
EST:     TGAGGATGTTCCTTTGCTACAG                         GCAGAGATTGTCCAAACATGTCGAAGCATGGAGAAACCAGTCATTGTCGCT
genomic: TGAGGATGTTCCTTTGCTACAGgtgagatcac ... tttttttcagGCAGAGATTGTCCAAACATGTCGAAGTATGGAGAAACCAGTCATTGTCGCT
EST: gi|67022089|gb|CO450838.1|CO450838
EST:     GTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAG                         GCAGAGATTGTCCAAACATGTCGAAGCATGGAGAAACCAGTCATTGTCGCT
genomic: GTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAGgtgagatcac ... tttttttcagGCAGAGATTGTCCAAACATGTCGAAGTATGGAGAAACCAGTCATTGTCGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAATGGTGGCGCGTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAGgtgagatcacattacatgtacagttataggtgcaccaagccatttcttgctgtatctagtaaagaacgctgtgtaaaaatgcaaccaagcagcagcataatataaattgtgactgttttacttttttttcag

- - - - - -  GTGGAG
- - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - -  AGGATG