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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGTCCATGTTGATACTGTTGTCATGAATCCTCCCTTTGGTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAGgtcagaaccggtgcttgtttgcgactagcagtttcctttggaagatgatatttgacattttaagtgcccatttgctactgacag

Basic information

species Zea mays
transcript GRMZM2G113640_T03
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113640_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os06g06730.1 (Oryza sativa), 5'ss of exon 6
GCGTCCATGTTGATACTGTTGTCATGAATCCTCCCTTTGGTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAGgtcaga--accggtgcttgtttgcgacta-gcagtttcct----ttggaagatgatatttgacattttaagtgcccatttgctactgacag
|| | | |||||| |||||||||||||||||||||||||| ||| | || || ||||| |||||||| ||| | ||||||| | || |||| ||   || ||       |||| |  |  ||  |  ||    ||     ||||| ||| | ||||| | |  | ||| |||| |  |||
GCCTTCTTGTTGACACTGTTGTCATGAATCCTCCCTTTGGGACAAGCAGAAAAGGAGCTGACATGGAATTCATTTCTATGGGCATGAAGgtgagggcactgggcagcagttgccatcatacacatgactgagattattgcatgatgtttaaaatttttaatatctatt-gctatttgcag

upper sequence: GRMZM2G113640_T03 (Zea mays), 5'ss of exon 5
lower sequence: AT4G28830.1 (Arabidopsis thaliana), 5'ss of exon 6
GCGTCCATGTTGATACTGTTGTCATGAATCCTCCCTTTGGTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAGgt------cagaaccggtgcttgtttgcgactagcagtttcctttggaagatgatatttgacattttaagtgcccatttg-ctactgacag
|| |   ||| ||||| ||||| ||||| ||||| ||||||||||| | ||| ||||| ||||||||||| ||||||  |||  || ||||      |||||  |    |   ||   |||      |   || | |  |     ||  |  |||  | |     |||| ||||   |||
GCCTGATTGTGGATACGGTTGTAATGAACCCTCCATTTGGTACACGGAAGAAAGGAGCTGACATGGAGTTTCTCTCTGCGGCAATGAAGgtaaacaacagaaaagaatatctctttttactgttttctaatttcgtatcactcggttacatgtttacattcgatgtttggctac--gcag

upper sequence: GRMZM2G113640_T03 (Zea mays), 5'ss of exon 5
lower sequence: Vv11s0016g03520.t01 (Vitis vinifera), 5'ss of exon 6
GCGTCCA--TGTTGATACTGTTGTCATGAATCCTCCCTTTGGTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAGgtcagaaccggtgcttgtttgcgactagcagtttcct-ttggaagatgatatttgacattttaagtgcccatttgctactgacag----------
  ||| |  ||||||||||||||| ||||||||||| ||||| ||||| | ||| || || |||||||| || ||| || |||| ||| |||| |  |  |   | | ||  |   |  ||| | | |  | |    | |||||||   || ||| |   |  ||   | | |  |          
--GTCAAATTGTTGATACTGTTGTAATGAATCCTCCATTTGGAACACGGAAGAAGGGGGCTGACATGGATTTTCTCGCTGTGGCTTTGAAGgtaaagatggtaccattttctcatttttcagatacatgcttgtgatttatatttg---ttctaattaatctattttcattaattggttgtgtcag

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|211270654|gb|FL248444.1|FL248444
EST:     GTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGMAG                         GTTGCTTCTCAAGCTGTCTATTCTCTACACAAGACTTCCACTAGAGAA
genomic: GTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAGgtcagaaccg ... ctactgacagGTTGCTTCTCAAGCTGTCTATTCTCTACACAAGACTTCCACTAGAGAA
EST: gi|32928356|gb|CF033168.1|CF033168
EST:     ACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAG                         GTTGCTTCTCAAGCTGTCTATTCTCTACACAAGACTTCCACTAGAGAA
genomic: ACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAGgtcagaaccg ... ctactgacagGTTGCTTCTCAAGCTGTCTATTCTCTACACAAGACTTCCACTAGAGAA
EST: gi|213171204|gb|FM188301.1|FM188301
EST:     GTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAG                         GTTGCTTCTCAAGCTGTCTATTCTCTACACAAGACTTCCACTAGAGAA
genomic: GTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAGgtcagaaccg ... ctactgacagGTTGCTTCTCAAGCTGTCTATTCTCTACACAAGACTTCCACTAGAGAA
EST: gi|78110824|gb|DV529222.1|DV529222
EST:     GTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAG                         GTTGCTTCTCAAGCTGTCTATTCTCTACACA
genomic: GTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAGgtcagaaccg ... ctactgacagGTTGCTTCTCAAGCTGTCTATTCTCTACACA
EST: gi|6227108|gb|AW155812.1|AW155812
EST:     GTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAG                         GTTGCTTCTCAAGCTGTCTATTCTCTACACAAGACTTCCACTAGAGAA
genomic: GTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAGgtcagaaccg ... ctactgacagGTTGCTTCTCAAGCTGTCTATTCTCTACACAAGACTTCCACTAGAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGTCCATGTTGATACTGTTGTCATGAATCCTCCCTTTGGTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAGgtcagaaccggtgcttgtttgcgactagcagtttcctttggaagatgatatttgacattttaagtgcccatttgctactgacag

- - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA