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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaatctgccctatcttgattagtccacgttgtgtttgtcgtcgatgttcagacacattttgctcaattccttgttacatttaacgctgcttggtatcgtctattag

Basic information

species Zea mays
transcript GRMZM5G848768_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G848768_T03 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os02g57260.1 (Oryza sativa), 5'ss of exon 10
GCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaatctgccctatcttgattagtccacgttgtgtttgtcgtcgatgttcagacacattttgctcaattccttgttacatttaacgctgcttggtatcgtctattag
|||| || ||||||||||| ||||||||||||||||||||||||||||  ||    || ||  ||||||| || || || |||||||||||||||||||    || | |||  |  ||||  ||  |  | ||  |||          ||    |||  | || || ||| |  | | | ||   || |    |  |      ||| | 
GCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGAGGGACGTAGCGATGAAGAAGGGACTTCCTATTCTTGGTGTTTTCAGgtgctgcattttgcatttccttgtatatacagcatttggttca--------gtcttaacatgtgttcctgaatgctgtatgagat---actccctctattccaaaatataa-

upper sequence: GRMZM5G848768_T03 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA20G18980.1 (Glycine max), 5'ss of exon 10
GCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaatctgccctatcttga--ttagtccacgtt-gtgtttgt-cgtcgatgttcagac--acattttgctcaattccttgttacatttaacgctgcttggtatcgtctattag
| ||||| ||||| |||||||||||||||| ||||||||| || |||||||||  ||| ||  || | || ||||| |||||||||||||| |||||||  |   || ||   |||   |   |||||||  |   || ||| |  |  ||| | || |   ||||  ||     |   |    | ||  |   |   |                
GTAATTCTAGTCAGGTGAGTGATGGTGCTGCAGCTGTTCTGCTGATGAAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAGgt-acttcatttgtaatatagaggctttagtccctggcagtatttatatgctgat-tccaaattgacatgctgtgtgctctatgaagaaatgaaggaccaat----------------

upper sequence: GRMZM5G848768_T03 (Zea mays), 5'ss of exon 10
lower sequence: AT1G04710.1 (Arabidopsis thaliana), 5'ss of exon 10
GCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgccc----aatc--tgccctatcttgattagtccacgttgtgtttgtcgtcgatgttcagacacattttgctcaattccttgttacatttaacgctgcttggtatcgtctattag
| ||||| || ||| | ||||| ||||||||||||||||| || ||||  |||  ||| ||  || ||||||| || |||||||||||||| ||||||| | |     | |   | | |||| ||||    ||   | |   |||     |     ||    |||  || |                                            
GGAATTCTAGCCAATTAAGTGACGGTGCTGGAGCTGTTCTCCTTATGAGGAGAAATGTCGCAATGCAGAAAGGCCTTCCCATTCTTGGTGTATTCAGgtgggcttgatagttgatactctatattgacctttctttgcttcatttagtaacagcactcttggacacattacag------------------------------------------

upper sequence: GRMZM5G848768_T03 (Zea mays), 5'ss of exon 10
lower sequence: AT2G33150.1 (Arabidopsis thaliana), 5'ss of exon 10
GCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaatctgccctatcttgattagtccacgttgtgtttgtcgtcgatgttcagacacattttgctcaattccttgttacattta-acgctgcttggtatcgtctattag-------------------------------------------------------
| |||||||| ||||| ||||||||||| ||||| ||||| || ||||| |||  ||| ||  || | ||||| || ||| |||||||||| ||||||| |   |   |  | ||    | |  | |   |      |      |||        || |   |  | | |||| | |||||   | | |||  |     | |   ||                                                          
GAAATTCCAGCCAAGTAAGTGATGGTGCAGGAGCGGTTCTCCTAATGAAGAGAAGTGTTGCAATGCAAAAAGGACTTCCCGTTCTTGGTGTATTCAGgtgggtaataattacttacaaagctacgactgtggaagtctgaaaaccgaaaaaactgcagaggcttgtgatttccat-ttacacagatatgctagtatacgtggaaaatacattgttctttctgtatttggctttttctaagtagcacactattggacatattgcag

upper sequence: GRMZM5G848768_T03 (Zea mays), 5'ss of exon 10
lower sequence: Vv05s0051g00720.t01 (Vitis vinifera), 5'ss of exon 10
GCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaatctgccctatcttgattagtccacgtt-gtgtttgtcg-tcgatgt-tcagacacattttgctcaattccttgttacatttaacgctgcttggtatcgtctattag
| ||||| || ||||||||||||||||||||||||||||| |||||||| |||  ||| ||  ||   |||||| | || ||||||||||| |||||||     |||   || ||  |  ||  || ||  ||  ||  | | | |  |||  || |     ||| ||| |     | | ||   || |  || ||||||||          
GGAATTCTAGCCAAGTGAGTGATGGTGCTGGAGCTGTTCTCCTCATGAAGAGAAGTGTTGCAATGCGTAAAGGGTTACCTATTCTTGGTGTATTCAGgtatataaat---ccttagatgtatatgtacatatttatgaatttaggtaaatgcctctggtgtctttagctta---tatggatatggtttatact-cttggtataa--------

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|71769910|gb|DR967847.1|DR967847
EST:     AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAG                         GAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC
genomic: AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaat ... cgtctattagGAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC
EST: gi|60346439|gb|DN213412.1|DN213412
EST:     AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAG                         GAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC
genomic: AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaat ... cgtctattagGAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC
EST: gi|32868231|gb|CF007913.1|CF007913
EST:     AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAG                         GAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGTGTTGGTCCTGC
genomic: AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaat ... cgtctattagGAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC
EST: gi|6994094|gb|AW453308.1|AW453308
EST:     AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAG                         GAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGTGTTGGTCCTGC
genomic: AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaat ... cgtctattagGAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC
EST: gi|7031294|gb|AW461032.1|AW461032
EST:     AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAG                         GAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGTGTTGGTCCTGC
genomic: AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaat ... cgtctattagGAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC
EST: gi|149076676|gb|EE165319.2|EE165319
EST:     AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAG                         GAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC
genomic: AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaat ... cgtctattagGAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC
EST: gi|91874450|gb|EB404407.1|EB404407
EST:     AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAG                         GAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC
genomic: AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaat ... cgtctattagGAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC
EST: gi|213184067|gb|FM191388.1|FM191388
EST:     AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAG                         GAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGTGTTGGTCCTGC
genomic: AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaat ... cgtctattagGAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC
EST: gi|211292683|gb|FL176851.1|FL176851
EST:     AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAG                         GAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGTGTTGGTCCTGC
genomic: AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaat ... cgtctattagGAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC
EST: gi|74238395|gb|DT646309.1|DT646309
EST:     AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAG                         GAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC
genomic: AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaat ... cgtctattagGAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC
EST: gi|33942354|gb|CF348954.1|CF348954
EST:     AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAG                         GAGCCTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGTGTTGGTCCTGC
genomic: AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaat ... cgtctattagGAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC
EST: gi|148946680|gb|EC891943.2|EC891943
EST:     AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAG                         GAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC
genomic: AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaat ... cgtctattagGAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC
EST: gi|149100616|gb|EE186704.2|EE186704
EST:     AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAG                         GAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC
genomic: AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaat ... cgtctattagGAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC
EST: gi|32859198|gb|CD998879.1|CD998879
EST:     AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAG                         GAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGTGTTGGTCCTGC
genomic: AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaat ... cgtctattagGAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC
EST: gi|60672291|gb|DN475055.1|DN475055
EST:     AAA-GATCTGTGGCTCTGAA-AAAGGGCTGCCCATTCTTGGTGTTTTCAG                         GAGCTTTGCGGCTGTTGGA
genomic: AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaat ... cgtctattagGAGCTTTGCGGCTGTTGGA
EST: gi|78074202|gb|DV502636.1|DV502636
EST:     AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAG                         GAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC
genomic: AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaat ... cgtctattagGAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC
EST: gi|88752432|gb|DY536573.1|DY536573
EST:     AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAG                         GAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC
genomic: AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaat ... cgtctattagGAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC
EST: gi|211323452|gb|FL157684.1|FL157684
EST:     AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAG                         GAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGTGTTGGTCCTGC
genomic: AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaat ... cgtctattagGAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC
EST: gi|32859848|gb|CD999529.1|CD999529
EST:     AAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTNTGGTGTTTTCAG                         GAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGT-ATGGGTGTTGGTCCTGC
genomic: AAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCT-TGGTGTTTTCAGgttgcccaat ... cgtctattagGAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC
EST: gi|149101630|gb|EE187762.2|EE187762
EST:     AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAG                         GAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC
genomic: AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaat ... cgtctattagGAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC
EST: gi|101388206|gb|EB816117.1|EB816117
EST:     AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAG                         GAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC
genomic: AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaat ... cgtctattagGAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC
EST: gi|60345789|gb|DN212762.1|DN212762
EST:     AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAG                         GAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC
genomic: AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaat ... cgtctattagGAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC
EST: gi|101394624|gb|EB819247.1|EB819247
EST:     AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAG                         GAGCTTGGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC
genomic: AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaat ... cgtctattagGAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaatctgccctatcttgattagtccacgttgtgtttgtcgtcgatgttcagacacattttgctcaattccttgttacatttaacgctgcttggtatcgtctattag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA