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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtgtcgattgccttgatctacaccctcttctctcacctatttatccataacatctgattactgaatcatccatgcttagGCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC

Basic information

species Zea mays
transcript GRMZM5G848768_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G848768_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os02g57260.1 (Oryza sativa), 3'ss of exon 11
gtctgtgtcgattgccttgatctacaccctcttctctcacctatttatccataacatctgattactgaatcatccatgct------tagGCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC----------------------------------------------------
|| |||  |  ||  |   ||   | | ||| | |    | ||  || | | ||    ||||  |     ||||  |  |      ||||||||||| || ||||| || ||||||||||||||| |||| ||||||                                                    
gtttgttactttttacaatattagctcactcgtttact-cgtacctagctacaatggttgatacccatgccatctgtattcttgtatagGCCTTCGCTTCGCAGTTCGTGTATTGCTGCAACAAGCTGGGACTGGACAGGTCAAAAGTAAACGTGAATGGAGGCGCAATCGCCCTAGGACATCCTCTTG
















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:     AGTCTGCAGGCCTTGAGATTGGAGACATTGATTTGTTTGAACTGAATGAG                         GCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC
genomic: AGTCTGCAGGCCTTGAGATTGGAGACATTGATTTGTTTGAACTGAATGAGgtctgtgtcg ... ccatgcttagGCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC
EST: gi|60346439|gb|DN213412.1|DN213412
EST:     AGTCTGCAGGCCTTGAGATTGGAGACATTGATTTGTTTGAACTGAATGAG                         GCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC
genomic: AGTCTGCAGGCCTTGAGATTGGAGACATTGATTTGTTTGAACTGAATGAGgtctgtgtcg ... ccatgcttagGCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC
EST: gi|32868231|gb|CF007913.1|CF007913
EST:     AGTCTGCAGGCCTTGAGATTGGCGACATTGATCTGTTTGAACTGAATGAG                         GCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGGTGGGGCTGGAC
genomic: AGTCTGCAGGCCTTGAGATTGGAGACATTGATTTGTTTGAACTGAATGAGgtctgtgtcg ... ccatgcttagGCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC
EST: gi|6994094|gb|AW453308.1|AW453308
EST:     AGTCTGCAGGCCTTGAGATTGGCGACATTGATCTGTTTGAACTGAATGAG                         GCCTTCGCCTCTCAGTTTGTCTATTGCTGC
genomic: AGTCTGCAGGCCTTGAGATTGGAGACATTGATTTGTTTGAACTGAATGAGgtctgtgtcg ... ccatgcttagGCCTTCGCCTCTCAGTTTGTCTATTGCTGC
EST: gi|7031294|gb|AW461032.1|AW461032
EST:     AGTCTGCAGGCCTTGAGATTGGCGACATTGATCTGTTTGAACTGAATGAG                         GCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC
genomic: AGTCTGCAGGCCTTGAGATTGGAGACATTGATTTGTTTGAACTGAATGAGgtctgtgtcg ... ccatgcttagGCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC
EST: gi|149076676|gb|EE165319.2|EE165319
EST:     AGTCTGCAGGCCTTGAGATTGGAGACATTGATTTGTTTGAACTGAATGAG                         GCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC
genomic: AGTCTGCAGGCCTTGAGATTGGAGACATTGATTTGTTTGAACTGAATGAGgtctgtgtcg ... ccatgcttagGCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC
EST: gi|91874450|gb|EB404407.1|EB404407
EST:     AGTCTGCAGGCCTTGAGATTGGAGACATTGATTTGTTTGAACTGAATGAG                         GCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC
genomic: AGTCTGCAGGCCTTGAGATTGGAGACATTGATTTGTTTGAACTGAATGAGgtctgtgtcg ... ccatgcttagGCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC
EST: gi|211361818|gb|FL432329.1|FL432329
EST:     AGTCTGCAGGCCTTGAGATTGGCGACATTGATCTGTTTGAACTGAATGAG                         GCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC
genomic: AGTCTGCAGGCCTTGAGATTGGAGACATTGATTTGTTTGAACTGAATGAGgtctgtgtcg ... ccatgcttagGCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC
EST: gi|211292683|gb|FL176851.1|FL176851
EST:     AGTCTGCAGGCCTTGAGATTGGCGACATTGATCTGTTTGAACTGAATGAG                         GCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGAGGCTGGAC
genomic: AGTCTGCAGGCCTTGAGATTGGAGACATTGATTTGTTTGAACTGAATGAGgtctgtgtcg ... ccatgcttagGCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC
EST: gi|74238395|gb|DT646309.1|DT646309
EST:     AGTCTGCAGGCCTTGAGATTGGAGACATTGATTTGTTTGAACTGAATGAG                         GCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC
genomic: AGTCTGCAGGCCTTGAGATTGGAGACATTGATTTGTTTGAACTGAATGAGgtctgtgtcg ... ccatgcttagGCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC
EST: gi|33942354|gb|CF348954.1|CF348954
EST:     AGTCTGCAGGCCTTGAGATTGGCGACATTGATCTGTTTGAACTGAATGAG                         GCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC
genomic: AGTCTGCAGGCCTTGAGATTGGAGACATTGATTTGTTTGAACTGAATGAGgtctgtgtcg ... ccatgcttagGCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC
EST: gi|148946680|gb|EC891943.2|EC891943
EST:     AGTCTGCAGGCCTTGAGATTGGAGACATTGATTTGTTTGAACTGAATGAG                         GCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC
genomic: AGTCTGCAGGCCTTGAGATTGGAGACATTGATTTGTTTGAACTGAATGAGgtctgtgtcg ... ccatgcttagGCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC
EST: gi|149100616|gb|EE186704.2|EE186704
EST:     AGTCTGCAGGCCTTGAGATTGGAGACATTGATTTGTTTGAACTGAATGAG                         GCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC
genomic: AGTCTGCAGGCCTTGAGATTGGAGACATTGATTTGTTTGAACTGAATGAGgtctgtgtcg ... ccatgcttagGCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC
EST: gi|32859198|gb|CD998879.1|CD998879
EST:     AGTCTGCAGGCCTTGAGATTGGCGACATTGATCTGTTTGAACTGAATGAG                         GCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC
genomic: AGTCTGCAGGCCTTGAGATTGGAGACATTGATTTGTTTGAACTGAATGAGgtctgtgtcg ... ccatgcttagGCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC
EST: gi|78074202|gb|DV502636.1|DV502636
EST:     AGTCTGCAGGCCTTGAGATTGGAGACATTGATTTGTTTGAACTGAATGAG                         GCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC
genomic: AGTCTGCAGGCCTTGAGATTGGAGACATTGATTTGTTTGAACTGAATGAGgtctgtgtcg ... ccatgcttagGCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC
EST: gi|88752432|gb|DY536573.1|DY536573
EST:     AGTCTGCAGGCCTTGAGATTGGAGACATTGATTTGTTTGAACTGAATGAG                         GCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC
genomic: AGTCTGCAGGCCTTGAGATTGGAGACATTGATTTGTTTGAACTGAATGAGgtctgtgtcg ... ccatgcttagGCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC
EST: gi|211323452|gb|FL157684.1|FL157684
EST:     AGTCTGCAGGCCTTGAGATTGGCGACATTGATCTGTTTGAACTGAATGAG                         GCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAG
genomic: AGTCTGCAGGCCTTGAGATTGGAGACATTGATTTGTTTGAACTGAATGAGgtctgtgtcg ... ccatgcttagGCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAG
EST: gi|149101630|gb|EE187762.2|EE187762
EST:     AGTCTGCAGGCCTTGAGATTGGAGACATTGATTTGTTTGAACTGAATGAG                         GCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC
genomic: AGTCTGCAGGCCTTGAGATTGGAGACATTGATTTGTTTGAACTGAATGAGgtctgtgtcg ... ccatgcttagGCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC
EST: gi|101388206|gb|EB816117.1|EB816117
EST:     AGTCTGCAGGCCTTGAGATTGGAGACATTGATTTGTTTGAACTGAATGAG                         GCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC
genomic: AGTCTGCAGGCCTTGAGATTGGAGACATTGATTTGTTTGAACTGAATGAGgtctgtgtcg ... ccatgcttagGCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC
EST: gi|60345789|gb|DN212762.1|DN212762
EST:     AGTCTGCAGGCCTTGAGATTGGAGACATTGATTTGTTTGAACTGAATGAG                         GCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC
genomic: AGTCTGCAGGCCTTGAGATTGGAGACATTGATTTGTTTGAACTGAATGAGgtctgtgtcg ... ccatgcttagGCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC
EST: gi|101394624|gb|EB819247.1|EB819247
EST:     AGTCTGCAGGCCTTGAGATTGGAGACATTGATTTGTTTGAACTGAATGAG                         GCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC
genomic: AGTCTGCAGGCCTTGAGATTGGAGACATTGATTTGTTTGAACTGAATGAGgtctgtgtcg ... ccatgcttagGCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcttctctcacctatttatccataacatctgattactgaatcatccatgcttagGCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC
             tatttat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtgtcgattgccttgatctacaccctcttctctcacctatttatccataacatctgattactgaatcatccatgcttagGCCTTCGCCTCTCAGTTTGTCTATTGCTGCAACAAGTTGGGGCTGGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA