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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGCCGGAGCAGCCGGGAGCGCGGGGTTCGGAGCACGGGACGCGGAACTCGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTGgtgaggctcagctatccatgcattcaaattcaatcaatcctcccggctaatctgtcgatgtctgcactgcacag

Basic information

species Zea mays
transcript GRMZM2G005859_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005859_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g01014.1 (Oryza sativa), 5'ss of exon 1
GCCGCCGGAGCAGCCGGGAGCGCGGGGTTCGGAGCACGGGACGCGGAACTCGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTGgtg-----aggctcagctatcca---tgcattca--aattcaatcaatcctcccggctaatctgtcgatgtctgcactgcacag------------------------------------
 ||| |||||  |  ||  ||| ||| |||| ||| ||||||||||| || ||||||||||| | ||| || ||||| ||||||||||||||||||||||||           | | |||      | | || |  | || ||| ||| |         |    ||||||     |    |||                                     
ACCGGCGGAGGCGGAGGAGGCGGGGGCTTCGCAGCCCGGGACGCGGAGCTGGCCATGTGGGAGAGGCTGGGAGCGGTTGTCAGGCTCAGCTATGGCATTGgtactaacgactcctgttatttcatctacttttagtatttaaattaattccattttagtaataatcgatgctactatgcaacaattaagtaataatagaataataatctgatgggtgcag
















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|50335119|gb|CO530245.1|CO530245
EST:     CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTG                         GGATCTACGGGGCCATGGCACTCGCCGGGAGATTCATATGCCAAATGGCCG
genomic: CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTGgtgaggctca ... cactgcacagGGATCTACGGGGCCATGGCACTCGCCGGGAGATTCATATGCCAAATGGCCG
EST: gi|149043962|gb|EE047444.2|EE047444
EST:     CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTG                         GGATCTACGGGGCCATGGCACTCGCCGGGAGATTCATATGCCAAATGGCCG
genomic: CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTGgtgaggctca ... cactgcacagGGATCTACGGGGCCATGGCACTCGCCGGGAGATTCATATGCCAAATGGCCG
EST: gi|101392576|gb|EB818218.1|EB818218
EST:     CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTG                         GGATCTACGGGGCCATGGCACTCGCCGGGAGATTCATATGCCAAATGGCCG
genomic: CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTGgtgaggctca ... cactgcacagGGATCTACGGGGCCATGGCACTCGCCGGGAGATTCATATGCCAAATGGCCG
EST: gi|211010141|gb|FL113888.1|FL113888
EST:     CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTG                         GGATCTACGGGGCCATGGCACTCGCCGGGAGATTCATATGCCAAATGGCCG
genomic: CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTGgtgaggctca ... cactgcacagGGATCTACGGGGCCATGGCACTCGCCGGGAGATTCATATGCCAAATGGCCG
EST: gi|71445181|gb|DR826231.1|DR826231
EST:     CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTG                         GGATCTACGGGGCCATGGCACTCGCCGGGAGATTCATATGCCAAATGGCCG
genomic: CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTGgtgaggctca ... cactgcacagGGATCTACGGGGCCATGGCACTCGCCGGGAGATTCATATGCCAAATGGCCG
EST: gi|78109220|gb|DV527636.1|DV527636
EST:     CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTG                         GGATCTACGGGGCCATGGCACTCGCCGGGAGATTCATATGCCAAATGGCCG
genomic: CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTGgtgaggctca ... cactgcacagGGATCTACGGGGCCATGGCACTCGCCGGGAGATTCATATGCCAAATGGCCG
EST: gi|149090531|gb|EE179841.2|EE179841
EST:     CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTG                         GGATCTACGGGGCCATGGCACTCGCCGGGAAATTCATATGCCAAATG
genomic: CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTGgtgaggctca ... cactgcacagGGATCTACGGGGCCATGGCACTCGCCGGGAGATTCATATGCCAAATG
EST: gi|50338466|gb|CO533592.1|CO533592
EST:     CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTG                         GGATCTACGGGGCCATGGCACTCGCCGGGAGATTCATATGCCAAATGGCCG
genomic: CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTGgtgaggctca ... cactgcacagGGATCTACGGGGCCATGGCACTCGCCGGGAGATTCATATGCCAAATGGCCG
EST: gi|76020246|gb|DT947416.1|DT947416
EST:     CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTG                         GGATCTACGGGGCCATGGCACTCCCCGGGAGATTCATATGCCAAATGGCCG
genomic: CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTGgtgaggctca ... cactgcacagGGATCTACGGGGCCATGGCACTCGCCGGGAGATTCATATGCCAAATGGCCG
EST: gi|7844544|gb|AW787766.1|AW787766
EST:     CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTG                         GGATCTACGGGGCCATGGCACTCGCCGGGAGATTCATATGCCAAATGGCCG
genomic: CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTGgtgaggctca ... cactgcacagGGATCTACGGGGCCATGGCACTCGCCGGGAGATTCATATGCCAAATGGCCG
EST: gi|211423764|gb|FL057577.1|FL057577
EST:     CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTG                         GGATCTACGGGGCCATGGCACTCGCCGGGAGATTCATATGCCAAATGGCCG
genomic: CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTGgtgaggctca ... cactgcacagGGATCTACGGGGCCATGGCACTCGCCGGGAGATTCATATGCCAAATGGCCG
EST: gi|78180235|gb|DV550608.1|DV550608
EST:     CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTG                         GGATCTACGGGGCCATGGCACTCGCCGGGAGATTCATATGCCAAATGGCCG
genomic: CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTGgtgaggctca ... cactgcacagGGATCTACGGGGCCATGGCACTCGCCGGGAGATTCATATGCCAAATGGCCG
EST: gi|211041393|gb|FL113883.1|FL113883
EST:     CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTG                         GGATCTACGGGGCCCTGGCACTCGCCGGGAGATTCATATGCCAAATGGCCC
genomic: CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTGgtgaggctca ... cactgcacagGGATCTACGGGGCCATGGCACTCGCCGGGAGATTCATATGCCAAATGGCCG
EST: gi|76290855|gb|DV030423.1|DV030423
EST:     CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTG                         GGATCTACGGGGCCATGGCACTCGCCGGGAGATTCATATGCCAAATGGCCG
genomic: CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTGgtgaggctca ... cactgcacagGGATCTACGGGGCCATGGCACTCGCCGGGAGATTCATATGCCAAATGGCCG
EST: gi|78091085|gb|DV519459.1|DV519459
EST:     CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTG                         GGATCTACGGGGCCATGGCACTCGCCGGGAGATTCATATGCCAAATGGCCG
genomic: CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTGgtgaggctca ... cactgcacagGGATCTACGGGGCCATGGCACTCGCCGGGAGATTCATATGCCAAATGGCCG
EST: gi|91874018|gb|EB403975.1|EB403975
EST:     CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTG                         GGATCTACGGGGCCATGGCACTCGCCGGGAGATTC-TATGCCA
genomic: CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTGgtgaggctca ... cactgcacagGGATCTACGGGGCCATGGCACTCGCCGGGAGATTCATATGCCA
EST: gi|148964395|gb|EC905771.2|EC905771
EST:     CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTG                         GGATCTACGGGGCCATGGCACTCGCCGGGAGATTCATATGCCAAATGGCCG
genomic: CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTGgtgaggctca ... cactgcacagGGATCTACGGGGCCATGGCACTCGCCGGGAGATTCATATGCCAAATGGCCG
EST: gi|149074609|gb|EE163014.2|EE163014
EST:     CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTG                         GGATCTACGGGGCCATGGCACTCGCCGGGAGATTCATATGCCAAATGGCCG
genomic: CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTGgtgaggctca ... cactgcacagGGATCTACGGGGCCATGGCACTCGCCGGGAGATTCATATGCCAAATGGCCG
EST: gi|211010144|gb|FL113891.1|FL113891
EST:     CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTG                         GGATCTACGGGGCCATG
genomic: CGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTGgtgaggctca ... cactgcacagGGATCTACGGGGCCATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCGCCGGAGCAGCCGGGAGCGCGGGGTTCGGAGCACGGGACGCGGAACTCGCCATGTGGGACAAGCTCGGGGCGGTCGTCAGGCTCAGCTATGGCATTGgtgaggctcagctatccatgcattcaaattcaatcaatcctcccggctaatctgtcgatgtctgcactgcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT