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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtagctagccaatctctcctgctttctctctctctctcaagtctgaatcgactattctccgtcattttcttgagcatttctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCTTAT

Basic information

species Zea mays
transcript GRMZM2G168143_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168143_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g01850.1 (Oryza sativa), 3'ss of exon 2
gtcagtagctagccaatct-ctcctgctttctctctctc---tctcaagtctgaatcgactattctccgtca-------ttttcttgagcatttctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCTTAT
||||||  |   |   ||| ||||| |||  ||  ||||    ||       | |||||      | | |||       |  || |   || || | |||  |||| || || || |||||||||||| | |||||||||||    |||||||| |||||||||||||||||||||||| | |
gtcagtccccctcttctcttctcctccttattcaatctcattccttctcatcggatcgatctcctttcttcacaccagataatcatcttcacttgtacctctagGTTTCACTCTGCGTCAAGAGGCTCGTTTACACCAACGACCAGGGAGAGATTGTCAAAGGAGTCTGCTCCAACTTCCTCT

upper sequence: GRMZM2G168143_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT5G66190.2 (Arabidopsis thaliana), 3'ss of exon 3
gtcagtagctagccaatctctcctgctttctctctctctctcaagtctgaatcgactattctccgtcattttcttgagcatttctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCTTAT
    |||   |   |||| |||   |     ||  ||   | | |  | |    |  ||  ||  | || |     |     ||    ||||||| || || ||||||||||| ||  | ||||| || |||| ||||||||| || || || ||||||||||||||||| |
----gtaagcaaataatccctctaac---aactaactaaataatgatttacaaaatgatcttctcttatctgg--aaatggatccttttgcagGTTTCTCTCTGTGTCAAGAGACTAGTTTACACAAATGATGGCGGAGAGATTGTTAAGGGGGTCTGCTCCAACTTCTTGT
















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|71441572|gb|DR822622.1|DR822622
EST:     TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACA                         GTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
EST: gi|6696066|gb|AW289174.1|AW289174
EST:     TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACA                         GTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
EST: gi|91056042|gb|EB166460.1|EB166460
EST:     TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACA                         GTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
EST: gi|6194972|gb|AW147076.1|AW147076
EST:     TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACA                         GTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
EST: gi|89758955|gb|DY687935.1|DY687935
EST:     TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACA                         GTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
EST: gi|149083857|gb|EE173232.2|EE173232
EST:     TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACA                         GTCTCGCTGTGTGTCAAGAGGCTCATCTACCCCAACGATGCCGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
EST: gi|8929977|gb|BE224741.1|BE224741
EST:     TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACA                         GTCTCGCTGTGTGTCATGTAGGCTCATCTACACCAACGATGCCGGAGAGAT
genomic: TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAG-AGGCTCATCTACACCAACGATGCCGGAGAGAT
EST: gi|93015751|gb|EB641271.1|EB641271
EST:     TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACA                         GTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
EST: gi|148932036|gb|EC875356.2|EC875356
EST:     TCTACTCCATCGCCAGCAGCGCGATCGGCGAATTCGGCGACTTCAAGACA                         GTCTCGCTGTGTGTCAAGAGGCTCATCTACCCCAA-GAATGCCGGAGAGAT
genomic: TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGA-TGCCGGAGAGAT
EST: gi|148939854|gb|EC884563.2|EC884563
EST:     TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACA                         GTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
EST: gi|76923047|gb|DV169308.1|DV169308
EST:     TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACA                         GTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
EST: gi|148952933|gb|EE152405.2|EE152405
EST:     TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACA                         GTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
EST: gi|50327429|gb|CO522555.1|CO522555
EST:     TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACA                         GTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
EST: gi|9956136|gb|BE643570.1|BE643570
EST:     TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACA                         GTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
EST: gi|76280879|gb|DV020447.1|DV020447
EST:     TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACA                         GTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
EST: gi|89756101|gb|DY686266.1|DY686266
EST:     TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACA                         GTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
EST: gi|149112200|gb|EE191272.2|EE191272
EST:     TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACA                         GTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
EST: gi|74242655|gb|DT650569.1|DT650569
EST:     TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACA                         GTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
EST: gi|71304994|gb|DR788635.1|DR788635
EST:     TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACA                         GTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
EST: gi|94475152|gb|EB704110.1|EB704110
EST:     TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACA                         GTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
EST: gi|91047927|gb|EB158345.1|EB158345
EST:     TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACA                         GTCTCGCTGTGTGTCAAGAGGCTCATCTA
genomic: TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcaagtctgaatcgactattctccgtcattttcttgagcatttctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCTTAT
                                          tttctgcct  CT-rich tract
                             attttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtagctagccaatctctcctgctttctctctctctctcaagtctgaatcgactattctccgtcattttcttgagcatttctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCTTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG