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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCTGAAAGAAGATGAGTCACCCTGTATTTTTGGTCCAATCGTGAAACAACGATGGTCCTATGCTTGCGCGAAGCAACTTATTGAGAGACTTATATTTGgtcagtagagtaaaattttgcactgtgccgctgatggccttcttgttctaacacttcttttatgtttttgtcattttgatttgagtatctgccag

Basic information

species Zea mays
transcript GRMZM2G167872_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G167872_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g73790.1 (Oryza sativa), 5'ss of exon 4
GTTCTGAAAGAAGATGAGTCACCCTGTATTTTTGGTCCAATCGTGAAACAACGATGGTCCTATGCTTGCGCGAAGCAACTTATTGAGAGACTTATATTTGgtcagtagagtaaaattttgcact-gtgccgctga-tggccttcttgttctaacacttcttttatgtttttgtcattttgatttgagtatctgccag
|| |||||||||||||| || ||||| |||||||||||||| |||||||| |||||||| ||||| || |||||||| ||||||||||| ||||| |||||| |||  |||||  |||   | |  || |  |   ||  |   ||||           ||||  | |||   ||                      
GTACTGAAAGAAGATGAATCCCCCTGCATTTTTGGTCCAATTGTGAAACAGCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTGgtgagtgcagtaacttttgttattcatgtcattacctgaacactttgtaaccgtgtgctttttgagctttaaccag---------------------

upper sequence: GRMZM2G167872_T02 (Zea mays), 5'ss of exon 2
lower sequence: AT1G08200.1 (Arabidopsis thaliana), 5'ss of exon 4
GTTCTGAAAGAAGATGAGTCACCCTGTATTTTTGGTCCAATCGTGAAACAACGATGGTCCTATGCTTGCGCGAAGCAACTTATTGAGAGACTTATATTTGgtcagtagagtaaaattttgcactgtgccgctgatggccttcttgtt-ctaacacttcttttatgtttttgtcattttgatttgagtatctgccag
|| || |||||||||   || || || || |||||| |||| | ||| ||  | ||||| |||||||| || ||||||||||||||||||||| | |  |||  ||||  |    | || |||        |  |    |||| |   | || |  | | | | ||   | |  || || ||  ||          
GTACTCAAAGAAGATATATCCCCTTGCATCTTTGGTTCAATTGAGAAGCAGAGGTGGTCATATGCTTGTGCAAAGCAACTTATTGAGAGACTTGTTTACGgtatgtagttt----tcttacacgaaagaaattttttgtttctagacacaaaaaagtttctcacgtcact-tttttctggttgcag----------
















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|148943583|gb|EC888646.2|EC888646
EST:     CGATGGTCCTATGCTTGCGCGAAGNCA-CTTATTGAGAGACTTATATTTG                         CTGAGGGTGCAGAAAATGGCCTTTGAAT-CACAATCGTGAGACCTTTT
genomic: CGATGGTCCTATGCTTGCGCGAAG-CAACTTATTGAGAGACTTATATTTGgtcagtagag ... tatctgccagCTGAGGGTGCAGAAAATGGCCTT-GAATTCACAATCGTGAGACCTTTT
EST: gi|148962548|gb|EE013424.2|EE013424
EST:     ACGATGGTCCTATGCTTGCGCGAAGCAACTTATTGAGAGACTTATATTTG                         CTGAGGGTGCAGAAAATGGCCTTGAATTCACAATCGTGAGACCTTTTAATT
genomic: ACGATGGTCCTATGCTTGCGCGAAGCAACTTATTGAGAGACTTATATTTGgtcagtagag ... tatctgccagCTGAGGGTGCAGAAAATGGCCTTGAATTCACAATCGTGAGACCTTTTAATT
EST: gi|148970721|gb|EE021451.2|EE021451
EST:     ACGATGGTCCTATGCTTGCGCGAAGCAACTTATTGAGAGACTTATATTTG                         CTGAGGGTGCAGAAAATGGCCTTGAATTCACAATCGTGAGACCTTTTAATT
genomic: ACGATGGTCCTATGCTTGCGCGAAGCAACTTATTGAGAGACTTATATTTGgtcagtagag ... tatctgccagCTGAGGGTGCAGAAAATGGCCTTGAATTCACAATCGTGAGACCTTTTAATT
EST: gi|149086979|gb|EE176522.2|EE176522
EST:     ACGATGGTCCTATGCTTGCGCGAAGCAACTTATTGAGAGACTTATATTTG                         CTGAGGGTGCAGAAAATGGCCTTGAATTTCACA-TCGTGAGACCTTTTTAT
genomic: ACGATGGTCCTATGCTTGCGCGAAGCAACTTATTGAGAGACTTATATTTGgtcagtagag ... tatctgccagCTGAGGGTGCAGAAAATGGCCTTGAATT-CACAATCGTGAGACCTTTTAAT
EST: gi|67029504|gb|CO458253.1|CO458253
EST:     CGATGGTCCTATGCTTGCGCNGAAGCA-CTTATTGAGAGGCTTATATTTG                         CTGAGGGTGCAGAAA-TGGCCTTGAATTCACA-TCGTGAGACCTTTTA-TT
genomic: CGATGGTCCTATGCTTGCGC-GAAGCAACTTATTGAGAGACTTATATTTGgtcagtagag ... tatctgccagCTGAGGGTGCAGAAAATGGCCTTGAATTCACAATCGTGAGACCTTTTAATT
EST: gi|67010325|gb|CO439074.1|CO439074
EST:     ACGATGGTCCTATGCTTGCGCGAAGCAACTTATTGAGAGGCTTATATTTG                         CTGAGGGTGCAGAAAATGGCCTTGAATTCACAATCGTGAGACCTTTTAATT
genomic: ACGATGGTCCTATGCTTGCGCGAAGCAACTTATTGAGAGACTTATATTTGgtcagtagag ... tatctgccagCTGAGGGTGCAGAAAATGGCCTTGAATTCACAATCGTGAGACCTTTTAATT
EST: gi|33099170|gb|CF059130.1|CF059130
EST:     ACGATGGTCCTATGCTTGCGCGAAGCAACTTATTGAGAGGCTTATATTTG                         CTGAGGGTGCAGAAAATGGCCTTGAATTCACAATCGTGAGACCTTTTAATT
genomic: ACGATGGTCCTATGCTTGCGCGAAGCAACTTATTGAGAGACTTATATTTGgtcagtagag ... tatctgccagCTGAGGGTGCAGAAAATGGCCTTGAATTCACAATCGTGAGACCTTTTAATT
EST: gi|61118009|gb|DN558970.1|DN558970
EST:     ACGATGGTCCTATGCTTGCGCGAAGCAACTTATTGAGAGGCTTATATTTG                         CTGAGGGTGCAGAAAATGGCCTT
genomic: ACGATGGTCCTATGCTTGCGCGAAGCAACTTATTGAGAGACTTATATTTGgtcagtagag ... tatctgccagCTGAGGGTGCAGAAAATGGCCTT
EST: gi|148936214|gb|EC880288.2|EC880288
EST:     ACGATGGTCCTATGCTTGCGCGAAGCAACTTATTGAGAGACTTATATTTG                         CTGAGGGTGCAGAAAATGGCCTTGAATTCACAATCGTGAGACCTTTTAATT
genomic: ACGATGGTCCTATGCTTGCGCGAAGCAACTTATTGAGAGACTTATATTTGgtcagtagag ... tatctgccagCTGAGGGTGCAGAAAATGGCCTTGAATTCACAATCGTGAGACCTTTTAATT
EST: gi|61118010|gb|DN558971.1|DN558971
EST:     ACGATGGTCCTATGCTTGCGCGAAGCAACTTATTGAGAGGCTTATATTTG                         CTGAGGGTGCAGAAAATGGCCTTG
genomic: ACGATGGTCCTATGCTTGCGCGAAGCAACTTATTGAGAGACTTATATTTGgtcagtagag ... tatctgccagCTGAGGGTGCAGAAAATGGCCTTG
EST: gi|61118011|gb|DN558972.1|DN558972
EST:     ACGATGGTCCTATGCTTGCGCGAAGCAACTTATTGAGAGGCTTATATTTG                         CTGAGGGTGCAGAAAATGGCCTT
genomic: ACGATGGTCCTATGCTTGCGCGAAGCAACTTATTGAGAGACTTATATTTGgtcagtagag ... tatctgccagCTGAGGGTGCAGAAAATGGCCTT
EST: gi|149048837|gb|EE048337.2|EE048337
EST:     ACGATGGTCCTATGCTTGCGCGAAGCAACTTATTGAGAGACTTATATTTG                         CTGAGGGTGCAGAAAATGGCCTTGAATTCACAATCGTGAGACCTTTTAATT
genomic: ACGATGGTCCTATGCTTGCGCGAAGCAACTTATTGAGAGACTTATATTTGgtcagtagag ... tatctgccagCTGAGGGTGCAGAAAATGGCCTTGAATTCACAATCGTGAGACCTTTTAATT
EST: gi|71439581|gb|DR820631.1|DR820631
EST:     ACGATGGTCCTATGCTTGCGCGAAGCAACTTATTGAGAGACTTATATTTG                         CTGAGGGTGCAGAAAATGGCCTTGAATTCACAATCGTGAGACCTTTTAATT
genomic: ACGATGGTCCTATGCTTGCGCGAAGCAACTTATTGAGAGACTTATATTTGgtcagtagag ... tatctgccagCTGAGGGTGCAGAAAATGGCCTTGAATTCACAATCGTGAGACCTTTTAATT
EST: gi|149013844|gb|EE043324.2|EE043324
EST:     ACGATGGTCCTATGCTTGCGCGAAGCAACTTATTGAGAGACTTATATTTG                         CTGAGGGTGCAGAAAATGGCCTTGAATTCACAATCGTGAGACCTTTTTATT
genomic: ACGATGGTCCTATGCTTGCGCGAAGCAACTTATTGAGAGACTTATATTTGgtcagtagag ... tatctgccagCTGAGGGTGCAGAAAATGGCCTTGAATTCACAATCGTGAGACCTTTTAATT
EST: gi|78088132|gb|DV516525.1|DV516525
EST:     ACGATGGTCCTATGCTTGCGCGAAGCAACTTATTGAGAGACTTATATTTG                         CTGAGGGTGCAGAAAATGGCCTTGAATTCACAATCGTGAGACCTTTT
genomic: ACGATGGTCCTATGCTTGCGCGAAGCAACTTATTGAGAGACTTATATTTGgtcagtagag ... tatctgccagCTGAGGGTGCAGAAAATGGCCTTGAATTCACAATCGTGAGACCTTTT
EST: gi|149080038|gb|EE169058.2|EE169058
EST:     ACGATGGTCCTATGCTTGCGCGAAGCAACTTATTGAGAGACTTATATTTG                         CTGAGGGTGCAGAAAATGGCCTTGAATTCACAATCGTGAGACCTTTTAATT
genomic: ACGATGGTCCTATGCTTGCGCGAAGCAACTTATTGAGAGACTTATATTTGgtcagtagag ... tatctgccagCTGAGGGTGCAGAAAATGGCCTTGAATTCACAATCGTGAGACCTTTTAATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCTGAAAGAAGATGAGTCACCCTGTATTTTTGGTCCAATCGTGAAACAACGATGGTCCTATGCTTGCGCGAAGCAACTTATTGAGAGACTTATATTTGgtcagtagagtaaaattttgcactgtgccgctgatggccttcttgttctaacacttcttttatgtttttgtcattttgatttgagtatctgccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA