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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGAAACCGAGGTCCAGCTTGATGCTGAGAGGGCATCTGTCTTCTATGCGGAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAGgtattattgttgttggaaaggctcgtgtctcttaagtttcttgcataatgcttctagtctatgcagcagccttcagacgctaacattgacactaacagtttgtaacatgactccttttatctttgtgttgatctttag

Basic information

species Zea mays
transcript GRMZM2G060464_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G060464_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g35700.2 (Oryza sativa), 5'ss of exon 2
AAGAAACCGAGGTCCAGCTTGATGCTGAGAGGGCATCTGTCTTCTATGCGGAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAGgtattattgttgttggaaaggctcgtgtctcttaagtttcttgcataa-tgcttctagtctatgcagcagccttcagacgctaacattgacactaacagtttgt-aacatgactccttttatctttgtgttgatctttag
||||  | | ||| ||||| ||||| |||||||||||  |||||||||||||||||||   |||||||||||||||||| || || ||||| || ||||||||   |||| |    |||| || |||| | ||  ||| ||||| ||| | ||   ||||       ||| ||  ||    |    | |||| | |     | | |||||||                            
AAGAGGCAGTGGTTCAGCTGGATGCGGAGAGGGCATCACTCTTCTATGCGGAGCATTCTGGGAGAAGCTTCTTTGACAGTCTGGTGAAGTATATGACAAGgtacctttgtcg----aaagacttgtgtatttt--gttccttgcttaagtcctcacagtc------acaggctatagtgaatcgtttcgacagtgaggccatatcaacatga----------------------------
















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|78106343|gb|DV524761.1|DV524761
EST:     GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAG                         TGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
genomic: GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAGgtattattgt ... tgatctttagTGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
EST: gi|60356826|gb|DN223799.1|DN223799
EST:     GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAG                         TGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
genomic: GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAGgtattattgt ... tgatctttagTGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
EST: gi|50330122|gb|CO525248.1|CO525248
EST:     GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAG                         TGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
genomic: GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAGgtattattgt ... tgatctttagTGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
EST: gi|211375638|gb|FL110756.1|FL110756
EST:     GAS-ATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAG                         TGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
genomic: GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAGgtattattgt ... tgatctttagTGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
EST: gi|16916528|gb|BM072881.1|BM072881
EST:     GTCAAGTACATAACAAG                         TGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
genomic: GTCAAGTACATAACAAGgtattattgt ... tgatctttagTGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
EST: gi|211477830|gb|FL110767.1|FL110767
EST:     GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAG                         TGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
genomic: GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAGgtattattgt ... tgatctttagTGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
EST: gi|91873960|gb|EB403917.1|EB403917
EST:     GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAG                         TGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
genomic: GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAGgtattattgt ... tgatctttagTGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
EST: gi|60358496|gb|DN225469.1|DN225469
EST:     GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAG                         TGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
genomic: GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAGgtattattgt ... tgatctttagTGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
EST: gi|211375642|gb|FL110760.1|FL110760
EST:     GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAG                         TGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
genomic: GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAGgtattattgt ... tgatctttagTGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
EST: gi|78090669|gb|DV519043.1|DV519043
EST:     GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAG                         TGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
genomic: GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAGgtattattgt ... tgatctttagTGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
EST: gi|78106342|gb|DV524760.1|DV524760
EST:     GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAG                         TGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
genomic: GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAGgtattattgt ... tgatctttagTGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
EST: gi|26457519|gb|CA829102.1|CA829102
EST:     CTTTGACAGCCTAGTCAAGTACATAACAAG                         -GGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
genomic: CTTTGACAGCCTAGTCAAGTACATAACAAGgtattattgt ... tgatctttagTGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
EST: gi|78090668|gb|DV519042.1|DV519042
EST:     GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAG                         TGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
genomic: GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAGgtattattgt ... tgatctttagTGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
EST: gi|60351869|gb|DN218842.1|DN218842
EST:     GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAG                         TGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
genomic: GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAGgtattattgt ... tgatctttagTGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
EST: gi|211375643|gb|FL110761.1|FL110761
EST:     GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAG                         TGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
genomic: GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAGgtattattgt ... tgatctttagTGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
EST: gi|60339376|gb|DN206349.1|DN206349
EST:     GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAG                         TGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG
genomic: GAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAGgtattattgt ... tgatctttagTGGTCCAGTTCTTGCTATGGTTCTGGAAAGACCTGACGCCGTTGCGCAATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGAAACCGAGGTCCAGCTTGATGCTGAGAGGGCATCTGTCTTCTATGCGGAGCATTCCCAGAGAAGCTTCTTTGACAGCCTAGTCAAGTACATAACAAGgtattattgttgttggaaaggctcgtgtctcttaagtttcttgcataatgcttctagtctatgcagcagccttcagacgctaacattgacactaacagtttgtaacatgactccttttatctttgtgttgatctttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC