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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATCGGCTTATCAACGTTGATGAGAGCATTTACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAATgtaagtagcatgccccgtactcctgtttttatcaccaatccttccttgtacaggtgcttctttgcaactagccttttttttcattgttattgtttgaaca...

Basic information

species Zea mays
transcript GRMZM2G155662_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155662_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os06g05350.1 (Oryza sativa), 5'ss of exon 5
--------AATCGGCTTATCAACGTTGATGAGAGCATTTACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAATgtaagtagcatgccccgtactcctgtttttatcaccaatccttccttgtacaggtgcttctttgcaactagccttttttt-tcattgttattgtttgaaca--
        || || ||  | ||| | |||||||  |||||||||||||||||||| ||||| |||||||| |||||||| |||||||||||| ||| ||| ||| |   |  | ||| |    | ||         | |    ||  |   ||| | | |   || |   ||| ||||    |  |   |  
GTGTTCAAAACCGTCTCCTGAACATCGATGAGAATATTTACATCCCTATAACCAAAGGAGAATTTGCTGTGATTGTATCGACTTTCAATgtatgtaacataccctgctatattatttattgttctaacagagaagagaatgcatgaat---tgccattggttcttataaatcaatgttcacttgcgtttact
















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|71427013|gb|DR808063.1|DR808063
EST:     ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCA-T                         TACATCATACCGCACCTCATGGGC
genomic: ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAATgtaagtagca ... acttgtgcagTACATCATACCGCACCTCATGGGC
EST: gi|71311953|gb|DR792477.1|DR792477
EST:     ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAAT                         TACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAA
genomic: ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAATgtaagtagca ... acttgtgcagTACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAA
EST: gi|89247407|gb|DY619193.1|DY619193
EST:     ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAAT                         TACATCATACCGCCAC-TCATGGGCTGGAGCACATTTGTAAGTTCAATCAA
genomic: ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAATgtaagtagca ... acttgtgcagTACATCATACCGC-ACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAA
EST: gi|89247406|gb|DY619192.1|DY619192
EST:     ATTGTATTAACTTTCAAT                         TACATCATACCGCACCTCATGGGCGGGAGCACATTTGTAAGTTCAATCAAA
genomic: ATTGTATCAACTTTCAATgtaagtagca ... acttgtgcagTACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAA
EST: gi|91054380|gb|EB164798.1|EB164798
EST:     ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAAT                         TACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAAT
genomic: ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAATgtaagtagca ... acttgtgcagTACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAAT
EST: gi|20301062|gb|BQ164005.1|BQ164005
EST:     ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAAT                         TACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAA
genomic: ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAATgtaagtagca ... acttgtgcagTACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAA
EST: gi|91050359|gb|EB160777.1|EB160777
EST:     ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAAT                         TACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAA
genomic: ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAATgtaagtagca ... acttgtgcagTACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAA
EST: gi|78075430|gb|DV503864.1|DV503864
EST:     ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAAT                         TACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAA
genomic: ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAATgtaagtagca ... acttgtgcagTACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAA
EST: gi|71448588|gb|DR829638.1|DR829638
EST:     ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAAT                         TACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAA
genomic: ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAATgtaagtagca ... acttgtgcagTACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAA
EST: gi|76019635|gb|DT946805.1|DT946805
EST:     ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAAT                         TACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAA
genomic: ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAATgtaagtagca ... acttgtgcagTACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAA
EST: gi|78078777|gb|DV507189.1|DV507189
EST:     ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAAT                         TACATCATACCGCACCTCATGGGCTGGAGCACATTT-TGAAGTTCAATCAA
genomic: ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAATgtaagtagca ... acttgtgcagTACATCATACCGCACCTCATGGGCTGGAGCACATTTGT-AAGTTCAATCAA
EST: gi|213179367|gb|FM192339.1|FM192339
EST:     ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAAT                         TACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAA
genomic: ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAATgtaagtagca ... acttgtgcagTACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAA
EST: gi|50336696|gb|CO531822.1|CO531822
EST:     ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAAT                         TACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCA
genomic: ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAATgtaagtagca ... acttgtgcagTACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCA
EST: gi|76925400|gb|DV170433.1|DV170433
EST:     ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAAT                         TACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAA
genomic: ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAATgtaagtagca ... acttgtgcagTACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAA
EST: gi|31909569|gb|CD650984.1|CD650984
EST:     ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAAT                         TACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAA
genomic: ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAATgtaagtagca ... acttgtgcagTACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAA
EST: gi|31909099|gb|CD650749.1|CD650749
EST:     ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAAT                         TACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAA
genomic: ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAATgtaagtagca ... acttgtgcagTACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAA
EST: gi|93015158|gb|EB640678.1|EB640678
EST:     ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAAT                         TACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAA
genomic: ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAATgtaagtagca ... acttgtgcagTACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAA
EST: gi|78075431|gb|DV503865.1|DV503865
EST:     ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAAT                         TACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAA
genomic: ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAATgtaagtagca ... acttgtgcagTACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATCGGCTTATCAACGTTGATGAGAGCATTTACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAATgtaagtagcatgccccgtactcctgtttttatcaccaatccttccttgtacaggtgcttctttgcaactagccttttttttcattgttattgtttgaaca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccgtac