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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGTTTTTGACTTGCCCTTTCATATGGCCAGAGATCAGATAGAAGAGAGTTTGCGCACAAAAATGACTTCAATCAAGgtaggagccactggattgagactataagcatcgtacaattgctatttctcccatacacacttgttttcattacatgatgataattatttctgatgacaaccag

Basic information

species Zea mays
transcript GRMZM2G147500_T02
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147500_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os08g14460.1 (Oryza sativa), 5'ss of exon 11
GATGTTTTTGACTTGCCCTTTCATATGGCCAGAGATCAGATAGAAGAGAGTTTGCGCACAAAAATGACTTCAATCAAGgtaggagccactggattgagactataagcat--cgtacaattgctatttctcc--catacacacttgttttcattacatgatgataattatttctgatgacaaccag---------------
||||| ||||| ||||||||||| ||||| ||||| ||||| ||||||||||||||||| |||||| |||| || ||||||| |   |||| ||  |||| |    | |  |     || | |  | ||||  ||| || |||| |  |||||   | |   |  |  ||||   |   ||  |                
GATGTCTTTGATTTGCCCTTTCACATGGCTAGAGACCAGATTGAAGAGAGTTTGCGCACTAAAATGGCTTCCATAAAGgtagaa-tgactgaat-aagacaactcacctgacccctcatggttgatgctccagcatgcaaactt-tcatcattgattcactgtgctcctttcaactttgaaaaaacaaattactatgcag

upper sequence: GRMZM2G147500_T02 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA17G07040.1 (Glycine max), 5'ss of exon 12
GATGTTTTTGACTTGCCCTTTCATATGGCCAGAGATCAGATAGAAGAGAGTTTGCGCACAAAAATGACTTCAATCAAGgtaggagcc-actggattgagactataagcatcgtacaattgctatttctcccatacacacttgttttcattacatgatga-taattatttctgatgacaaccag
||||| |||||| | || ||||| |||||||||||||| |||||||| ||| | ||||  |||||| |||| || ||||||    |  | | |  | |   |  ||      |    |   |||||  |  |||   |||  || || ||   || | | |  ||     |    | |   ||
GATGTATTTGACCTTCCTTTTCACATGGCCAGAGATCAAATAGAAGAAAGTCTTCGCAACAAAATGGCTTCTATAAAGgtaattacttattagtatcactttccaatttgtatcttttaagtatttg-cagatatgaactgtttgtctttggttgttaactgcttgaaaattgaaatatgaag
















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|71427991|gb|DR809041.1|DR809041
EST:     CCAGAGATCAGATAGAAGAGAGTTTGCGCACAAAAATGACTTCAATCAAG                         GCACGAATGACACAACTTCAAGATGCTCAGAAAGGTGCAGAAGTGACTTCT
genomic: CCAGAGATCAGATAGAAGAGAGTTTGCGCACAAAAATGACTTCAATCAAGgtaggagcca ... tgacaaccagGCACGAATGACACAACTTCAAGATGCTCAGAAAGGTGCAGAAGTGACTTCT
EST: gi|31405728|gb|CD484460.1|CD484460
EST:     CCAGAGATCAGATAGAAGAGAGTTTGCGCACAAAAATGACTTCAATCAAG                         GCACGAATGACACAACTTCAAGATGCTCAGAAAGGTGCAGAAGTGACTTCT
genomic: CCAGAGATCAGATAGAAGAGAGTTTGCGCACAAAAATGACTTCAATCAAGgtaggagcca ... tgacaaccagGCACGAATGACACAACTTCAAGATGCTCAGAAAGGTGCAGAAGTGACTTCT
EST: gi|60342233|gb|DN209206.1|DN209206
EST:     CCAGAGATCAGATAGAAGAGAGTTTGCGCACAAAAATGACTTCAATCAAG                         GCACGAATGACACAACTTCAAGATGCTCAGAAAGGTGCAGAAGTGACTTCT
genomic: CCAGAGATCAGATAGAAGAGAGTTTGCGCACAAAAATGACTTCAATCAAGgtaggagcca ... tgacaaccagGCACGAATGACACAACTTCAAGATGCTCAGAAAGGTGCAGAAGTGACTTCT
EST: gi|32943705|gb|CF048524.1|CF048524
EST:     CCAGAGATCAGATAGAAGAGAGTTTGCGCACAAAAATGACTTCAATCAAG                         GCACGAATGACACAACTTCAAGATGCTCAGAAAGGTGCAGAAGTGACTTCT
genomic: CCAGAGATCAGATAGAAGAGAGTTTGCGCACAAAAATGACTTCAATCAAGgtaggagcca ... tgacaaccagGCACGAATGACACAACTTCAAGATGCTCAGAAAGGTGCAGAAGTGACTTCT
EST: gi|60350197|gb|DN217170.1|DN217170
EST:     CCAGAGATCAGATAGAAGAGAGTTTGCGCACAAAAATGACTTCAATCAAG                         GCACGAATGACACAACTTCAAGATGCTCAGAAAGGTGCAGAAGTGACTTCT
genomic: CCAGAGATCAGATAGAAGAGAGTTTGCGCACAAAAATGACTTCAATCAAGgtaggagcca ... tgacaaccagGCACGAATGACACAACTTCAAGATGCTCAGAAAGGTGCAGAAGTGACTTCT
EST: gi|32911044|gb|CF015856.1|CF015856
EST:     GACTTCAATCAAG                         GCACGAATGACACAACTTCAAGATGCTCAGAAAGGTGCAGAAGTGACTTCT
genomic: GACTTCAATCAAGgtaggagcca ... tgacaaccagGCACGAATGACACAACTTCAAGATGCTCAGAAAGGTGCAGAAGTGACTTCT
EST: gi|91872286|gb|EB402243.1|EB402243
EST:     GTTTGCGCACAAAAATGACTTCAATCAAG                         GCACGAATGACACAACTTCAAGATGCTCAGAAAGGTGCAGAAGTGACTTCT
genomic: GTTTGCGCACAAAAATGACTTCAATCAAGgtaggagcca ... tgacaaccagGCACGAATGACACAACTTCAAGATGCTCAGAAAGGTGCAGAAGTGACTTCT
EST: gi|148955451|gb|EC901042.2|EC901042
EST:     CCAGAGATCAGATAGAAGAGAGTTTGCGCACAAAAATGACTTCAATCAAG                         GCACGAATGACACAACTTCAAGATGTTCAGAAAGGTGCAGAAGTGACTTTT
genomic: CCAGAGATCAGATAGAAGAGAGTTTGCGCACAAAAATGACTTCAATCAAGgtaggagcca ... tgacaaccagGCACGAATGACACAACTTCAAGATGCTCAGAAAGGTGCAGAAGTGACTTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGTTTTTGACTTGCCCTTTCATATGGCCAGAGATCAGATAGAAGAGAGTTTGCGCACAAAAATGACTTCAATCAAGgtaggagccactggattgagactataagcatcgtacaattgctatttctcccatacacacttgttttcattacatgatgataattatttctgatgacaaccag

- - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - -  AAGAGA