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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGAAGGAGAAGTCCCTGGCCGAGAGGAAGAAGTCCATCGAGAACCGGAAGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctcctgatcctgctcgatctaacctccttgtagactattcgtgcggggtgggtcgtagggcttcgcgtgcggcgtgttattttcatctcaaag...

Basic information

species Zea mays
transcript GRMZM5G868433_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G868433_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os04g51630.2 (Oryza sativa), 5'ss of exon 2
GAAGAAGGAGAAGTCCCTGGCCGAGAGGAAGAAGTCCATCGAGAACCGGAAGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctcctgatcctgctcgatctaacctc-cttgtagactat-tcgtgcggggtgggtcgtagggcttcgcgtgcggcgtgttattttcatctcaaag
||  ||||||||| || | ||||||| ||||||||||||||||| ||| |||||||||||| ||||||||||||||||||||||||||||||| |||||||| |||||    |  ||  |  |||| |  | |   |  |   ||| |  |||| ||        || | ||| |||| |   ||   ||   |   | || 
GAGCAAGGAGAAGGCCGTCGCCGAGAAGAAGAAGTCCATCGAGAGCCGCAAGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAGgttagatcgttggcccccacatgatccattcccgtctcgatgttatattttgcgtggcaaag-acagcgattc-cgtgggatctgggtttggtactcccaaa

upper sequence: GRMZM5G868433_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os08g13690.1 (Oryza sativa), 5'ss of exon 2
GAAGAAGGAGAAGTCCCTGGCCGAGAGGAAGAAGTCCATCGAGAACCGGAAGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgt---cagatctcctgatcctgctcgatctaacctccttgtagactatt-cgtgc-ggggtgggtcgtagggcttcgcgtgcggcgtgttattttcatctcaaag
 | |||||||||| | || ||||||| ||||||| || |||||| ||| |||||||||||| |||||||||||||||||||| |||||||||| || |||||   |||| |  |    || |||     |    ||   | |  || |  |||   ||  ||| ||||   | || ||||   |||  |      ||||   || 
CAGGAAGGAGAAGGCGCTCGCCGAGAAGAAGAAGGCCGTCGAGAGCCGCAAGCTCATCTTCGCCCGCGCCAAGCAGTACGCCCAGGAGTACGACGCGCAGgtgagcagagcaacct-ccccgctgcccgttgattcgcggaaccctgtggcgtctaggaatggttcgtttagatttgcgtt--gcgcatcgacg-catcgtgaa-
















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|15632349|gb|BI679442.1|BI679442
EST:     AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|211171434|gb|FK956282.1|FK956282
EST:     AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|5915128|gb|AW052769.1|AW052769
EST:     GGAGTACGATGCCCAG                         GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: GGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|76922808|gb|DV169184.1|DV169184
EST:     AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|15554187|gb|BI644185.1|BI644185
EST:     CCGC-CCAAGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: CCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|9733002|gb|BE511754.1|BE511754
EST:     AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|60350172|gb|DN217145.1|DN217145
EST:     CAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: CAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|211173119|gb|FK956304.1|FK956304
EST:     GCTCATCTTCACCCGCGCCAATGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACT-GTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: GCTCATCTTCACCCGCGCCAA-GCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|15590144|gb|BI674760.1|BI674760
EST:     AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|148940442|gb|EC885240.2|EC885240
EST:     AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|211173115|gb|FK956300.1|FK956300
EST:     AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|94477419|gb|EB706377.1|EB706377
EST:     AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|148941047|gb|EC885904.2|EC885904
EST:     AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|5915120|gb|AW052761.1|AW052761
EST:     GGAG-ACGA-GCCCAG                         GAGAAGGAACTGG-ACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: GGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|20299953|gb|BQ162896.1|BQ162896
EST:     AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|148935172|gb|EC879210.2|EC879210
EST:     AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|71438751|gb|DR819801.1|DR819801
EST:     AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|21987690|gb|BQ779218.1|BQ779218
EST:     AGCTCATCTTCACCCGCGCCTAGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|71444618|gb|DR825668.1|DR825668
EST:     AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|211173114|gb|FK956299.1|FK956299
EST:     AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|20301133|gb|BQ164076.1|BQ164076
EST:     AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|31350410|gb|CD434767.1|CD434767
EST:     AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|78084905|gb|DV513298.1|DV513298
EST:     AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|6021537|gb|AW066465.1|AW066465
EST:     AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|15313739|gb|BI478933.1|BI478933
EST:     AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGAAGGAGAAGTCCCTGGCCGAGAGGAAGAAGTCCATCGAGAACCGGAAGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctcctgatcctgctcgatctaacctccttgtagactattcgtgcggggtgggtcgtagggcttcgcgtgcggcgtgttattttcatctcaaag

- - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG