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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCATGGTATGCCTACACAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAGgtgtggtctcaagatttcttgtcacatcatgctactcttcaaccccacatatgaagttccggatttgctttcctcagatttcatgaatatctaagagtatgcttcatccatttttgcttatgaattggattctcgtactgatcag

Basic information

species Zea mays
transcript GRMZM2G101217_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101217_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g68390.1 (Oryza sativa), 5'ss of exon 4
CCATGGTATGCCTACACAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAGgtgtggtctcaagatttcttgtcacatcatgctac-tcttcaaccccacatatg-------aagttccggatttgctttcctcagatttcatgaatatctaagagtatgcttcatccatttttgcttatgaattggattctcgtactgatcag
||||||||||||||  ||||||| ||||| || || |||||||||||||||||||||||| ||||||||   ||| ||  |         |||  | |||   || || || | ||| ||       |||  ||  |   |||  | |  ||||| || |||                                                         
CCATGGTATGCCTATGCAATAGCTGCATCAATCCTCCGTACAGCAAATCTTTCAGTCCCACTGAAGgtgcattcttaacttcctcctcagcatagttctagacctccatccacccatttgctcttacaagcgccataaccgctcacatatgatttaataaatgatg-----------------------------------------------------
















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|211531113|gb|FL426903.1|FL426903
EST:     CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAG                         ATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGCATACTTGAT
genomic: CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAGgtgtggtctc ... tactgatcagATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGCATACTTGAT
EST: gi|211153475|gb|FL406036.1|FL406036
EST:     CAATAGCAGCATCGATTCTGCGTACAGCAAATCYTTCAGTCCCATTGAAG                         ATATACGAGATTGG
genomic: CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAGgtgtggtctc ... tactgatcagATATACGAGATTGG
EST: gi|211057983|gb|FL426573.1|FL426573
EST:     CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAG                         ATATACGAGATTGGTGGTGGCTC
genomic: CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAGgtgtggtctc ... tactgatcagATATACGAGATTGGTGGTGGCTC
EST: gi|211269212|gb|FL410574.1|FL410574
EST:     CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAG                         ATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGC
genomic: CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAGgtgtggtctc ... tactgatcagATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGC
EST: gi|76924073|gb|DV169790.1|DV169790
EST:     CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAG                         ATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGCATACTTGAT
genomic: CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAGgtgtggtctc ... tactgatcagATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGCATACTTGAT
EST: gi|93012306|gb|EB637826.1|EB637826
EST:     CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAG                         ATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGCATACTTGAT
genomic: CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAGgtgtggtctc ... tactgatcagATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGCATACTTGAT
EST: gi|71312573|gb|DR792811.1|DR792811
EST:     CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAG                         ATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGCATACTTGAT
genomic: CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAGgtgtggtctc ... tactgatcagATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGCATACTTGAT
EST: gi|50325602|gb|CO520728.1|CO520728
EST:     CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAG                         ATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGCATACTTGAT
genomic: CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAGgtgtggtctc ... tactgatcagATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGCATACTTGAT
EST: gi|211209580|gb|FL394645.1|FL394645
EST:     CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAG                         ATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGCATACTTGA
genomic: CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAGgtgtggtctc ... tactgatcagATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGCATACTTGA
EST: gi|89250708|gb|DY622494.1|DY622494
EST:     CAATAGCAGCATCCATTCTGCGTACAGCAAATCTTTCAGTCCCCTTGAAG                         ATATACCAGATTGGTGGTGGGTCTGG
genomic: CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAGgtgtggtctc ... tactgatcagATATACGAGATTGGTGGTGGCTCTGG
EST: gi|37417541|gb|CF646424.1|CF646424
EST:     CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAG                         ATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGCATACTTGAT
genomic: CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAGgtgtggtctc ... tactgatcagATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGCATACTTGAT
EST: gi|93012540|gb|EB638060.1|EB638060
EST:     CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAG                         ATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGCATACTTGAT
genomic: CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAGgtgtggtctc ... tactgatcagATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGCATACTTGAT
EST: gi|101391071|gb|EB817469.1|EB817469
EST:     CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAG                         ATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGCATACTTGAT
genomic: CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAGgtgtggtctc ... tactgatcagATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGCATACTTGAT
EST: gi|211197467|gb|FL425782.1|FL425782
EST:     CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAG                         ATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGC
genomic: CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAGgtgtggtctc ... tactgatcagATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGC
EST: gi|211164475|gb|FL391064.1|FL391064
EST:     CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAG                         ATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGCATACTT
genomic: CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAGgtgtggtctc ... tactgatcagATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGCATACTT
EST: gi|211428747|gb|FL388358.1|FL388358
EST:     CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAG                         ATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAA
genomic: CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAGgtgtggtctc ... tactgatcagATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAA
EST: gi|211524044|gb|FL387968.1|FL387968
EST:     CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAG                         ATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGCATACTTGAT
genomic: CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAGgtgtggtctc ... tactgatcagATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGCATACTTGAT
EST: gi|76281532|gb|DV021100.1|DV021100
EST:     CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAG                         ATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGCATACTTGAT
genomic: CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAGgtgtggtctc ... tactgatcagATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGCATACTTGAT
EST: gi|148959299|gb|EE010710.2|EE010710
EST:     CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAG                         ATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGCATACTTGAT
genomic: CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAGgtgtggtctc ... tactgatcagATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGCATACTTGAT
EST: gi|148960597|gb|EE011219.2|EE011219
EST:     ATAGCAGCATCGATTCTGCGTACAGCAAATTCTTTCAGTCCCCATTGAAG                         ATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGCATACTTGA
genomic: ATAGCAGCATCGATTCTGCGTACAGCAAAT-CTTTCAGTCCC-ATTGAAGgtgtggtctc ... tactgatcagATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGCATACTTGA
EST: gi|211085712|gb|FL420035.1|FL420035
EST:     CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAG                         ATATACGAGATTGGTGGTGGCTCTGGGAACATGCGCAAAGTGCATACTTG
genomic: CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAGgtgtggtctc ... tactgatcagATATACGAGATTGGTGGTGGCTCTGG-AACATGCGCAAAGTGCATACTTG
EST: gi|71418854|gb|DR804568.1|DR804568
EST:     CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAG                         ATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGCATACTTGAT
genomic: CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAGgtgtggtctc ... tactgatcagATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGCATACTTGAT
EST: gi|50337135|gb|CO532261.1|CO532261
EST:     CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAG                         ATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGCATACTTGAT
genomic: CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAGgtgtggtctc ... tactgatcagATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGCATACTTGAT
EST: gi|71327533|gb|DR800378.1|DR800378
EST:     CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAG                         ATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGCATACTTGAT
genomic: CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAGgtgtggtctc ... tactgatcagATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGCATACTTGAT
EST: gi|50336106|gb|CO531232.1|CO531232
EST:     CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAG                         ATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGCATACTTGAT
genomic: CAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAGgtgtggtctc ... tactgatcagATATACGAGATTGGTGGTGGCTCTGGAACATGCGCAAAGTGCATACTTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCATGGTATGCCTACACAATAGCAGCATCGATTCTGCGTACAGCAAATCTTTCAGTCCCATTGAAGgtgtggtctcaagatttcttgtcacatcatgctactcttcaaccccacatatgaagttccggatttgctttcctcagatttcatgaatatctaagagtatgcttcatccatttttgcttatgaattggattctcgtactgatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG