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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTATCAGCTACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgatggctgctttgctataaaccttcctatgtttttttagttaccctgattctattgtctgcatgtacatttag

Basic information

species Zea mays
transcript GRMZM2G121790_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G121790_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g14130.1 (Oryza sativa), 5'ss of exon 3
ACTATCAGCTACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgatggctgctttgctataaaccttcctatgtttttttagttaccctgattctattgtctgcatgtacatttag
|| || ||||||||||||||  |||||||||||||||||||||||||||||||||| ||||||     |   ||||  ||  | |       |  |     |||| ||  |     | |  | | |   |   |||| ||
ACGATTAGCTACATGGCAGAACGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTTCAGgta----aacttctgcagtgtaacattgtcctcctttaaagtttatttgtctcttatttggtatttcttttatcattcag

upper sequence: GRMZM2G121790_T01 (Zea mays), 5'ss of exon 3
lower sequence: EFJ10962 (Selaginella moellendorffii), 5'ss of exon 3
ACTATCAGCTACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgatggctgctttgctataaaccttcctatgtttttttagttaccctgattctattgtctgcatgtacatttag
|| || |||||  | || ||  | ||||| ||||||||||| ||||| ||||||||||||||         ||    | ||| ||| | |||     |    ||  ||  |||| |    ||  || ||           
ACGATTAGCTATGTCGCGGAACGTGTTGTAGGAACTGGATCGTTTGGCATCGTCTTCCAGgtgt-------gcaaactcgctttaatcattctaggctaacgtttctt--cctgttgggcttcacttcag----------
















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|148952787|gb|EC898773.2|EC898773
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgat ... gtacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
EST: gi|211542449|gb|FL405555.1|FL405555
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgat ... gtacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
EST: gi|211406230|gb|FL424177.1|FL424177
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTNGCGATTAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgat ... gtacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
EST: gi|148932530|gb|EC876330.2|EC876330
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgat ... gtacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
EST: gi|71443963|gb|DR825013.1|DR825013
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgat ... gtacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
EST: gi|30031861|gb|CB833712.1|CB833712
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgat ... gtacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
EST: gi|76287882|gb|DV027450.1|DV027450
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgat ... gtacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
EST: gi|211116869|gb|FL397790.1|FL397790
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgat ... gtacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
EST: gi|211082958|gb|FL420011.1|FL420011
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgat ... gtacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
EST: gi|211238101|gb|FL372796.1|FL372796
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgat ... gtacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
EST: gi|211508681|gb|FL378807.1|FL378807
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgat ... gtacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
EST: gi|71441697|gb|DR822747.1|DR822747
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgat ... gtacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
EST: gi|211363564|gb|FL402332.1|FL402332
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgat ... gtacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
EST: gi|211204459|gb|FL397416.1|FL397416
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgat ... gtacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
EST: gi|94476799|gb|EB705757.1|EB705757
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgat ... gtacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
EST: gi|211129185|gb|FL389047.1|FL389047
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTNCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgat ... gtacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
EST: gi|149112787|gb|EE191425.2|EE191425
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgat ... gtacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
EST: gi|71430638|gb|DR811688.1|DR811688
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgat ... gtacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
EST: gi|91057059|gb|EB167477.1|EB167477
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgat ... gtacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
EST: gi|211431312|gb|FL387544.1|FL387544
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgat ... gtacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
EST: gi|31351371|gb|CD435728.1|CD435728
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgat ... gtacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
EST: gi|71443964|gb|DR825014.1|DR825014
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgat ... gtacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
EST: gi|211273308|gb|FL386903.1|FL386903
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgat ... gtacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
EST: gi|211426820|gb|FL420659.1|FL420659
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgat ... gtacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
EST: gi|211080138|gb|FL417805.1|FL417805
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgat ... gtacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
EST: gi|211072098|gb|FL423947.1|FL423947
EST:     CATGGCAGAGAGAGTTGTGGGAACTGGGATCATTTGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
genomic: CATGGCAGAGAGAGTTGTGGGAACTGG-ATCATTTGGAATCGTCTTCCAGgtaccgtgat ... gtacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
EST: gi|211525018|gb|FL424288.1|FL424288
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAG                         GGCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCA
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgat ... gtacatttagG-CAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCA
EST: gi|211323232|gb|FL374207.1|FL374207
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgat ... gtacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
EST: gi|211042522|gb|FL401598.1|FL401598
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgat ... gtacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
EST: gi|211189308|gb|FL380832.1|FL380832
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGA
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgat ... gtacatttagGCAAAATGTCTGGAGACTGGTGAGA
EST: gi|211360527|gb|FL385280.1|FL385280
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCGAYYAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgat ... gtacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
EST: gi|148931707|gb|EC874917.2|EC874917
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgat ... gtacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
EST: gi|76922778|gb|DV169169.1|DV169169
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgat ... gtacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 424

ACTATCAGCTACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgat ... gtacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAGGACAAGCGCTACAAGAACAGGGAGCTACAAATCATGCGATCCATGGATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 463

ACTATCAGCTACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgat ... gtacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAGGACAAGCGCTACAAGAACAGGGAGCTACAAATCATGCGATCCATGGATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 482

ACTATCAGCTACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgat ... gtacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAGGACAAGCGCTACAAGAACAGGGAGCTACAAATCATGCGATCCATGGATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 334

ACTATCAGCTACATGGCAGAGAGAGTTGTGGGAACTGGATCATTTGGAATCGTCTTCCAGgtaccgtgat ... gtacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCGATTAAGAAGGTTTTGCAGGACAAGCGCTACAAGAACAGGGAGCTACAAATCATGCGATCCATGGATC