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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGCACAATACCCGCGGCGAGCCTGACTCCATCGTCGCGCTGGCCAAATGGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGGgtgagcccgtaggttgcagtatcgtgtttgggaaaaaaaaatgatacaatggcgatgtgcctgaatttggagtgctgacatggtaatatgcgctcttctcgacag

Basic information

species Zea mays
transcript GRMZM2G085747_T04
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085747_T04 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os10g35960.2 (Oryza sativa), 5'ss of exon 3
GGAGCACAATACCCGCGGCGAGCCTGACTCCATCGTCGCGCTGGCCAAATGGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGGgtgagcccgtaggttgcagtatcgtgtttgggaaaaaaaaatgatacaatggcgatgtgcctgaatttggagtgctgacatggtaatatgcg-ctcttctcgacag
||||||||| ||||| || ||||| ||| ||||||||||||||||||| |||||||||||||||||| |||||||||||||||||||  |||||||||| |||||| ||     | |  | | |   | | ||      | | ||    |   | |||    |  ||||     ||||   |||  | | || || || | | |||
GGAGCACAACACCCGGGGAGAGCCCGACACCATCGTCGCGCTGGCCAAGTGGAGGATCCTCAACAGGCTGCACGACCGGAACGAGACGCTGTACTACAGAgtgagcgcgctctct-cgatgttgcagtggcgatggttgattcatgagctcaaggtgtttgcgtgtttgattgtctgatgcggtggtgttcgtctgtttttgccag
















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|76919658|gb|DV167819.1|DV167819
EST:     GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGG                         GTGCTAATTGACAATATCAAGGATTTTGCCCCGATAA
genomic: GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGGgtgagcccgt ... ttctcgacagGTGCTAATTGACAATATCAAGGATTTTGCCCCGATAA
EST: gi|211274711|gb|FL015918.1|FL015918
EST:     GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGG                         GTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
genomic: GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGGgtgagcccgt ... ttctcgacagGTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
EST: gi|211274712|gb|FL015919.1|FL015919
EST:     GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGG                         GTGCTAATTGACAATA
genomic: GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGGgtgagcccgt ... ttctcgacagGTGCTAATTGACAATA
EST: gi|74238358|gb|DT646272.1|DT646272
EST:     GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGG                         GTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
genomic: GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGGgtgagcccgt ... ttctcgacagGTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
EST: gi|29130557|gb|CB381261.1|CB381261
EST:     GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGG                         GTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
genomic: GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGGgtgagcccgt ... ttctcgacagGTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
EST: gi|29130494|gb|CB381198.1|CB381198
EST:     GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGG                         GTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
genomic: GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGGgtgagcccgt ... ttctcgacagGTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
EST: gi|149102281|gb|EE287658.2|EE287658
EST:     GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGG                         GTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
genomic: GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGGgtgagcccgt ... ttctcgacagGTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
EST: gi|211384290|gb|FL369291.1|FL369291
EST:     GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGG                         GTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
genomic: GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGGgtgagcccgt ... ttctcgacagGTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
EST: gi|211048980|gb|FL422995.1|FL422995
EST:     GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGG                         GTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
genomic: GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGGgtgagcccgt ... ttctcgacagGTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
EST: gi|211016654|gb|FL375789.1|FL375789
EST:     GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGG                         GTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
genomic: GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGGgtgagcccgt ... ttctcgacagGTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
EST: gi|211527375|gb|FL402913.1|FL402913
EST:     GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGG                         GTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
genomic: GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGGgtgagcccgt ... ttctcgacagGTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
EST: gi|32801635|gb|CD953871.1|CD953871
EST:     GATCCCCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGG                         GTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
genomic: GATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGGgtgagcccgt ... ttctcgacagGTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
EST: gi|71437509|gb|DR818559.1|DR818559
EST:     GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGG                         GTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT
genomic: GGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGGgtgagcccgt ... ttctcgacagGTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGCACAATACCCGCGGCGAGCCTGACTCCATCGTCGCGCTGGCCAAATGGAGGATCCTCAACAGGTTGCACGACCGGAACGAGACATTGTACTACAGGgtgagcccgtaggttgcagtatcgtgtttgggaaaaaaaaatgatacaatggcgatgtgcctgaatttggagtgctgacatggtaatatgcgctcttctcgacag

- - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT