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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATTTTAACATTGGTCCATTAGTTGATTTAGACGTCCCTCGGAGCTTTTGGAGTCAGGTTTCAGGGAAGTATGGGAACATGTTCTACTGGAAAGAAAAGgtaacattttattgtttgacctattagaacatcttcaagagtttccaaatttagtccaaatcattgagttttccaagttgccagaaacaattgggaacaa...

Basic information

species Zea mays
transcript GRMZM2G022876_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G022876_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os07g34950.1 (Oryza sativa), 5'ss of exon 5
AAATTTTAACATTGGTCCATTAGTTGATTTAGACGTCCCTCGGAGCTTTTGGAGTCAGGTTTCAGGGAAGTATGGGAACATGTTCTACTGGAAAGAAAAGgtaacattttattgtttgacctattagaacatcttcaagagtttccaaatttagtccaaa----tcattgagttttccaagttgccagaaacaattgggaacaa-
|||||| ||  ||||| ||||||||||||||||| | |||||||||||||||||||  |||||||||||||| || |||||||||| ||||||||||||||||||||||| || ||  | |||  ||    |   ||| |  || || ||| |     |     |  ||  ||  |||   || | | ||  |   | | || | 
AAATTTCAATGTTGGTGCATTAGTTGATTTAGACATTCCTCGGAGCTTTTGGAGTCGTGTTTCAGGGAAGTACGGAAACATGTTCTTCTGGAAAGAAAAGgtaacattttgttattcaatctagcag----ttaacaataaattacatattcatagtgatgttttttttttgtcctcctgatt-ctacaattagaagagcactaa

upper sequence: GRMZM2G022876_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA10G06430.2 (Glycine max), 5'ss of exon 5
AAATTTTAACATTGGTCCATTAGTTGATTTAGACGTCCCTCGGAGCTTTTGGAGTCAGGTTTCAGGGAAGTATGGGAACATGTTCTACTGGAAAGAAAAGgtaacattttattgtttgacctattagaacatcttcaag--agtttccaaatttagtccaaatcattgagttttccaagttgccagaaacaattgggaacaa
 ||||| ||  ||||| |    |||||||| || ||||| || |||||||||| ||   |  | ||||||||||||||||| ||||| |||||||||||||||   | ||  |  |     ||        |  | |    ||||  |   ||||    ||  ||   | |  | ||                         
GAATTTCAATGTTGGTGCTACGGTTGATTTGGATGTCCCACGTAGCTTTTGGAATCGCTTGGCTGGGAAGTATGGGAACATTTTCTATTGGAAAGAAAAGgtagtctcttgcttctcagtgtagctatttttaattagcctagttaacgg-tttaacttaa--caccaaatgatacag------------------------
















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|211123601|gb|FL454343.1|FL454343
EST:     GGAGTCAGGTTTCAGGGAAGTATGGGAACATGTTCTACTGGAAAGAAAAG                         GGAGAGGACGCCTCAATCGAAGCTGCTGTGACGGCAATATCTCGATGTCTA
genomic: GGAGTCAGGTTTCAGGGAAGTATGGGAACATGTTCTACTGGAAAGAAAAGgtaacatttt ... catggatcagGGAGAGGACGCCTCAATCGAAGCTGCTGTGACGGCAATATCTCGATGTCTA
EST: gi|16377665|gb|BI992046.1|BI992046
EST:     GGAGTCAGGTTTCAGGGAAGTATGGGAACATGTTCTACTGGAAAGAAAAG                         GGAGAGGACGCCTCAATCGAAGCTGCTGTGACGGCAATATCTCGATGTCTA
genomic: GGAGTCAGGTTTCAGGGAAGTATGGGAACATGTTCTACTGGAAAGAAAAGgtaacatttt ... catggatcagGGAGAGGACGCCTCAATCGAAGCTGCTGTGACGGCAATATCTCGATGTCTA
EST: gi|149071910|gb|EE160296.2|EE160296
EST:     GGAGTCAGGTTTCAGGGAAGTATGGGAACATGTTCTACTGGAAAGAAAAG                         GGAGAGGACGCCTCAATCGAAGCTGCTGTGACGGCAATATCTCGATGTCTA
genomic: GGAGTCAGGTTTCAGGGAAGTATGGGAACATGTTCTACTGGAAAGAAAAGgtaacatttt ... catggatcagGGAGAGGACGCCTCAATCGAAGCTGCTGTGACGGCAATATCTCGATGTCTA
EST: gi|113650042|gb|DW807261.1|DW807261
EST:     GGAGTCAGGTTTCAGGGAAGTATGGGAACATGTTCTACTGGAAAGAAAAG                         GGGAGAGGACGCCTC
genomic: GGAGTCAGGTTTCAGGGAAGTATGGGAACATGTTCTACTGGAAAGAAAAGgtaacatttt ... catggatcagGG-AGAGGACGCCTC
EST: gi|21809641|gb|BQ667959.1|BQ667959
EST:     GGAGTCAGGTTTCAGGGAAGTATGGGAACATGTTCTACTGGAAAGAAAAG                         GGAGAGGACGCCTCGATCGAAGCTGCTGTGACGGCAATATCTCGATGTCTA
genomic: GGAGTCAGGTTTCAGGGAAGTATGGGAACATGTTCTACTGGAAAGAAAAGgtaacatttt ... catggatcagGGAGAGGACGCCTCAATCGAAGCTGCTGTGACGGCAATATCTCGATGTCTA
EST: gi|6342689|gb|AW165513.1|AW165513
EST:     GGAGTCAGGTTTCAGGGAAGTATGGGAACATGTTCTACTGGAAAGAAAAG                         GGAGAGGACGCCTCAATCGAAGCTGCTGTGACGGCAATATCTCGATGTCTA
genomic: GGAGTCAGGTTTCAGGGAAGTATGGGAACATGTTCTACTGGAAAGAAAAGgtaacatttt ... catggatcagGGAGAGGACGCCTCAATCGAAGCTGCTGTGACGGCAATATCTCGATGTCTA
EST: gi|14243662|gb|BG841333.2|BG841333
EST:     GGAGTCAGGTTTCAGGGAAGTATGGGAACATGTTCTACTGGAAAGAAAAG                         GGAGAGGACGCCTCAATCGAAGCTGCTGTGACGGCAATATCTCGATGTCTA
genomic: GGAGTCAGGTTTCAGGGAAGTATGGGAACATGTTCTACTGGAAAGAAAAGgtaacatttt ... catggatcagGGAGAGGACGCCTCAATCGAAGCTGCTGTGACGGCAATATCTCGATGTCTA
EST: gi|211190443|gb|FL432725.1|FL432725
EST:     GGAGTCAGGTTTCAGGGAAGTATGGGAACATGTTCTACTGGAAAGAAAAG                         GGAGAGGACGCCTCAATCGAAGCTGCTGTGACGGCAATATCTCGATGTCTA
genomic: GGAGTCAGGTTTCAGGGAAGTATGGGAACATGTTCTACTGGAAAGAAAAGgtaacatttt ... catggatcagGGAGAGGACGCCTCAATCGAAGCTGCTGTGACGGCAATATCTCGATGTCTA

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAATTTTAACATTGGTCCATTAGTTGATTTAGACGTCCCTCGGAGCTTTTGGAGTCAGGTTTCAGGGAAGTATGGGAACATGTTCTACTGGAAAGAAAAGgtaacattttattgtttgacctattagaacatcttcaagagtttccaaatttagtccaaatcattgagttttccaagttgccagaaacaattgggaacaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA