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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTAACACTTTGATGGCACATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCTgtaaggccctgtttagatgcaaagtttttttagttttagaaaataccatggttttgtgtaatagttttgttttggcaaaccatgagttgtttgaatgtaa...

Basic information

species Zea mays
transcript GRMZM2G111713_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G111713_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os07g45300.1 (Oryza sativa), 5'ss of exon 9
GTTAACACTTTGATGGCACATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCTgtaaggccctgtttagatgcaaagtttttttagttttagaaaataccatggttttgtgtaatagttttgttttggcaaaccatgagttgtttgaatgtaa
||||||||  ||||||||||||||||||||||||| || || |||||  |||||||||| |||||||| |||||        |   ||  |     | ||||    | ||| |      |   ||     || | || | |   |     ||| ||             
GTTAACACACTGATGGCACATGGAGACACATCATCTCTCCGTAAAATATTGACAGAGAGAATGCATTCGgtaagttttcaccttactgtgagtggatgttag----acaaacttttggaggcatgctatttattcttctctcttctttttatgggtgaag---------
















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|88758132|gb|DY542273.1|DY542273
EST:     ATGGAGACACATCATCGCTTCGGAAAATTTTGACAGAGAGGATGCATTCT                         ACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
genomic: ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCTgtaaggccct ... ttggctgaagACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
EST: gi|76923556|gb|DV169545.1|DV169545
EST:     ATGGAGACACATCATCGTTTTGGAAAATTCTGACAGAGAGGATGCATTCT                         ACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
genomic: ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCTgtaaggccct ... ttggctgaagACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
EST: gi|211177445|gb|FL359118.1|FL359118
EST:     ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCT                         ACTATAAAAAATGAACTAAAGAGAAGACAG
genomic: ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCTgtaaggccct ... ttggctgaagACTATAAAAAATGAACTAAAGAGAAGACAG
EST: gi|4827723|gb|AI668415.1|AI668415
EST:     ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCT                         ACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
genomic: ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCTgtaaggccct ... ttggctgaagACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
EST: gi|50337822|gb|CO532948.1|CO532948
EST:     AGGATGCATTCT                         ACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
genomic: AGGATGCATTCTgtaaggccct ... ttggctgaagACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
EST: gi|89251080|gb|DY622866.1|DY622866
EST:     AAATTCTGACAGAGAGGATGCATTCT                         TCTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
genomic: AAATTCTGACAGAGAGGATGCATTCTgtaaggccct ... ttggctgaagACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
EST: gi|71443106|gb|DR824156.1|DR824156
EST:     ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCT                         ACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
genomic: ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCTgtaaggccct ... ttggctgaagACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
EST: gi|89248722|gb|DY620508.1|DY620508
EST:     ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCT                         ACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
genomic: ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCTgtaaggccct ... ttggctgaagACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
EST: gi|71420007|gb|DR804974.1|DR804974
EST:     ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCT                         ACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
genomic: ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCTgtaaggccct ... ttggctgaagACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
EST: gi|61119623|gb|DN560584.1|DN560584
EST:     ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCT                         ACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGG
genomic: ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCTgtaaggccct ... ttggctgaagACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGG
EST: gi|211237149|gb|FL440871.1|FL440871
EST:     ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCT                         CCTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
genomic: ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCTgtaaggccct ... ttggctgaagACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
EST: gi|89758224|gb|DY687488.1|DY687488
EST:     ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCT                         ACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
genomic: ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCTgtaaggccct ... ttggctgaagACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
EST: gi|88758133|gb|DY542274.1|DY542274
EST:     ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCT                         ACTATAAAAAATGAACTA
genomic: ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCTgtaaggccct ... ttggctgaagACTATAAAAAATGAACTA
EST: gi|148938688|gb|EC883024.2|EC883024
EST:     ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCT                         ACTATAAAAAATGAACTAAAGA
genomic: ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCTgtaaggccct ... ttggctgaagACTATAAAAAATGAACTAAAGA
EST: gi|71420010|gb|DR804975.1|DR804975
EST:     ATGGAGACACATCATCGCTTCGGAAA-TTCTGACAGAGAGGATGCATTCT                         ACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTTGGA-TTCTGTACA
genomic: ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCTgtaaggccct ... ttggctgaagACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGT-GGAATTCTGTACA
EST: gi|148989211|gb|EE031705.2|EE031705
EST:     ATGGAGACACATCATCGCTTCGGGAAATTCTGACAGAGAGGATGCATTCT                         ACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTA
genomic: ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCTgtaaggccct ... ttggctgaagACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTA
EST: gi|32913045|gb|CF017857.1|CF017857
EST:     ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCT                         ACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
genomic: ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCTgtaaggccct ... ttggctgaagACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
EST: gi|76923558|gb|DV169546.1|DV169546
EST:     ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCT                         ACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
genomic: ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCTgtaaggccct ... ttggctgaagACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTAACACTTTGATGGCACATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCTgtaaggccctgtttagatgcaaagtttttttagttttagaaaataccatggttttgtgtaatagttttgttttggcaaaccatgagttgtttgaatgtaa

- - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG