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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcctcgcccacgcgcgtctcttactcccccgcggaccagatctggtcgccccaggcctaattctcaccgcaatggagtggttttggggtggcgtgtgcctctgattgcgtgtatgcgcgtctgattctgcagGCGATTAACGACAAGATCGTGTCCATGGGTATCGACCGGGCGGAGATCAAGGCGGTGGACGCGCAGGAATCGCTCTGTGGCGGCGTCAGCGTGCTCGTCA

Basic information

species Zea mays
transcript GRMZM2G069174_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069174_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g30430.1 (Oryza sativa), 3'ss of exon 2
gtaagttcctcgcccacgcgcgtctcttactcccccgcggaccagatctggtcgccccaggcctaattctcaccgcaatggagtggt--tttggggtggcgtgtgcctctgattgcgtgtatgcgcgtctgattctgcagGCGATTAACGACAAGATCGTGTCCATGGGTATCGACCGGGCGGAGATCAAGGCGGTGGACGCGCAGGAATCGCTCTGTGGCGGCGTCAGCGTGCTCGTCA
                     ||||||  |||  ||          || ||   || |||  ||    ||| |||     ||||| |  |||  || || | | |  |   | ||  |||    |    || |  || ||||||||||||  ||||||||||||||||  ||||  |||||||||||||||||||||||||||||||| |||||  | || |||||||  ||||||||||
---------------------gtctctctctcttccat--------tccgg---cctcagatctgggcctccccgtggccgagtgatggttttcgggggagggggatttgaactgtttgt---tgttgttgttgttgtagGCGATTAACGCGAAGATCGTGTCCATGGACATCGTGCGGGCGGAGATCAAGGCGGTGGACGCGCAGGAGTCGCTGGGCGGGGGCGTCACGGTGCTCGTCA
















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|211305900|gb|FL324273.1|FL324273
EST:     GCCCCGCCGGCACCGGTGCCGACGGCATGGACACGGTCACCAC-ATGGAC                         GCGATTAACGACAAGATCGTGTCCATGGGTATCGACCGGGCGGAGATCAAG
genomic: GCCCCGCCGGCACCGGTGCCGACGGCATGGACACGGTCACCACCATGGACgtaagttcct ... gattctgcagGCGATTAACGACAAGATCGTGTCCATGGGTATCGACCGGGCGGAGATCAAG
EST: gi|37425819|gb|CF650658.1|CF650658
EST:     GCCCCGCCGGCACCGGTGCCGACGGCATGGACACGGTCACCACCATGGAC                         GCGATTAACGACAAGATCGTGTCCATGGGTATCGACCGGGCGGAGATCAAG
genomic: GCCCCGCCGGCACCGGTGCCGACGGCATGGACACGGTCACCACCATGGACgtaagttcct ... gattctgcagGCGATTAACGACAAGATCGTGTCCATGGGTATCGACCGGGCGGAGATCAAG
EST: gi|78109549|gb|DV527965.1|DV527965
EST:     GCCCCGCCGGCACCGGTGCCGACGGCATGGACACGGTCACCACCATGGAC                         GCGATTAACGACAAGATCGTGTCCATGGGTATCGACCGGGCGGAGATCAAG
genomic: GCCCCGCCGGCACCGGTGCCGACGGCATGGACACGGTCACCACCATGGACgtaagttcct ... gattctgcagGCGATTAACGACAAGATCGTGTCCATGGGTATCGACCGGGCGGAGATCAAG
EST: gi|149015208|gb|EE044992.2|EE044992
EST:     GCCCCGCCGGCACCGGTGCCGACGGCATGGACACGGTCACCACCATGGAC                         GCGATTAACGACAAGATCGTGTCCATGGGTATCGACCGGGCGGAGATCAAG
genomic: GCCCCGCCGGCACCGGTGCCGACGGCATGGACACGGTCACCACCATGGACgtaagttcct ... gattctgcagGCGATTAACGACAAGATCGTGTCCATGGGTATCGACCGGGCGGAGATCAAG
EST: gi|50337377|gb|CO532503.1|CO532503
EST:     GCCCCGCCGGCACCGGTGCCGACGGCATGGACACGGTCACCACCATGGAC                         GCGATTAACGACAAGATCGTGTCCATGGGTATCGACCGGGCGGAGATCAAG
genomic: GCCCCGCCGGCACCGGTGCCGACGGCATGGACACGGTCACCACCATGGACgtaagttcct ... gattctgcagGCGATTAACGACAAGATCGTGTCCATGGGTATCGACCGGGCGGAGATCAAG
EST: gi|89249461|gb|DY621247.1|DY621247
EST:     GCCCCGCCGGCACCGGTGCCGACGGCATGGACACGGTCACCACCATGGAC                         GCGATTAACGACAAGATCGTGTCCATGGGTATCGACCGGGCGGAGATCAAG
genomic: GCCCCGCCGGCACCGGTGCCGACGGCATGGACACGGTCACCACCATGGACgtaagttcct ... gattctgcagGCGATTAACGACAAGATCGTGTCCATGGGTATCGACCGGGCGGAGATCAAG
EST: gi|101391403|gb|EB817636.1|EB817636
EST:     GCCCCGCCGGCACCGGTGCCGACGGCATGGACACGGTCACCACCATGGAC                         GCGATTAACGACAAGATCGTGTCCATGGGTATCGACCGGGCGGAGATCAAG
genomic: GCCCCGCCGGCACCGGTGCCGACGGCATGGACACGGTCACCACCATGGACgtaagttcct ... gattctgcagGCGATTAACGACAAGATCGTGTCCATGGGTATCGACCGGGCGGAGATCAAG
EST: gi|71310294|gb|DR791439.1|DR791439
EST:     GCCCCGCCGGCACCGGTGCCGACGGCATGGACACGGTCACCACCATGGAC                         GCGATTAACGACAAGATCGTGTCCATGGGTATCGACCGGGCGGAGATCAAG
genomic: GCCCCGCCGGCACCGGTGCCGACGGCATGGACACGGTCACCACCATGGACgtaagttcct ... gattctgcagGCGATTAACGACAAGATCGTGTCCATGGGTATCGACCGGGCGGAGATCAAG
EST: gi|33467081|gb|CF244130.1|CF244130
EST:     GCCCCGCCGGCACCGGTGCCGACGGCATGGACACGGTCACCACCATGGAC                         GCGATTAACGACAAGATCGTGTCCATGGGTATCGACCGGGCGGAGATCAAG
genomic: GCCCCGCCGGCACCGGTGCCGACGGCATGGACACGGTCACCACCATGGACgtaagttcct ... gattctgcagGCGATTAACGACAAGATCGTGTCCATGGGTATCGACCGGGCGGAGATCAAG
EST: gi|50324320|gb|CO519446.1|CO519446
EST:     GCCCCGCCGGCACCGGTGCCGACGGCATGGACACGGTCACCACCATGGAC                         GCGATTAACGACAAGATCGTGTCCATGGGTATCGACCGGGCGGAGATCAAG
genomic: GCCCCGCCGGCACCGGTGCCGACGGCATGGACACGGTCACCACCATGGACgtaagttcct ... gattctgcagGCGATTAACGACAAGATCGTGTCCATGGGTATCGACCGGGCGGAGATCAAG
EST: gi|211216044|gb|FL339267.1|FL339267
EST:     GCCCCGCCGGCACCGGTGCCGACG-CATGGACACGGTCACCACCATGGAC                         GCGATTAACGACAAGATCGTGTCCATGGGTATCGACCGGGCGAAGATCAAG
genomic: GCCCCGCCGGCACCGGTGCCGACGGCATGGACACGGTCACCACCATGGACgtaagttcct ... gattctgcagGCGATTAACGACAAGATCGTGTCCATGGGTATCGACCGGGCGGAGATCAAG
EST: gi|89756695|gb|DY686633.1|DY686633
EST:     GCCCCGCCGGCACCGGTGCCGACGGCATGGACACGGTCACCACCATGGAC                         GCGATTAACGACAAGATCGTGTCCATGGGTATCGACCGGGCGGAGATCAAG
genomic: GCCCCGCCGGCACCGGTGCCGACGGCATGGACACGGTCACCACCATGGACgtaagttcct ... gattctgcagGCGATTAACGACAAGATCGTGTCCATGGGTATCGACCGGGCGGAGATCAAG
EST: gi|50329790|gb|CO524916.1|CO524916
EST:     GCCCCGCCGGCACCGGTGCCGACGGCATGGACACGGTCACCACCATGGAC                         GCGATTAACGACAAGATCGTGTCCATGGGTATCGACCGGGCGGAGATCAAG
genomic: GCCCCGCCGGCACCGGTGCCGACGGCATGGACACGGTCACCACCATGGACgtaagttcct ... gattctgcagGCGATTAACGACAAGATCGTGTCCATGGGTATCGACCGGGCGGAGATCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggttttggggtggcgtgtgcctctgattgcgtgtatgcgcgtctgattctgcagGCGATTAACGACAAGATCGTGTCCATGGGTATCGACCGGGCGGAGATCAAGGCGGTGGACGCGCAGGAATCGCTCTGTGGCGGCGTCAGCGTGCTCGTCA
                                         gtctgat  putative branch site (score: 4)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcctcgcccacgcgcgtctcttactcccccgcggaccagatctggtcgccccaggcctaattctcaccgcaatggagtggttttggggtggcgtgtgcctctgattgcgtgtatgcgcgtctgattctgcagGCGATTAACGACAAGATCGTGTCCATGGGTATCGACCGGGCGGAGATCAAGGCGGTGGACGCGCAGGAATCGCTCTGTGGCGGCGTCAGCGTGCTCGTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA