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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggtaagcgaccgcgccgcactccattgctgctttctctgttcgctgcgcatttcgatctttggctaagaagttgcggtttggtttggccgtgctcgtgggtcgtgtagATGTCGTCCGAGGCGGTGAAGGTGGCGGTGCCGGAGTCGGTACTCCGCAAGCGGAAGCGCGAGGAGCAGTGGGCCGCCGAGAAGAAGGAGAAGTCCCTGG

Basic information

species Zea mays
transcript GRMZM5G868433_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 1
gtaaggtaagcgaccg-cgccgcactccattgctgcttt-ctctgttcgctgcgcatttcgatctttggctaagaagttgcggtttggtttggccgtgctcgtgggtcgtgtagATGTCGTCCGAGGCGGTGAAGGTGGCGGTGCCGGAGTCGGTACTCCGCAAGCGGAAGCGCGAGGAGCAGTGGGCCGCCGAGAAGAAGGAGAAGTCCCTGG
     ||||| |  || |||||    ||||||| ||  | |||   ||  | |||   |||  |  |  | |         |||  ||||| || || |      |  | | ||||| ||||||||||||  ||||||| |||||||||||| || ||||||||| ||||||| ||||||  |||||| |||| ||  ||||||||| || | |
-----gtaagagctcgtcgccggtagccattgccgccctgctcctctctgttcgctcgtcgccccgtcccgatctgaccctggtg-ggtttcgctgttc------gctgcgcagATGGCGTCCGAGGCGGCCAAGGTGGTGGTGCCGGAGTCCGTGCTCCGCAAGAGGAAGCGGGAGGAGGTGTGGGCGGCCGCGAGCAAGGAGAAGGCCGTCG

upper sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os08g13690.1 (Oryza sativa), 3'ss of exon 1
gtaaggtaagcgaccgcgccgcactccattgctgctttctctgttcgctgcgcatttcgatctttggctaagaagttgcggtttggtttggccgtgctcgtgggtcgtgtagATGTCGTCCGAGGCGGTGAAGGTGGCGGTG---CCGGAGTCGGTACTCCGCAAGCGGAAGCGCGAGGAGCAGTGGGCCGCCGAGAAGAAGGAGAAGTCCCTGG
                                |    || |    |   || |  | |      || ||  |  ||   | | |   |  || |||   ||| || ||| ||||| || | |||| || ||||| |||||||   ||||||||||| ||    ||||||||||| |||||||||||||| || || | |||||||||| | |   
-------------------------------gtaagctcccgaaccctagctcgatccagcgactg-ctcggccgtgcggatct--ctgagcggtgtgtgtgtgt-gtgcagATGGCGGCGGAGGTGGCGAAGGCGGCGGTGGTGCCGGAGTCGGTGCTGAAGAAGCGGAAGCGGGAGGAGCAGTGGGCGGCGGACAGGAAGGAGAAGGCGC---
















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|211171434|gb|FK956282.1|FK956282
EST:     TCTCCTACGCAGATCGTCCAG                         ATGTCGTCCGAGGCGGTGAAGGTGGCGGTGCCGGAGTCGGTACTCCGCAAG
genomic: TCTCCTACGCAGATCGTCCAGgtaaggtaag ... ggtcgtgtagATGTCGTCCGAGGCGGTGAAGGTGGCGGTGCCGGAGTCGGTACTCCGCAAG
EST: gi|76922808|gb|DV169184.1|DV169184
EST:     TCTCCTACGCAGATCGTCCAGGTAAG                     
genomic: TCTCCTACGCAGATCGTCC-----AGgtaaggtaag ... ggtcgt
EST: gi|148940442|gb|EC885240.2|EC885240
EST:     CCCGCGTCCCCCCTCTCCTACGCAGATCGTCCAGGTAAG                     
genomic: CCCGCGTCCCCCCTCTCCTACGCAGATCGTCC-----AGgtaaggtaag ... ggtcgt
EST: gi|211173115|gb|FK956300.1|FK956300
EST:     TCTCCTACGCAGATCGTCCAGGTAAG                     
genomic: TCTCCTACGCAGATCGTCC-----AGgtaaggtaag ... ggtcgt
EST: gi|94477419|gb|EB706377.1|EB706377
EST:     CCCCTCTCCTACGCAGATCGTCCAGGTAAG                     
genomic: CCCCTCTCCTACGCAGATCGTCC-----AGgtaaggtaag ... ggtcgt
EST: gi|148941047|gb|EC885904.2|EC885904
EST:     CCCGCGTCCCCCCTCTCCTACGCAGATCGTCCAGGTAAG                     
genomic: CCCGCGTCCCCCCTCTCCTACGCAGATCGTCC-----AGgtaaggtaag ... ggtcgt
EST: gi|148935172|gb|EC879210.2|EC879210
EST:     CCCGCGTCCCCCCTCTCCTACGCAGATCGTCCAGGTAAG                     
genomic: CCCGCGTCCCCCCTCTCCTACGCAGATCGTCC-----AGgtaaggtaag ... ggtcgt
EST: gi|71438751|gb|DR819801.1|DR819801
EST:     CCCGCGTCCCCCCTCTCCTACGCAGATCGTCCAG                         ATGTCGTCCGAGGCGGTGAAGGTGGCGGTGCCGGAGTCGGTACTCCGCAAG
genomic: CCCGCGTCCCCCCTCTCCTACGCAGATCGTCCAGgtaaggtaag ... ggtcgtgtagATGTCGTCCGAGGCGGTGAAGGTGGCGGTGCCGGAGTCGGTACTCCGCAAG
EST: gi|78084905|gb|DV513298.1|DV513298
EST:     TCTCCTACGCAGATCGTCCAGGTAAG                     
genomic: TCTCCTACGCAGATCGTCC-----AGgtaaggtaag ... ggtcgt

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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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggtaagcgaccgcgccgcactccattgctgctttctctgttcgctgcgcatttcgatctttggctaagaagttgcggtttggtttggccgtgctcgtgggtcgtgtagATGTCGTCCGAGGCGGTGAAGGTGGCGGTGCCGGAGTCGGTACTCCGCAAGCGGAAGCGCGAGGAGCAGTGGGCCGCCGAGAAGAAGGAGAAGTCCCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT