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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgcagtatgtggttcacatagttcccagtatccttttggacttagatttagtttgatatatggttatgtttattgacagaatgctttttagctttacagATAAAATCTTGAGCAAAATGGGAGAAGGTTTGGGTTTTCTGCAATCTGTCGTCTCCTCTTCTGCTGGGTATCTCCGTTATTATTCTAATGAAGAGGGCTA

Basic information

species Zea mays
transcript GRMZM2G094039_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094039_T06 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g40840.1 (Oryza sativa), 3'ss of exon 2
-atgcagtatgtggttcacatagttcccagtatccttttggacttagatttagtttgata-tatggttatgtttattgacagaatgctttt--tagctttacagATAAAATCTTGAGCAAAATGGGAGAAGGTTTGGGTTTTCTGCAATCTGTCGTCTCCTCTTCTGCTGGGTATCTCCGTTATTATTCTAATGAAGAGGGCTA
 ||||    | | ||| | || |    || || || |  ||  ||| |  || || | |  | ||    ||||  |||| |   | || ||  | ||| | |||| |||||||||||||||||||||||||                                                                         
gatgctaattttagttgaaattg----caataaccgtagggctttatagctatttaggttctgtgagattgttcgttgatattcttctcttcttggctatgcagACAAAATCTTGAGCAAAATGGGAGAAG-------------------------------------------------------------------------
















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|60339751|gb|DN206724.1|DN206724
EST:     CCGTGATGGACACTTCGTATTCGACCTTGGCGAGAACTTGACCCGCCGAT                         ATAAAATCTTGAGCAAAATGGGAGAAGGTTTGGGTTTTCTGCAATCTGTCG
genomic: CCGTGATGGACACTTCGTATTCGACCTTGGCGAGAACTTGACCCGCCGATgtgagttccc ... agctttacagATAAAATCTTGAGCAAAATGGGAGAAGGTTTGGGTTTTCTGCAATCTGTCG
EST: gi|148969962|gb|EE020875.2|EE020875
EST:     CCGTGATGGACACTTCGTATTCGACCTTGGCGAGAACTTGACCCGCCGAT                         ATAAAATCTTGAGCAAAATGGGAGAAGGTTTGGGTTTTCTGCAATCTGTCG
genomic: CCGTGATGGACACTTCGTATTCGACCTTGGCGAGAACTTGACCCGCCGATgtgagttccc ... agctttacagATAAAATCTTGAGCAAAATGGGAGAAGGTTTGGGTTTTCTGCAATCTGTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatttagtttgatatatggttatgtttattgacagaatgctttttagctttacagATAAAATCTTGAGCAAAATGGGAGAAGGTTTGGGTTTTCTGCAATCTGTCGTCTCCTCTTCTGCTGGGTATCTCCGTTATTATTCTAATGAAGAGGGCTA
                          tattgac  putative branch site (score: 2)
                                       cttttta  putative PPT
                   ttatgtttatt  TA-rich tract
















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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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgcagtatgtggttcacatagttcccagtatccttttggacttagatttagtttgatatatggttatgtttattgacagaatgctttttagctttacagATAAAATCTTGAGCAAAATGGGAGAAGGTTTGGGTTTTCTGCAATCTGTCGTCTCCTCTTCTGCTGGGTATCTCCGTTATTATTCTAATGAAGAGGGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG