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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATCAATGAAAAGATTGGTGCTGCTGGTGTAGTCAGCCAGGAGTGCAAGACTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAGgtttgtatattccaaaccatggatttgtttttctgattgctggtttgatcaattgctcttgaagctctgcggtaactcaacttgctattgggttattttgcag

Basic information

species Zea mays
transcript GRMZM2G035636_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G035636_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os05g49200.2 (Oryza sativa), 5'ss of exon 8
AATCAATGAAAAGATTGGTGCTGCTGGTGTAGTCAGCCAGGAGTGCAAGACTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAGgtttgtatattccaaaccatggatttgtttttctgattgctggtttgatcaattgc-tcttgaagctctgcggtaactcaacttgctattgggttattttgcag
||||||||| ||||| |||||| |||| ||||||||||| || |||||||| |||||||||||||||||||| |||||||||||||| ||||| |||||||||||||  || |          ||   |||||||    | | |||  ||||||   ||||  |    ||   |||  |||||| ||   || |||| ||||||
AATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGCCAAGAATGCAAGACAGTTGTTTCTCAATATGGACAACAGATCCTAGATCTGTTGCTTGCTGAGgtttgtaatttgc----------ttcaattttctggaaacagcttttgtcaattatatctttga----tgaattaaaacaactttctg--ggattatgttgcag
















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|6964727|gb|AW433420.1|AW433420
EST:     CTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAG                         ACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGC
genomic: CTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAGgtttgtatat ... tattttgcagACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGC
EST: gi|32850229|gb|CD989910.1|CD989910
EST:     CTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAG                         ACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGC
genomic: CTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAGgtttgtatat ... tattttgcagACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGC
EST: gi|32835904|gb|CD975582.1|CD975582
EST:     CTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAG                         ACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGC
genomic: CTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAGgtttgtatat ... tattttgcagACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGC
EST: gi|33092153|gb|CF052147.1|CF052147
EST:     CTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAG                         ACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACCTTTGATGGC
genomic: CTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAGgtttgtatat ... tattttgcagACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGC
EST: gi|32850207|gb|CD989888.1|CD989888
EST:     CTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAG                         ACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGCC
genomic: CTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAGgtttgtatat ... tattttgcagACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGC
EST: gi|32850559|gb|CD990240.1|CD990240
EST:     CTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAG                         ACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGC
genomic: CTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAGgtttgtatat ... tattttgcagACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGC
EST: gi|194716945|gb|FK934104.1|FK934104
EST:     CTGTTGTTTCTCAATATGAACAGCAGATCCTAGATCTTTTGCTAGCTGAG                         ACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGC
genomic: CTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAGgtttgtatat ... tattttgcagACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGC
EST: gi|8576947|gb|BE129584.1|BE129584
EST:     TCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAG                         ACACAACCAGCGAAGATCTGTTCCCAGGTTGGTCTGTGCACTTTTGATGGC
genomic: TCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAGgtttgtatat ... tattttgcagACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGC
EST: gi|7135183|gb|AW497972.1|AW497972
EST:     CTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAG                         ACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGC
genomic: CTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAGgtttgtatat ... tattttgcagACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGC
EST: gi|32850704|gb|CD990385.1|CD990385
EST:     CTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTNTGCTAGCTGAG                         ACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGC
genomic: CTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAGgtttgtatat ... tattttgcagACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGC
EST: gi|211224721|gb|FL222439.1|FL222439
EST:     CTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAG                         ACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGC
genomic: CTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAGgtttgtatat ... tattttgcagACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATCAATGAAAAGATTGGTGCTGCTGGTGTAGTCAGCCAGGAGTGCAAGACTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAGgtttgtatattccaaaccatggatttgtttttctgattgctggtttgatcaattgctcttgaagctctgcggtaactcaacttgctattgggttattttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA