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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTCTTAACTAGCCTCTGCTTCACTGCAGATGGTTGCAGGGAGATTTGTGAATGTGTACTCGAGAGATGACTGGATTCTCGGTGTAACCTTCCGAGCAAGgtgaacaaagtgggattgatttcgaattgattgatagtcagtgctggaacagttaagtcgatacctttgctgacttgctaattctctgatgtag

Basic information

species Zea mays
transcript GRMZM2G092776_T02
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G092776_T02 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os03g02170.3 (Oryza sativa), 5'ss of exon 13
TCTCTTAACTAGCCTCTGCTTCACTGCAGATGGTTGCAGGGAGATTTGTGAATGTGTACTCGAGAGATGACTGGATTCTCGGTGTAACCTTCCGAGCAAGgtgaacaaagtgggattgatttc-gaattgattgatagtcagtgctggaacagttaagtcgatacctttgctgacttgc-taattctctgatgtag-------------------------------
                             |||||||| || |||||||||||||||||||| | ||||||||||||||| ||||| || || || || |||| |||| | |     ||||||| ||  |  | || ||    |     | || |     | ||        ||||||   ||||  |||  || ||                               
-----------------------------ATGGTTGCTGGAAGATTTGTGAATGTGTACTCCACAGATGACTGGATTCTTGGTGTTACTTTTCGTGCGAGgtaaacagattta---tgatttcagagctcctagaaagctcatatc--accattcc--cccatgtgagctatgacttaagtaatcttctcgtgcagtctgctaacacaagggttggctggcatccag

upper sequence: GRMZM2G092776_T02 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os03g02170.1 (Oryza sativa), 5'ss of exon 13
TCTCTTAACTAGCCTCTGCTTCACTGCAGATGGTTGCAGGGAGATTTGTGAATGTGTACTCGAGAGATGACTGGATTCTCGGTGTAACCTTCCGAGCAAGgtgaacaaagtgggattgatttc-gaattgattgatagtcagtgctggaacagttaagtcgatacctttgctgacttgc-taattctctgatgtag
                             |||||||| || |||||||||||||||||||| | ||||||||||||||| ||||| || || || || |||| |||| | |     ||||||| ||  |  | || ||    |     | || |     | ||        ||||||   ||||  |||  || ||
-----------------------------ATGGTTGCTGGAAGATTTGTGAATGTGTACTCCACAGATGACTGGATTCTTGGTGTTACTTTTCGTGCGAGgtaaacagattta---tgatttcagagctcctagaaagctcatatc--accattcc--cccatgtgagctatgacttaagtaatcttctcgtgcag
















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|6865375|gb|AW360725.1|AW360725
EST:     AATGTGTACTCGAGAGATGACTGGATTCTCGGTGCAACCTTCCGAGCAAG                         CCTGCTTACCCAAGGACTGGCTGGCATCCAGGCCATTGATGTGCCTGGTGT
genomic: AATGTGTACTCGAGAGATGACTGGATTCTCGGTGTAACCTTCCGAGCAAGgtgaacaaag ... tctgatgtagCCTGCTTACCCAAGGACTGGCTGGCATCCAGGCCATTGATGTGCCTGGTGT
EST: gi|6538838|gb|AW224977.1|AW224977
EST:     AATGTGTACTCGAGAGATGACTGGATTCTCGGTGTAACCTTCCGAGCAAG                         CCTGCTTACCCAAGGACTGGCTGGCATCCAGGCCATTGATGTGCCTGGTGT
genomic: AATGTGTACTCGAGAGATGACTGGATTCTCGGTGTAACCTTCCGAGCAAGgtgaacaaag ... tctgatgtagCCTGCTTACCCAAGGACTGGCTGGCATCCAGGCCATTGATGTGCCTGGTGT
EST: gi|78120794|gb|DV539178.1|DV539178
EST:     AATGTGTACTCGAGAGATGACTGGATTCTCGGTGTAACCTTCCGAGCAAG                         CCTGCTTACCCAAGGACTGGCTGGCATCCAGGCCATTGATGTGCCTGGTGT
genomic: AATGTGTACTCGAGAGATGACTGGATTCTCGGTGTAACCTTCCGAGCAAGgtgaacaaag ... tctgatgtagCCTGCTTACCCAAGGACTGGCTGGCATCCAGGCCATTGATGTGCCTGGTGT
EST: gi|6865071|gb|AW360421.1|AW360421
EST:     AATGTGTACTCGAGAGATGACTGGATTCTCGGTGTAACCTTCCGAGCAAG                         CCTGCTTACCCAAGGACTGGCTGGCATCCAGGCCATTGATGTGCCTGGTGT
genomic: AATGTGTACTCGAGAGATGACTGGATTCTCGGTGTAACCTTCCGAGCAAGgtgaacaaag ... tctgatgtagCCTGCTTACCCAAGGACTGGCTGGCATCCAGGCCATTGATGTGCCTGGTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTCTTAACTAGCCTCTGCTTCACTGCAGATGGTTGCAGGGAGATTTGTGAATGTGTACTCGAGAGATGACTGGATTCTCGGTGTAACCTTCCGAGCAAGgtgaacaaagtgggattgatttcgaattgattgatagtcagtgctggaacagttaagtcgatacctttgctgacttgctaattctctgatgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG