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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTGTGCAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCACTTCAGgtaaaacccttatcttcagttaattgtgaattgtgttgacccatattgttgtgttattttctcatgaattcctaaggatgcaactgaacagcaggcacct...

Basic information

species Zea mays
transcript GRMZM2G052630_T02
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052630_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os05g03480.5 (Oryza sativa), 5'ss of exon 11
GATTGTGCAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCACTTCAGgtaaaacccttatcttcagttaattgtgaattgtgttgacccatattgttgtgttattttctcatgaattcctaaggatgcaactgaacagcaggcacct---------
|||||||| || || |||||||||||||||||||  |||||||| || ||||||||||| ||| |||| |||||| |  ||||      |||||  | |    |||| |    ||| ||||||||||  |  | |  | | |||   |     |  |         
GATTGTGCTGGTGTGATTCTCTTTGCTGCTGAAAGGGCAACCCAGGTTGCACTTCAGgtgaaaaccttgtcttcattacattggattccgtgttcgctc----tgtttt----tttcctcatgaattattcggaacacga-tgatttggccctatttagttttctt
















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|45847870|gb|CN071813.1|CN071813
EST:     CAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCACATCAG                         GCAATCCAGTGTCTTGGTGGAAATGGGTACATAAATGAGTACCCAACTGGT
genomic: CAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCACTTCAGgtaaaaccct ... actatggcagGCGATCCAGTGTCTTGGTGGAAATGGGTACATAAATGAGTACCCAACTGGT
EST: gi|24769404|gb|CA404533.1|CA404533
EST:     CAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCACTTCAG                         GCGATCCAGTGTCTTGGTGGAAATGGGTACATAAATGAGTACCCAACTGGT
genomic: CAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCACTTCAGgtaaaaccct ... actatggcagGCGATCCAGTGTCTTGGTGGAAATGGGTACATAAATGAGTACCCAACTGGT
EST: gi|110190881|gb|EC872779.1|EC872779
EST:     CAGGGGTAANNNNNNNNGCTGCTGAAAATGCAACCCAAGTGGCACTTCAG                         GCGATCCAGTGTTTTGGTGGAAATGGGTACATAAATGAGTACCCAACTGGT
genomic: CAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCACTTCAGgtaaaaccct ... actatggcagGCGATCCAGTGTCTTGGTGGAAATGGGTACATAAATGAGTACCCAACTGGT
EST: gi|31360769|gb|CD445126.1|CD445126
EST:     CAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCACTTCAG                         GCGATCCACTGTCTTGGTGGAAATGGGTACATAAATGAGTACCCAACTGG
genomic: CAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCACTTCAGgtaaaaccct ... actatggcagGCGATCCAGTGTCTTGGTGGAAATGGGTACATAAATGAGTACCCAACTGG
EST: gi|60347547|gb|DN214520.1|DN214520
EST:     CAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCACTTCAG                         GCGATCCAGTGTCTTGGTGGAAATGGGTACATAAATGAGTACCCAACTGGT
genomic: CAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCACTTCAGgtaaaaccct ... actatggcagGCGATCCAGTGTCTTGGTGGAAATGGGTACATAAATGAGTACCCAACTGGT
EST: gi|78027006|gb|DV495393.1|DV495393
EST:     CAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCACTTCAG                         GCGATCCAGTGTCTTGGTGGAAATGGGTACATAAATGAGTACCCAACTGGT
genomic: CAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCACTTCAGgtaaaaccct ... actatggcagGCGATCCAGTGTCTTGGTGGAAATGGGTACATAAATGAGTACCCAACTGGT
EST: gi|5108421|gb|AI740134.1|AI740134
EST:     CAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCACTTCAG                         GCGATCCAGTGTCTTGGTGGAAATGGGTACATAAATGAGTACCCAACTGGT
genomic: CAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCACTTCAGgtaaaaccct ... actatggcagGCGATCCAGTGTCTTGGTGGAAATGGGTACATAAATGAGTACCCAACTGGT
EST: gi|74240406|gb|DT648320.1|DT648320
EST:     CAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCACTTCAG                         GCGATCCAGTGTCTTGGTGGAAATGGGTACATAAATGAGTACCCAACTGGT
genomic: CAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCACTTCAGgtaaaaccct ... actatggcagGCGATCCAGTGTCTTGGTGGAAATGGGTACATAAATGAGTACCCAACTGGT
EST: gi|76936507|gb|DV174755.1|DV174755
EST:     CAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCACTTCAG                         GCGATCCAGTGTCTTGGTGGAAATGGGTACATAAATGAGTACCCAACTGGT
genomic: CAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCACTTCAGgtaaaaccct ... actatggcagGCGATCCAGTGTCTTGGTGGAAATGGGTACATAAATGAGTACCCAACTGGT
EST: gi|50336352|gb|CO531478.1|CO531478
EST:     CAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCACTTCAG                         GCGATCCAGTGTCTTGGTGGAAATGGGTACATAAATGAGTACCCAACTGGT
genomic: CAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCACTTCAGgtaaaaccct ... actatggcagGCGATCCAGTGTCTTGGTGGAAATGGGTACATAAATGAGTACCCAACTGGT
EST: gi|78124549|gb|DV542933.1|DV542933
EST:     CAGGGGTAATTTTCTTTGCTGCTGAAAATGCAACCCAAGTGGCACTTCAG                         GCGATCCAGTGTCTTGGTGGAAATGGGTACATAAATGAGTACCCAACTGGT
genomic: CAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCACTTCAGgtaaaaccct ... actatggcagGCGATCCAGTGTCTTGGTGGAAATGGGTACATAAATGAGTACCCAACTGGT
EST: gi|78105056|gb|DV523474.1|DV523474
EST:     CAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCACTTCAG                         GCGATCCAGTGTCTTGGTGGAAATGGGTACATAAATGAGTACCCAACTGGT
genomic: CAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCACTTCAGgtaaaaccct ... actatggcagGCGATCCAGTGTCTTGGTGGAAATGGGTACATAAATGAGTACCCAACTGGT
EST: gi|110525230|gb|EE029414.1|EE029414
EST:     CAGGGGTAANNNNNNNNGCTGCTGAAAATGCAACCCAAGTGGCACTTCAG                         GCGATCCAGTGTTTTGGTGGAAATGGGTACATAAATGAGTACCCAACTGGT
genomic: CAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCACTTCAGgtaaaaccct ... actatggcagGCGATCCAGTGTCTTGGTGGAAATGGGTACATAAATGAGTACCCAACTGGT
EST: gi|149076167|gb|EE164757.2|EE164757
EST:     CAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCACTTCAG                         GCGATCCAGTGTCTTGGTGGAAATGGGTACATAAATGAGTACCCAACTGGT
genomic: CAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCACTTCAGgtaaaaccct ... actatggcagGCGATCCAGTGTCTTGGTGGAAATGGGTACATAAATGAGTACCCAACTGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTGTGCAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCACTTCAGgtaaaacccttatcttcagttaattgtgaattgtgttgacccatattgttgtgttattttctcatgaattcctaaggatgcaactgaacagcaggcacct

- - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - GCTGCT