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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTCAAGGAGTTCCACGCCAACAACATCCGTGACACCTTCCGCGTCCTTCTCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAGgtacccaccgacacatcaaatccaccacctatttccggtcactaggcgtgccgattcgctagatctgacccgactttgctgtgcgcggtag

Basic information

species Zea mays
transcript GRMZM2G365160_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G365160_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os07g42960.1 (Oryza sativa), 5'ss of exon 1
TTTCAAGGAGTTCCACGCCAACAACATCCGTGACACCTTCCGCGTCCTTCTCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAGgtaccca---ccgacacatcaaatccaccacctatttccggtcactaggcgtgccgattcgctagatctgacccgactttgctgtgcgcggtag-
 |||||||||||| ||||||||||||||||||||||||||||| |||| ||||||||||||| ||| ||||||||||| ||||||||||| ||||||||||||||||    | | ||  |||| | | | | |  |||  |  | | |      |   || |  ||||||  || | |||  || ||| | |   
CTTCAAGGAGTTCAACGCCAACAACATCCGTGACACCTTCCGCATCCTGCTCCAGATGGGCGCCGTCCTCATGTTCGGCGGCCAGATGCCCGTCGTCAAGgtacccaaaatccaaaccccaaaacgagctcatccttcacgcgattcgcgagatctgatccc--gatctgctccaaattttgtgcgcgagtttag
















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|149066690|gb|EE286827.2|EE286827
EST:     TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAG                         GTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
genomic: TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAGgtacccaccg ... tgcgcggtagGTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
EST: gi|12970747|gb|BG267138.1|BG267138
EST:     TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAG                         GTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
genomic: TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAGgtacccaccg ... tgcgcggtagGTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
EST: gi|148937229|gb|EC881411.2|EC881411
EST:     TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAG                         GTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
genomic: TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAGgtacccaccg ... tgcgcggtagGTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
EST: gi|78026715|gb|DV495102.1|DV495102
EST:     TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAG                         GTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
genomic: TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAGgtacccaccg ... tgcgcggtagGTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
EST: gi|4886062|gb|AI677182.1|AI677182
EST:     TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAG                         GTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
genomic: TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAGgtacccaccg ... tgcgcggtagGTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
EST: gi|71310345|gb|DR791477.1|DR791477
EST:     TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAG                         GTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
genomic: TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAGgtacccaccg ... tgcgcggtagGTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
EST: gi|24764071|gb|CA399240.1|CA399240
EST:     TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAG                         GTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
genomic: TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAGgtacccaccg ... tgcgcggtagGTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
EST: gi|148960615|gb|EE011240.2|EE011240
EST:     TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAG                         GTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
genomic: TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAGgtacccaccg ... tgcgcggtagGTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
EST: gi|149112057|gb|EE191228.2|EE191228
EST:     TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAG                         GTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
genomic: TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAGgtacccaccg ... tgcgcggtagGTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
EST: gi|88748205|gb|DY532346.1|DY532346
EST:     TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAG                         GTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
genomic: TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAGgtacccaccg ... tgcgcggtagGTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
EST: gi|76923640|gb|DV169586.1|DV169586
EST:     TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAG                         GTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
genomic: TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAGgtacccaccg ... tgcgcggtagGTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
EST: gi|149100904|gb|EE187000.2|EE187000
EST:     TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAG                         GTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
genomic: TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAGgtacccaccg ... tgcgcggtagGTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
EST: gi|148950586|gb|EC896168.2|EC896168
EST:     TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAG                         GTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
genomic: TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAGgtacccaccg ... tgcgcggtagGTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
EST: gi|61119771|gb|DN560732.1|DN560732
EST:     TCCAGATGGGTGTCGTGCTCATGTTCGGTGGCCAGGTGCCGGTCGTCAAG                         GTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCCGAGCCGTTCGAG
genomic: TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAGgtacccaccg ... tgcgcggtagGTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
EST: gi|148970094|gb|EE021028.2|EE021028
EST:     TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAG                         GTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
genomic: TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAGgtacccaccg ... tgcgcggtagGTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
EST: gi|110218895|gb|EC900793.1|EC900793
EST:     TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAG                         GTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
genomic: TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAGgtacccaccg ... tgcgcggtagGTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
EST: gi|31353338|gb|CD437695.1|CD437695
EST:     TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAG                         GTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
genomic: TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAGgtacccaccg ... tgcgcggtagGTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
EST: gi|148937034|gb|EC881207.2|EC881207
EST:     TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAG                         GTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
genomic: TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAGgtacccaccg ... tgcgcggtagGTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
EST: gi|148944818|gb|EC889966.2|EC889966
EST:     TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAG                         GTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
genomic: TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAGgtacccaccg ... tgcgcggtagGTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
EST: gi|149073667|gb|EE161972.2|EE161972
EST:     TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAG                         GTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
genomic: TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAGgtacccaccg ... tgcgcggtagGTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
EST: gi|148964173|gb|EE015341.2|EE015341
EST:     TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAG                         GTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
genomic: TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAGgtacccaccg ... tgcgcggtagGTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
EST: gi|149038824|gb|EE155537.2|EE155537
EST:     TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAG                         GTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
genomic: TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAGgtacccaccg ... tgcgcggtagGTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
EST: gi|149083054|gb|EE172309.2|EE172309
EST:     TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAG                         GTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG
genomic: TCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAGgtacccaccg ... tgcgcggtagGTGGGGAGGATGGCTGGCCAGTTCGCCAAGCCAAGGTCTGAGCCGTTCGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTCAAGGAGTTCCACGCCAACAACATCCGTGACACCTTCCGCGTCCTTCTCCAGATGGGCGTCGTGCTCATGTTCGGTGGCCAGATGCCGGTCGTCAAGgtacccaccgacacatcaaatccaccacctatttccggtcactaggcgtgccgattcgctagatctgacccgactttgctgtgcgcggtag

- - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG