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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACCTATGATGCATTGAAGAGCTATACACCAGAAATGGTTGAAGTTCTCATTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatcactgaaaataaattgaagttctttttttcatccttttatgtactaatggcgttcttcgtttctacag

Basic information

species Zea mays
transcript GRMZM2G005036_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005036_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os05g44916.1 (Oryza sativa), 5'ss of exon 3
TACCTATGATGCATTGAAGAGCTATACACCAGAAATGGTTGAAGTTCTCATTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatcac--tgaaaataaattgaagttctttttttcatccttttatgtactaatggc-gttcttcgtttctacag
||| ||||||||| ||||| | ||| ||||||||||||||||||||||||| |||||||||||||| ||||||||  | || |||||||||||||||||||| | | ||||   |||  || |  |   | |  ||||       |||||   | || |    | |  | | ||||||||
TACTTATGATGCACTGAAGTGTTATGCACCAGAAATGGTTGAAGTTCTCATCGACAGTGTGAGGAACCCAGCATTTTTAGAATGGGAGGTCAAAGAGCAGgtgcatgatcattttgagcattatatttcgctaattttgcttcttttttactgattattatttgctaattgcttctacag

upper sequence: GRMZM2G005036_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT1G51980.2 (Arabidopsis thaliana), 5'ss of exon 3
TACCTATGATGCATTGAAGAGCTATACACCAGAAATGGTTGAAGTTCTCATTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatcactgaaaataaattgaagttcttt--------ttttcatccttttatgta---------ctaatggcgttcttcgtttctacag
 ||   ||||||  | |||| ||||   || ||||||||||||||||| ||||||||||| || || || || ||| | || ||||| || || ||  |||||  | ||   |         ||| | |  | |        | || |  |||||||||          |   || || |  || ||||  |||
CACTATTGATGCTCTTAAGACCTATGTCCCTGAAATGGTTGAAGTTCTTATTGACAGTGTTAGAAACCCTGCTTTCTTGGACTGGGAAGTGAATGAAGAGgtagatcattttttttttccttttgtattattctgataactgtgttgaaacttttatgtgacttttagccatgtgtcgatgatcttttccgcag
















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|31356317|gb|CD440674.1|CD440674
EST:     TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAG                         CTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
genomic: TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
EST: gi|89761459|gb|DY689465.1|DY689465
EST:     TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAG                         CTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
genomic: TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
EST: gi|31358559|gb|CD442916.1|CD442916
EST:     TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAG                         CTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
genomic: TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
EST: gi|88755226|gb|DY539367.1|DY539367
EST:     TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAG                         CTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
genomic: TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
EST: gi|19770121|gb|BQ034842.1|BQ034842
EST:     TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAG                         CTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
genomic: TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
EST: gi|32837193|gb|CD976871.1|CD976871
EST:     TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAG                         CTCCAGAACATAAAATCTGAAATAGCTGATGTGTCTGCTAATCCTCAAGGT
genomic: TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
EST: gi|19822381|gb|BQ048405.1|BQ048405
EST:     TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAG                         CTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
genomic: TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
EST: gi|30031572|gb|CB833423.1|CB833423
EST:     TTGACAG-GTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAG                         CTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
genomic: TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACCTATGATGCATTGAAGAGCTATACACCAGAAATGGTTGAAGTTCTCATTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatcactgaaaataaattgaagttctttttttcatccttttatgtactaatggcgttcttcgtttctacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG