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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCACGAAAGAAGGACAAGCTAAGATACCGCTACCCCCGTGGAGAATCTTACCTCGATGTGATACAGAGgtaaaaactatagtttctaattatacagacaaaaaatctccatagtttttttttcctaagaaaagtcgtgctggtttacttggtttttgtctgtcaaactatgacagatttcagttcccgtgtaactataccctaacagctgatgtcataataacccttag

Basic information

species Zea mays
transcript GRMZM2G021846_T01
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G021846_T02 (Zea mays), 5'ss of exon 19
lower sequence: LOC_Os05g07130.2 (Oryza sativa), 5'ss of exon 20
GTCACGAAAGAAGGACAAGCTAAGATACCGCTACCCCCGTGGAGAATCTTACCTCGATGTGATACAGAGgtaaaaactatagtttctaat--tatacagacaaaaaatctccatagtttttt--tttcctaagaaaagtcgtgctggtttacttggtttttgtctgtcaaactatgacagatttcagttcccgtgtaactataccctaacagctgatgtcataataacccttag
 ||||| |||||||||||  ||||||| || ||||||||||||||||||||||| |||||||| |||||||  || | ||   |||||||  ||| |||| ||||| | | || |||| |||    | |  |    | | |   |  |  | |       |   | |  |    | ||  | ||  | |   ||  ||     ||  |                          
ATCACGCAAGAAGGACAAATTAAGATATCGATACCCCCGTGGAGAATCTTACCTTGATGTGATTCAGAGgtttaatc-atttcttctaatattattcaga-aaaaacttttcacagttctttagactgcacaatgcaatggaaataatcaattctaccagtacgtcttcagtcttcactaacttgtgatttggtaaaat----cctcag-------------------------
















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|32925226|gb|CF030038.1|CF030038
EST:     CTAAGATACCGCTACCCCCGTGGAGAATCTTACCTCGATGTGATACAGAG                         GCTGGAACCCGTCATCATCGAGCTAGAACGCCAGCGTGCACCAGTGGTTGT
genomic: CTAAGATACCGCTACCCCCGTGGAGAATCTTACCTCGATGTGATACAGAGgtaaaaacta ... taacccttagGCTGGAACCCGTCATCATCGAGCTAGAACGCCAGCGTGCACCAGTGGTTGT
EST: gi|32926593|gb|CF031405.1|CF031405
EST:     CTAAGATACCGCTACCCCTGTGGAGAATCTTACCTCGATGTGATACAGAG                         GCTGGAACCCGTCATCATCGAGCTAGAACGCCAGCGTGCACCAGTGGTTGT
genomic: CTAAGATACCGCTACCCCCGTGGAGAATCTTACCTCGATGTGATACAGAGgtaaaaacta ... taacccttagGCTGGAACCCGTCATCATCGAGCTAGAACGCCAGCGTGCACCAGTGGTTGT
EST: gi|32838571|gb|CD978249.1|CD978249
EST:     CTAAGATACCGCTACCCCCGTGGAGAATCTTACCTCGATGTGATACAGAG                         GCTGGAACCCGTCATCATCGAGCTAGAACGCCAGCGTGCACCAGTGGTTGT
genomic: CTAAGATACCGCTACCCCCGTGGAGAATCTTACCTCGATGTGATACAGAGgtaaaaacta ... taacccttagGCTGGAACCCGTCATCATCGAGCTAGAACGCCAGCGTGCACCAGTGGTTGT
EST: gi|32941577|gb|CF046396.1|CF046396
EST:     CTAAGATGCCGCTACCCCCGTGGAGAATCTTACCTCGATGTGATACAGAG                         GCTGGAGTCCGTCATCATCGAGCTAGAACGCCAGCGTGCACCAGTGGTTGT
genomic: CTAAGATACCGCTACCCCCGTGGAGAATCTTACCTCGATGTGATACAGAGgtaaaaacta ... taacccttagGCTGGAACCCGTCATCATCGAGCTAGAACGCCAGCGTGCACCAGTGGTTGT
EST: gi|32941092|gb|CF045911.1|CF045911
EST:     CTAAGATACCGCTACCCCCGTGGAGAATCTTACCTCGATGTGATACAGAG                         GCTGGAACCCGTCATCATCGAGCTAGAACGCCAGCGTGCACCAGTGGTTGT
genomic: CTAAGATACCGCTACCCCCGTGGAGAATCTTACCTCGATGTGATACAGAGgtaaaaacta ... taacccttagGCTGGAACCCGTCATCATCGAGCTAGAACGCCAGCGTGCACCAGTGGTTGT
EST: gi|149062837|gb|EE157555.2|EE157555
EST:     CTAAGATACCGCTACCCCCGTGGAGAATCTTACCTCGATGTGATACAGAG                         GCTGGAACCCGTCATCATCGAGCTAGAACGCCAGCGTGCACCAGTGGTTGT
genomic: CTAAGATACCGCTACCCCCGTGGAGAATCTTACCTCGATGTGATACAGAGgtaaaaacta ... taacccttagGCTGGAACCCGTCATCATCGAGCTAGAACGCCAGCGTGCACCAGTGGTTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCACGAAAGAAGGACAAGCTAAGATACCGCTACCCCCGTGGAGAATCTTACCTCGATGTGATACAGAGgtaaaaactatagtttctaattatacagacaaaaaatctccatagtttttttttcctaagaaaagtcgtgctggtttacttggtttttgtctgtcaaactatgacagatttcagttcccgtgtaactataccctaacagctgatgtcataataacccttag

- - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - GGAGAA