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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGTCGTTAAGCTTCAAGAAGAGCTTGACATTGATGTGCTTGTGCATGGCGAGCCTGAGgtcagtgctcttgaatccattctgctggtttttgatgtctaagaagataaacccccataccatgagtgtagtcgcatttaattgactttattggcctatgttctacag

Basic information

species Zea mays
transcript GRMZM2G149751_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149751_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os12g42884.3 (Oryza sativa), 5'ss of exon 10
TGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGTCGTTAAGCTTCAAGAAGAGCTTGACATTGATGTGCTTGTGCATGGCGAGCCTGAGgtcagtgctcttgaatccattctgctggtttttgatgtcta--agaagataaacccccataccatgagtgtagtcgcatttaattgactttattggcctatgttctacag------------------------------------------------
|||||| || ||||||| |||||||||||||||||||| |||||| |||||| | || |||||||||||||||||||||||||| || ||||||||||||||||||   || |      | || || || |||  ||| ||  |  |||     | |    |  |  | | |  |  || | |||   ||||||| |  || |   | ||                                                
TGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGTTGTTAAGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcctcg----tgtactacttgtgtttagtgtttattactagactttacacttggctgtttgagaaaaca-atattattagatttattgactcat-taacaaagtttggtttgttctgcattgaagtaagctaactggcatgtattttacag

upper sequence: GRMZM2G149751_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os12g42876.1 (Oryza sativa), 5'ss of exon 9
TGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGTCGTTAAGCTTCAAGAAGAGCTTGACATTGATGTGCTTGTGCATGGCGAGCCTGAGgtcagtgctcttgaatccattctg------ctggtttttg-------atgtctaagaagataaa----------cccccataccatgagtgtagtc-----------gcatttaattgactttattggcctatgttctacag------
||||||||| ||| ||| |||||||||||||||||||| |||||| |||||| | || |||||||||||||| ||||| ||||| || ||||||||||||||||||   ||||  | |  | ||      || |  ||||        ||| | |||| | |||                 | ||| |    |||            ||||| || | |  | |||||| | | || || |       
TGAGGAGGAGTACATCAGTGCCATCAAGGAGGAAATCAGCAAGGTTGTTAAGATCCAGGAAGAGCTTGACATCGATGTCCTTGTTCACGGCGAGCCTGAGgtcagtatccttgtgtactgtttgtgttttctagactttgcacctggctgtttgagaaaacaaaataaatatatttattgaagcattaacaaagtttggtttgttctgcattgaagtaagctaattggcatgtattttatactttcag
















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|33100706|gb|CF060666.1|CF060666
EST:     AGCTTCAAGAAGAGCTTGACATTGATGTGCTTGTGCATGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTCTCCGGTTTTGCGTTC
genomic: AGCTTCAAGAAGAGCTTGACATTGATGTGCTTGTGCATGGCGAGCCTGAGgtcagtgctc ... tgttctacagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTCTCCGGTTTTGCGTTC
EST: gi|18963575|gb|BM660512.1|BM660512
EST:     AGCTCCAAGAAGAGCTTGACATTGATGTGCTTGTGCATGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTCTCCGGTTTTGCGTTC
genomic: AGCTTCAAGAAGAGCTTGACATTGATGTGCTTGTGCATGGCGAGCCTGAGgtcagtgctc ... tgttctacagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTCTCCGGTTTTGCGTTC
EST: gi|149087939|gb|EE177184.2|EE177184
EST:     AGCTTCAAGAAGAGCTTGACATTGATGTGCTTGTGCATGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTCTCCGGTTTTGCGTTC
genomic: AGCTTCAAGAAGAGCTTGACATTGATGTGCTTGTGCATGGCGAGCCTGAGgtcagtgctc ... tgttctacagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTCTCCGGTTTTGCGTTC
EST: gi|22473206|gb|BU037686.1|BU037686
EST:     AGCTTCAAGAAGAGCTTGACATTGATGTGCTTGTGCATGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTCTCCGGTTTTGCGTTC
genomic: AGCTTCAAGAAGAGCTTGACATTGATGTGCTTGTGCATGGCGAGCCTGAGgtcagtgctc ... tgttctacagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTCTCCGGTTTTGCGTTC
EST: gi|21432208|gb|BQ547698.1|BQ547698
EST:     TGTGCATGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTCTCCGGTTTTGCTGTT
genomic: TGTGCATGGCGAGCCTGAGgtcagtgctc ... tgttctacagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTCTCCGGTTTTGC-GTT
EST: gi|33100968|gb|CF060928.1|CF060928
EST:     AGCTTCAAGAAGAGCTTGACATTGATGTGCTTGTGCATGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTCTCCGGTTTTGCGTTC
genomic: AGCTTCAAGAAGAGCTTGACATTGATGTGCTTGTGCATGGCGAGCCTGAGgtcagtgctc ... tgttctacagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTCTCCGGTTTTGCGTTC
EST: gi|32802578|gb|CD954814.1|CD954814
EST:     AGCTTCAAGAAGAGCTTGTCATTGATGTGCTTGTGCATGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTCTCCGGTTTTGCGTTC
genomic: AGCTTCAAGAAGAGCTTGACATTGATGTGCTTGTGCATGGCGAGCCTGAGgtcagtgctc ... tgttctacagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTCTCCGGTTTTGCGTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGTCGTTAAGCTTCAAGAAGAGCTTGACATTGATGTGCTTGTGCATGGCGAGCCTGAGgtcagtgctcttgaatccattctgctggtttttgatgtctaagaagataaacccccataccatgagtgtagtcgcatttaattgactttattggcctatgttctacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT