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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccacctccaggctttcatcccaattaaacttcgagctgatctgacacccgttttgttgtgtggcgatgactggcagCCCGTATCAAGGTGCACGAGCTCCGGGGGAAGAGCAAGACGGACCTGCAGGCGCAGCTCAAGGAGCTGAAGTCTGAGCTCTCCCTCCTCCGCGTAGCCAA

Basic information

species Zea mays
transcript GRMZM2G043279_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G043279_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g30730.1 (Oryza sativa), 3'ss of exon 1
gtaagccacctccaggctt-------------tcatcccaattaaacttcgagctgatctgacacccgttttg-ttgtgtggcg-atgactggcagCCCGTATCAAGGTGCACGAGCTCCGGGGGAAGAGCAAGACGGACCTGCAGGCGCAGCTCAAGGAGCTGAAGTCTGAGCTCTCCCTCCTCCGCGTAGCCAA
||||||| || ||     |             ||||| | ||||   || |  || |       || | | ||   || |   | |  | || ||||||| |||||||||||||||||||||||||||| |||| |||| |||||||| ||||||||||| || ||| | |||||||||||||||||||| |||||
gtaagcctccccctcctctccctctctccggttcatctcgattagttttagctctcaatcccttccggatctgaccgtttcttggacaaatgtcagCCCGGATCAAGGTGCACGAGCTCCGGGGGAAGAACAAGGCGGAGCTGCAGGCCCAGCTCAAGGACCTCAAGGCGGAGCTCTCCCTCCTCCGCGTCGCCAA

upper sequence: GRMZM2G043279_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g30050.1 (Oryza sativa), 3'ss of exon 1
gtaagccacctccaggctttcatcccaattaaacttcgagctgatctgacacccgttttgttgtgtggcgatgactggcagCCCGTATCAAGGTGCACGAGCTCCGGGGGAAGAGCAAGACGGACCTGCAGGCGCAGCTCAAGGAGCTGAAGTCTGAGCTCTCCCTCCTCCGCGTAGCCAA
|||||| ||  |    | ||| || |       | ||  |||   |||   |   | |    ||| |    ||    |||||||| ||||||||  ||||||| |||||||||| |||| |||| |||||||| ||||||||||| || ||| | |||||||||||||||||||| |||||
gtaagctacaacattccgttcttctct------cctcccgctcgcctg---cggatctaaccgtgcgtgtgtggt--gcagCCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGGCCCAGCTCAAGGACCTCAAGGCGGAGCTCTCCCTCCTCCGCGTCGCCAA
















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|74243811|gb|DT651725.1|DT651725
EST:     CTGCCACCGCCGACGCCGCGCCGCCGCAGCAATTGTCACCGTCGCTATGG                         CCCGTATCAAGGTGCACGAGCTCCGGGGGAAGAGCAAGACGGACCTGCAGG
genomic: CTGCCACCGCCGACGCCGCGCCGCCGCAGCAATTGTCACCGTCGCTATGGgtaagccacc ... tgactggcagCCCGTATCAAGGTGCACGAGCTCCGGGGGAAGAGCAAGACGGACCTGCAGG
EST: gi|37425015|gb|CF650243.1|CF650243
EST:     CTGCCACCGCCGACGCCGCGCCGCCGCAGCAATTGTCACCGTCGCTATGG                         CCCGTATCAAGGTGCACGAGCTCCGGGGGAAGAGCAA
genomic: CTGCCACCGCCGACGCCGCGCCGCCGCAGCAATTGTCACCGTCGCTATGGgtaagccacc ... tgactggcagCCCGTATCAAGGTGCACGAGCTCCGGGGGAAGAGCAA
EST: gi|211186249|gb|FL001313.1|FL001313
EST:     CTGCCACCGCCGACGCCGCGCCGCCGCAGCAATTGTCACCGTCGCTATGG                         CCCGTATCAAGGTGCACGAGCTCCGGGGGAAGAGCAAGACGGACCTGCAGG
genomic: CTGCCACCGCCGACGCCGCGCCGCCGCAGCAATTGTCACCGTCGCTATGGgtaagccacc ... tgactggcagCCCGTATCAAGGTGCACGAGCTCCGGGGGAAGAGCAAGACGGACCTGCAGG
EST: gi|211188653|gb|FL001327.1|FL001327
EST:     CTGCCACCGCCGACGCCGCGCCGCCGCAGCAATTGTCACCGTCGCTATGG                         CCCGTATCAAGGTGCACGAGCTCCGGGGGAAGAGCAAGACGGACCTGCAGG
genomic: CTGCCACCGCCGACGCCGCGCCGCCGCAGCAATTGTCACCGTCGCTATGGgtaagccacc ... tgactggcagCCCGTATCAAGGTGCACGAGCTCCGGGGGAAGAGCAAGACGGACCTGCAGG
EST: gi|211186247|gb|FL001311.1|FL001311
EST:     CTGCCACCGCMGACGCCGCGCCGCCGCAGCAATTGTCACCGTCGCTATGG                         CCCGTATCAAGGTGCACGAGCTCCGGGGGAAGAGCAAGACGGACCTGCAGG
genomic: CTGCCACCGCCGACGCCGCGCCGCCGCAGCAATTGTCACCGTCGCTATGGgtaagccacc ... tgactggcagCCCGTATCAAGGTGCACGAGCTCCGGGGGAAGAGCAAGACGGACCTGCAGG
EST: gi|29130231|gb|CB380935.1|CB380935
EST:     CTGCCACCGCCGACGCCGCGCCGCCGCAGCAATTGTCACCGTCGCTATGG                         CCCGTATCAAGGTGCACGAGCTCCGGGGGAAGAGCAAGACGGACCTGCAGG
genomic: CTGCCACCGCCGACGCCGCGCCGCCGCAGCAATTGTCACCGTCGCTATGGgtaagccacc ... tgactggcagCCCGTATCAAGGTGCACGAGCTCCGGGGGAAGAGCAAGACGGACCTGCAGG
EST: gi|211188656|gb|FL001330.1|FL001330
EST:     CTGCCACCGCCGACGCCGCGCCGCCGCAGCAATTGTCACCGTCGCTATGG                         CCCGTATCAAGGTGCACGAGCTCCGGGGGAAGAGCAAGACGGACCTGCAGG
genomic: CTGCCACCGCCGACGCCGCGCCGCCGCAGCAATTGTCACCGTCGCTATGGgtaagccacc ... tgactggcagCCCGTATCAAGGTGCACGAGCTCCGGGGGAAGAGCAAGACGGACCTGCAGG
EST: gi|71768079|gb|DR966016.1|DR966016
EST:     CTGCCACCGCCGACGCCGCGCCGCCGCAGCAATTGTCACCGTCGCTATGG                         CCCGTATCAAGGTGCACGAGCTCCGGGGGAAGAGCAAGACGGACCTGCAGG
genomic: CTGCCACCGCCGACGCCGCGCCGCCGCAGCAATTGTCACCGTCGCTATGGgtaagccacc ... tgactggcagCCCGTATCAAGGTGCACGAGCTCCGGGGGAAGAGCAAGACGGACCTGCAGG
EST: gi|211330349|gb|FL295562.1|FL295562
EST:     CTGCCACCGCCGACGCCGCGCCGCCGCAGCAACTGTCACCGTCGCTATGG                         CCCGTATCAAGGTGCACGAGCTCCGGGGGAAGAGCAAGACGGACCTGCAGG
genomic: CTGCCACCGCCGACGCCGCGCCGCCGCAGCAATTGTCACCGTCGCTATGGgtaagccacc ... tgactggcagCCCGTATCAAGGTGCACGAGCTCCGGGGGAAGAGCAAGACGGACCTGCAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattaaacttcgagctgatctgacacccgttttgttgtgtggcgatgactggcagCCCGTATCAAGGTGCACGAGCTCCGGGGGAAGAGCAAGACGGACCTGCAGGCGCAGCTCAAGGAGCTGAAGTCTGAGCTCTCCCTCCTCCGCGTAGCCAA
                 atctgac  putative branch site (score: 3)
                             ttttgtt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagccacctccaggctttcatcccaattaaacttcgagctgatctgacacccgttttgttgtgtggcgatgactggcagCCCGTATCAAGGTGCACGAGCTCCGGGGGAAGAGCAAGACGGACCTGCAGGCGCAGCTCAAGGAGCTGAAGTCTGAGCTCTCCCTCCTCCGCGTAGCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC