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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGCTGCAGCGGGAGCCCGCCAACGCGCGCGACCGCCTCTACCAGTCCCACCGCGTGCGCCACATGCTCGACCTCGTCATCTCCACCTCCGGCAAGCTCgtaagcaacccccctcctccctccccccttccctcagcctagggttttcccggttgactcatggatgcactagattttgtttcgttctgagctatgttgc...

Basic information

species Oryza sativa
transcript LOC_Os03g50850.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g50850.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G178227_T02 (Zea mays), 5'ss of exon 1
GGAGCTGCAGCGGGAGCCCGCCAACGCGCGCGACCGCCTCTACCAGTCCCACCGCGTGCGCCACATGCTCGACCTCGTCATCTCCACCTCCGGCAAGCTCgtaagcaacccccctcctccctccccccttccctcagcctag--ggttttcccggttgactcatg--gatgcactagattttgtttcgttctgagctatgttgc
 |||||||| ||||||||||| ||| |||| ||||||||||  |||||||||||||| ||||||||||||||||||||| ||||||||||||||||||||||| |   ||   || || | ||      | |   |  | |     ||  |     ||| || |   | |   || | |   |||       |  | ||     
CGAGCTGCAACGGGAGCCCGCTAACCCGCGTGACCGCCTCTTTCAGTCCCACCGCGTCCGCCACATGCTCGACCTCGTCGTCTCCACCTCCGGCAAGCTCgtacgtg-ccattcttctgcttctaaggattcacgactccatccacttcacttcagtgattcgttttgcttagctgggtcaggttcgaacacggtcgatag---

upper sequence: LOC_Os03g50850.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G010515_T01 (Zea mays), 5'ss of exon 1
GGAGCTGCAGCGGGAGCCCGCCAACGCGCGCGACCGCCTCTACCAGTCCCACCGCGTGCGCCACATGCTCGACCTCGTCATCTCCACCTCCGGCAAGCTCgtaagcaacccccctcctccctccccccttccctcagcctagg-gttttcccggttgactcatggatgcactagattttgtttcgttctgagctatgttgc--
 |||||||| |||||||| |  ||| |||||| |||| | |  |||||||||||| | ||||||||||||||||||||| ||||||||||| ||||||||||| |   |     | |||  ||      | |   |  | |     |||   | ||  ||  | | |   |||  ||  |||| |   ||| |||| ||    
CGAGCTGCAACGGGAGCCTGATAACTCGCGCGGCCGCTTTTTTCAGTCCCACCGCATCCGCCACATGCTCGACCTCGTCGTCTCCACCTCCTGCAAGCTCgtacgtc-catttattctctttctgagggttcacgactccatccactttagtgattcgct--ttgtttagctattttaggtttggacatgatctatatttgtc

upper sequence: LOC_Os03g50850.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G087472_T01 (Zea mays), 5'ss of exon 1
GGAGCTGCAGCGGGAGCCCGCCAACGCGCGCGACCGCCTCTACCAGTCCCACCGCGTGCGCCACATGCTCGACCTCGTCATCTCCACCTCCGGCAAGCTCgtaagcaacccccctcctccctccccccttccctcagcctagggttttcccggttgactca--tggatgcactagattttgtttcgttctgagctatgttgc--
 ||||||||  |||||||||  ||| ||||||||||| | |  |||||||||||||| ||||||||||||||||||||| ||||||||||| ||||||||||| |   |     | |||  ||      | |   |  | |   |   ||    ||| ||   | | |   |||  ||  |||| |    || |||| ||    
CGAGCTGCAATGGGAGCCCGATAACCCGCGCGACCGCTTTTTTCAGTCCCACCGCGTCCGCCACATGCTCGACCTCGTCGTCTCCACCTCCTGCAAGCTCgtacgtc-catttattctctttctgagggttcacgactcca---tccaccttagtgattcgctttgtttagctattttaggtttggacacgatctatatttgtc

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|88415070|gb|CI583893.1|CI583893
EST:     ACCGCGTGCGCCACATGCTCGACCTCGTCATCTCCACCTCCGGCAAGCTC                         GTGGAAATCTACGAGGACAAGGATAATGCTAGGAAGGATGAGATCTCCAAC
genomic: ACCGCGTGCGCCACATGCTCGACCTCGTCATCTCCACCTCCGGCAAGCTCgtaagcaacc ... ttttacatagGTGGAAATCTACGAGGACAAGGATAATGCTAGGAAGGATGAGATCTCCAAC
EST: gi|86900664|gb|CI302081.1|CI302081
EST:     ACCGCGTGCGCCACATGCTCGACCTCGTCATCTCCACCTCCGGCAAGCTC                         GTGGAAATCTACGAGGACAAGGATAATGCTAGGAAGGATGAGATCTCCAAC
genomic: ACCGCGTGCGCCACATGCTCGACCTCGTCATCTCCACCTCCGGCAAGCTCgtaagcaacc ... ttttacatagGTGGAAATCTACGAGGACAAGGATAATGCTAGGAAGGATGAGATCTCCAAC
EST: gi|88350672|gb|CI617527.1|CI617527
EST:     ACCGCGTGCGCCACATGCTCGACCTCGTCATCTCCACCTCCGGCAAGCTC                         GTGGAAATCTACGAGGACAAGGATAATGCTAGGAAGGATGAGATCTCCAAC
genomic: ACCGCGTGCGCCACATGCTCGACCTCGTCATCTCCACCTCCGGCAAGCTCgtaagcaacc ... ttttacatagGTGGAAATCTACGAGGACAAGGATAATGCTAGGAAGGATGAGATCTCCAAC
EST: gi|58676557|gb|CK065244.1|CK065244
EST:     ACCGCGTGCGCCACATGCTCGACCTCGTCATCTCCACCTCCGGCAAGCTC                         GTGGAAATCTACGAGGACAAGGATAATGCTAGGAAGGATGAGATCTCCAAC
genomic: ACCGCGTGCGCCACATGCTCGACCTCGTCATCTCCACCTCCGGCAAGCTCgtaagcaacc ... ttttacatagGTGGAAATCTACGAGGACAAGGATAATGCTAGGAAGGATGAGATCTCCAAC
EST: gi|29664558|gb|CB660833.1|CB660833
EST:     ACCGCGTGCGCCACATGCTCGACCTCGTCATCTCCACCTCCGGCAAGCTC                         GTGGAAATCTACGAGGACAAGGATAATGCTAGGAAGGATGAGATCTCCAAC
genomic: ACCGCGTGCGCCACATGCTCGACCTCGTCATCTCCACCTCCGGCAAGCTCgtaagcaacc ... ttttacatagGTGGAAATCTACGAGGACAAGGATAATGCTAGGAAGGATGAGATCTCCAAC
EST: gi|88393433|gb|CI618321.1|CI618321
EST:     ACCGCGTGCGCCACATGCTCGACCTCGTCATCTCCACCTCCGGCAAGCTC                         GTGGAAATCTACGAGGACAAGGATAATGCTAGGAAGGATGAGATCTCCAAC
genomic: ACCGCGTGCGCCACATGCTCGACCTCGTCATCTCCACCTCCGGCAAGCTCgtaagcaacc ... ttttacatagGTGGAAATCTACGAGGACAAGGATAATGCTAGGAAGGATGAGATCTCCAAC
EST: gi|29664554|gb|CB660829.1|CB660829
EST:     ACCGCGTGCGCCACATGCTCGACCTCGTCATCTCCACCTCCGGCAAGCTC                         GTGGAAATCTACGAGGACAAGGATAATGCTAGGAAGGATGAGATCTCCAAC
genomic: ACCGCGTGCGCCACATGCTCGACCTCGTCATCTCCACCTCCGGCAAGCTCgtaagcaacc ... ttttacatagGTGGAAATCTACGAGGACAAGGATAATGCTAGGAAGGATGAGATCTCCAAC
EST: gi|88719454|gb|CI742964.1|CI742964
EST:     ACCGCGTGCGCCACATGCTCGACCTCGTCATCTCCACCTCCGGCAAGCTC                         GTGGAAATCTACGAGGACAAGGATAATGCTAGGAAGGATGAGATCTCCAAC
genomic: ACCGCGTGCGCCACATGCTCGACCTCGTCATCTCCACCTCCGGCAAGCTCgtaagcaacc ... ttttacatagGTGGAAATCTACGAGGACAAGGATAATGCTAGGAAGGATGAGATCTCCAAC
EST: gi|88745045|gb|CI768405.1|CI768405
EST:     ACCGCGTGCGCCACATGCTCGACCTCGTCATCTCCACCTCCGGCAAGCTC                         GTGGAAATCTACGAGGACAAGGATAATGCTAGGAAGGATGAGATCTCCAAC
genomic: ACCGCGTGCGCCACATGCTCGACCTCGTCATCTCCACCTCCGGCAAGCTCgtaagcaacc ... ttttacatagGTGGAAATCTACGAGGACAAGGATAATGCTAGGAAGGATGAGATCTCCAAC
EST: gi|88735755|gb|CI759263.1|CI759263
EST:     ACCGCGTGCGCCACATGCTCGACCTCGTCATCTCCACCTCCGGCAAGCTC                         GTGGAAATCTACGAGGACAAGGATAATGCTAGGAAGGATGAGATCTCCAAC
genomic: ACCGCGTGCGCCACATGCTCGACCTCGTCATCTCCACCTCCGGCAAGCTCgtaagcaacc ... ttttacatagGTGGAAATCTACGAGGACAAGGATAATGCTAGGAAGGATGAGATCTCCAAC
EST: gi|88739396|gb|CI762904.1|CI762904
EST:     ACCGNGTGCGCCACATGCTCGACCTCGTCATCTCCACCTCCGGCAAGCTC                         GTGGAAATCTACGAGGACAAGGATAATGCTAGGAAGGATGAGATCTCCAAC
genomic: ACCGCGTGCGCCACATGCTCGACCTCGTCATCTCCACCTCCGGCAAGCTCgtaagcaacc ... ttttacatagGTGGAAATCTACGAGGACAAGGATAATGCTAGGAAGGATGAGATCTCCAAC
EST: gi|58659954|gb|CK048634.1|CK048634
EST:     ACCGCGTGCGCCACATGCTCGACCTCGTCATCTCCACCTCCGGCAAGCTC                         GTGGAAATCTACGAGGACAAGGATAATGCTAGGAAGGATGAGATCTCCAAC
genomic: ACCGCGTGCGCCACATGCTCGACCTCGTCATCTCCACCTCCGGCAAGCTCgtaagcaacc ... ttttacatagGTGGAAATCTACGAGGACAAGGATAATGCTAGGAAGGATGAGATCTCCAAC
EST: gi|88399904|gb|CI585823.1|CI585823
EST:     ACCGCGTGCGCCACATGCTCGACCTCGTCATCTCCACCTCCGGCAAGCTC                         GTGGAAATCTACGAGGACAAGGATAATGCTAGGAAGGATGAGATCTCCAAC
genomic: ACCGCGTGCGCCACATGCTCGACCTCGTCATCTCCACCTCCGGCAAGCTCgtaagcaacc ... ttttacatagGTGGAAATCTACGAGGACAAGGATAATGCTAGGAAGGATGAGATCTCCAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGCTGCAGCGGGAGCCCGCCAACGCGCGCGACCGCCTCTACCAGTCCCACCGCGTGCGCCACATGCTCGACCTCGTCATCTCCACCTCCGGCAAGCTCgtaagcaacccccctcctccctccccccttccctcagcctagggttttcccggttgactcatggatgcactagattttgtttcgttctgagctatgttgc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccttcc