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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtacctgtcacaatcagtttatgtatgctcacttgtgttttgtttgttgtggtaaatgctgtggtagtctaggcaccaggggaatggattaaggtaccatattcttggttgtatagcaactcaataattttgagcatacttattttgcagAGTCAAGCAATCAAGGTATGCAATAGAGTATGCCAATGGATCAGGGACCTGGAAAACGAAATTTTCGTATACGGAGAAAGCACCCTTTCCTGGTGATATA

Basic information

species Oryza sativa
transcript LOC_Os01g74460.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g74460.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G179732_T03 (Zea mays), 3'ss of exon 5
gtttgtacctgtcacaatcagtttatgtatgctcacttgtgttttgtttgttgtg-gtaaatgctgtggtagtctaggcaccaggggaatggattaaggtaccatattcttggttgtatagcaactcaa---taattttgagcatacttattttgcagAGTCAAGCAATCAAGGTATGCAATAGAGTATGCCAATGGATCAGGGACCTGGAAAACGAAATTTTCGTATACGGAGAAAGCACCCTTTCCTGGTGATATA
||||| ||||| || |||| | ||||| || || | || | | | || | | | | || | | | || || |||||||| | | ||| || || ||||| ||| ||||| ||||||||||||| | ||||||||||||||||||||| | ||||| | ||||| || || ||||| || ||||||||||||||||||||||||
----------------gtcagtgcatgtacatgcagttgt-tgatgttttttttgtatggatcatatcacaacacagccgc--agtcatctttgtataatgcagttatcatgattgtatagggataatagtctaacttggattgtacttgttt-gcagACTCAAGCAATCAAGATGTGCAATAGAGTATGCCAATGGGTGAGGGATTTAGAAAATGAGATATTCGTGTATGGAGAAAGCACCCTTTCCTGGTGA----

upper sequence: LOC_Os01g74460.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G179732_T01 (Zea mays), 3'ss of exon 6
gtttgtacctgtcacaatcagtttatgtatgctcacttgtgttttgtttgttgtg-gtaaatgctgtggtagtctaggcaccaggggaatggattaaggtaccatattcttggttgtatagcaactcaa---taattttgagcatacttattttgcagAGTCAAGCAATCAAGGTATGCAATAGAGTATGCCAATGGATCAGGGACCTGGAAAACGAAATTTTCGTATACGGAGAAAGCACCCTTTCCTGGTGATATA
||||| ||||| || |||| | ||||| || || | || | | | || | | | | || | | | || || |||||||| | | ||| || || ||||| ||| ||||| ||||||||||||| | ||||||||||||||||||||| | ||||| | ||||| || || ||||| || |||||||||||||||||||||||||||
----------------gtcagtgcatgtacatgcagttgt-tgatgttttttttgtatggatcatatcacaacacagccgc--agtcatctttgtataatgcagttatcatgattgtatagggataatagtctaacttggattgtacttgttt-gcagACTCAAGCAATCAAGATGTGCAATAGAGTATGCCAATGGGTGAGGGATTTAGAAAATGAGATATTCGTGTATGGAGAAAGCACCCTTTCCTGGTGATATG

upper sequence: LOC_Os01g74460.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G179732_T02 (Zea mays), 3'ss of exon 6
gtttgtacctgtcacaatcagtttatgtatgctcacttgtgttttgtttgttgtg-gtaaatgctgtggtagtctaggcaccaggggaatggattaaggtaccatattcttggttgtatagcaactcaa---taattttgagcatacttattttgcagAGTCAAGCAATCAAGGTATGCAATAGAGTATGCCAATGGATCAGGGACCTGGAAAACGAAATTTTCGTATACGGAGAAAGCACCCTTTCCTGGTGATATA
||||| ||||| || |||| | ||||| || || | || | | | || | | | | || | | | || || |||||||| | | ||| || || ||||| ||| ||||| ||||||||||||| | ||||||||||||||||||||| | ||||| | ||||| || || ||||| || ||||||||||||||||||||
----------------gtcagtgcatgtacatgcagttgt-tgatgttttttttgtatggatcatatcacaacacagccgc--agtcatctttgtataatgcagttatcatgattgtatagggataatagtctaacttggattgtacttgttt-gcagACTCAAGCAATCAAGATGTGCAATAGAGTATGCCAATGGGTGAGGGATTTAGAAAATGAGATATTCGTGTATGGAGAAAGCACCCTTTCCTG--------

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|29665848|gb|CB662123.1|CB662123
EST:     TAACCCAGGATTTTGAGTTGTACGCCGCTTTTAATCCACTGGCTGACAAG                         AGTCAAGCAATCAAGGTATGCAATAGAGTATGCCAATGGATCAGGGACCTG
genomic: TAACCCAGGATTTTGAGTTGTACGCCGCTTTTAATCCACTGGCTGACAAGgtttgtacct ... tattttgcagAGTCAAGCAATCAAGGTATGCAATAGAGTATGCCAATGGATCAGGGACCTG
EST: gi|88503388|gb|CI430894.1|CI430894
EST:     TACGCCGCTTTTAATCCACTGGCTGACAAG                         AGTCAAGCAATCAAGGTATGCAATAGAGTATGCCAATGGATCAGGGACCTG
genomic: TACGCCGCTTTTAATCCACTGGCTGACAAGgtttgtacct ... tattttgcagAGTCAAGCAATCAAGGTATGCAATAGAGTATGCCAATGGATCAGGGACCTG
EST: gi|86486002|gb|CI128635.1|CI128635
EST:     TAACCCAGGATTTTGAGTTGTACGCCGCTCTTAATCCGCTGGCTGACAAG                         AGTCAAGCCATCAAGGTATNCAATAGAGTATGCCAATGGATCAGGGACCTG
genomic: TAACCCAGGATTTTGAGTTGTACGCCGCTTTTAATCCACTGGCTGACAAGgtttgtacct ... tattttgcagAGTCAAGCAATCAAGGTATGCAATAGAGTATGCCAATGGATCAGGGACCTG
EST: gi|87029236|gb|CI276504.1|CI276504
EST:     TAACCCAGGATTTTGAGTTGTACGCCGCTTTTAATCCACTGGCTGACAAG                         AGTCAAGCAATCAAGGTATGCAATAGAGTATGCCAATGGATCAGGGACCTG
genomic: TAACCCAGGATTTTGAGTTGTACGCCGCTTTTAATCCACTGGCTGACAAGgtttgtacct ... tattttgcagAGTCAAGCAATCAAGGTATGCAATAGAGTATGCCAATGGATCAGGGACCTG
EST: gi|88997559|gb|CI390225.1|CI390225
EST:     TAACCCAGGATTTTGAGTTGTACGCCGCTTTTAATCCACTGGCTGACAAG                         AGTCAAGCAATCAAGGTATGCAATAGAGTATGCCAATGGATCAGGGACCTG
genomic: TAACCCAGGATTTTGAGTTGTACGCCGCTTTTAATCCACTGGCTGACAAGgtttgtacct ... tattttgcagAGTCAAGCAATCAAGGTATGCAATAGAGTATGCCAATGGATCAGGGACCTG
EST: gi|86861206|gb|CI326645.1|CI326645
EST:     TAACCCAGGATTTTGAGTTGTACCCCGCTTTTAATCCACTGGCTGACAAG                         AGTCAAGCAATCAAGGTATGCAATAGAGTATGCCAATGGATCAGGGACCTG
genomic: TAACCCAGGATTTTGAGTTGTACGCCGCTTTTAATCCACTGGCTGACAAGgtttgtacct ... tattttgcagAGTCAAGCAATCAAGGTATGCAATAGAGTATGCCAATGGATCAGGGACCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accatattcttggttgtatagcaactcaataattttgagcatacttattttgcagAGTCAAGCAATCAAGGTATGCAATAGAGTATGCCAATGGATCAGGGACCTGGAAAACGAAATTTTCGTATACGGAGAAAGCACCCTTTCCTGGTGATATA
                                           cttatttt  CT-rich tract
 aactcaataatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtacctgtcacaatcagtttatgtatgctcacttgtgttttgtttgttgtggtaaatgctgtggtagtctaggcaccaggggaatggattaaggtaccatattcttggttgtatagcaactcaataattttgagcatacttattttgcagAGTCAAGCAATCAAGGTATGCAATAGAGTATGCCAATGGATCAGGGACCTGGAAAACGAAATTTTCGTATACGGAGAAAGCACCCTTTCCTGGTGATATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA