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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtgcctgttgatcacttgatcttgccctggctcccatcgtttgattctcttgctattttcatccattaatgattgattgtattttcatcaattctcagGTCAAGAATATCTCGATGGAAATTTTGGACTTCTATGACACCTACAAGATTGATCCTCAAAGAGGGCTCCCAGAGGACAAAATAGCCCCTGTGATGAACA

Basic information

species Oryza sativa
transcript LOC_Os09g32680.4
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g32680.4 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G408242_T03 (Zea mays), 3'ss of exon 8
gtaagtgtgcctgttgatcacttgatcttgccctggct-cccatcgtttgattctcttgctattttcatccattaatgattgattgtattttcatcaattctcagGTCAAGAATATCTCGATGGAAATTTTGGACTTCTATGACACCTACAAGATTGATCCTCAAAGAGGGCTCCCAGAGGACAAAATAGCCCCTGTGATGAACA
                 | |   | |||     ||| | |||  |  || ||||| |   | ||||| ||    ||        |||   ||   |||||| ||||| ||||||||||| |||||||| || ||||||||||||||||||||||||||||||||||| ||  |||| ||||| || |||  ||| ||||||||||
----------------gtaagcagttctattattggtttcccggctatttattctgt-attgttttcttcacccaact-----ctgtgacttg--caattcccagGTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATTGATCCTCAAAGGGGCATCCCTGAGGATAAGATAAGCCCCGTGATGAACA
















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|24468776|gb|CA305725.1|CA305725
EST:     ACAAGGACATAACTCTGTGGTTTGAAGAGCTCCGTGTTGACATGAACATT                         GTCAAGAATATCTCGATGGAAATTTTGGACTTCTATGACACCTACAAGATT
genomic: ACAAGGACATAACTCTGTGGTTTGAAGAGCTCCGTGTTGACATGAACATTgtaagtgtgc ... caattctcagGTCAAGAATATCTCGATGGAAATTTTGGACTTCTATGACACCTACAAGATT
EST: gi|86493556|gb|CI136189.1|CI136189
EST:     ACAAGGACATAACTCTGTGGTTTGAAGAGCTCCGTGTTGACATGAACATT                         GTCAAGAATATCTCGATGGAAATTTTGGACTTCTATGACACCTACAAGATT
genomic: ACAAGGACATAACTCTGTGGTTTGAAGAGCTCCGTGTTGACATGAACATTgtaagtgtgc ... caattctcagGTCAAGAATATCTCGATGGAAATTTTGGACTTCTATGACACCTACAAGATT
EST: gi|29660228|gb|CB656503.1|CB656503
EST:     ACAAGGACATAACTCTGTGGTTTGAAGAGCTCCGTGTTGACATGAACATT                         GTCAAGAATATCTCGATGGAAATTTTGGACTTCTATGACACCTACAAGATT
genomic: ACAAGGACATAACTCTGTGGTTTGAAGAGCTCCGTGTTGACATGAACATTgtaagtgtgc ... caattctcagGTCAAGAATATCTCGATGGAAATTTTGGACTTCTATGACACCTACAAGATT
EST: gi|88833089|gb|CI369979.1|CI369979
EST:     ACAAGGACATAACTCTGTGGTTTGAAGAGCTCCGTGTTGACATGAACATT                         GTCAAGAATATCTCGATGGAAATTTTGGACTTCTATGACACCTACAAGATT
genomic: ACAAGGACATAACTCTGTGGTTTGAAGAGCTCCGTGTTGACATGAACATTgtaagtgtgc ... caattctcagGTCAAGAATATCTCGATGGAAATTTTGGACTTCTATGACACCTACAAGATT
EST: gi|88258947|gb|CI363240.1|CI363240
EST:     ACAAGGACATAACTCTGTGGTTTGAAGAGCTCCGTGTTGACATGAACATT                         GTCAAGAATATCTCGATGGAAATTTTGGACTTCTATGACACCTACAAGATT
genomic: ACAAGGACATAACTCTGTGGTTTGAAGAGCTCCGTGTTGACATGAACATTgtaagtgtgc ... caattctcagGTCAAGAATATCTCGATGGAAATTTTGGACTTCTATGACACCTACAAGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctcttgctattttcatccattaatgattgattgtattttcatcaattctcagGTCAAGAATATCTCGATGGAAATTTTGGACTTCTATGACACCTACAAGATTGATCCTCAAAGAGGGCTCCCAGAGGACAAAATAGCCCCTGTGATGAACA
                                      ttttcatc  CT-rich tract
                     attaatgattgattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgtgcctgttgatcacttgatcttgccctggctcccatcgtttgattctcttgctattttcatccattaatgattgattgtattttcatcaattctcagGTCAAGAATATCTCGATGGAAATTTTGGACTTCTATGACACCTACAAGATTGATCCTCAAAGAGGGCTCCCAGAGGACAAAATAGCCCCTGTGATGAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA