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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaaaaatacatccttttgttgttccacaacaaactgtcatggacatcctttttttaattgatactattgtgttctagACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACTCACTGGGGTGATGCAGGGTCCAATAATCCAAACCCATCAACTCATTCAA

Basic information

species Oryza sativa
transcript LOC_Os01g60040.2
intron # 47
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 47
lower sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 30
gtaaaaaaaatacatccttttgttgttccacaacaaactgtc-atggacatcctttttttaattgatact----attgt------gttctagACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACTCACTGGGGTGATGCAGGGTCCAATAATCCAAACCCATCAACTCATTCAA
||| || |   | | ||  | ||| ||  ||||||  ||  |    | | | ||||||||  ||| ||      |||||      ||| ||||||||||| || ||||||||| |||| ||||| ||| ||||||| |||||||||||||||||||| |  || || |||||||| ||||| ||||| ||| 
gtagaacatgcaaaaccact-gttatta-acaacattcttcctgcagcctttctttttttctttggtaaccaacattgttcggtcgttgtagACCCTTGCTGCTGCTAGAATGTTGACGCCATCGGGACCTATGGGTCAAACTCACTGGGGTGATGCTGCTTCAAACAATCCAAATCCATCTACTCACTCAG

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 47
lower sequence: GRMZM2G068755_T01 (Zea mays), 3'ss of exon 48
--------------------------------------------gtaaaaaaaatacatccttttgttgttccac-------aacaaactgtcatggacatcctttttttaattgatact----attgt------gttctagACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACTCACTGGGGTGATGCAGGGTCCAATAATCCAAACCCATCAACTCATTCAA
                                            |     | | |     |  |||     ||||       |||||  |     | | | |||||||||  ||| ||      |||||      ||| ||||||||||| || ||||||||| |||| ||||| ||  ||||||| |||||||||||||||||||| |  || || |||||||| ||||| ||||| ||| 
gtagaacttgcaaaaccactgttctgttgttgtagACCCTTGCAGCCGCTAGATTGTTGACCCTTGCAAAACCACCATTAGCAACAAGATTCTTCGCAAAGCCTTTTTTTTCTTGGTAACCAACATTGTTCGGTTGTTGTAGACCCTTGCAGCCGCTAGAATGTTGACGCCATCGGGGCCTATGGGTCAAACTCACTGGGGTGATGCTGCATCGAACAATCCAAATCCATCTACTCACTCAG
















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|58658439|gb|CK047119.1|CK047119
EST:     ATGCTGAACCTCAGCCAATCATTNTGGCATACATGGATCTTAATCTTCAG                         ACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACT
genomic: ATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAGgtaaaaaaaa ... tgtgttctagACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACT
EST: gi|58601380|gb|CK011908.1|CK011908
EST:     ATGCTGAACCTCAGCCAATCATTTNGGCATACATTGATCTTAATCTTCAG                         ACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACT
genomic: ATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAGgtaaaaaaaa ... tgtgttctagACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACT
EST: gi|58600986|gb|CK011514.1|CK011514
EST:     ATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAG                         ACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAAGT
genomic: ATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAGgtaaaaaaaa ... tgtgttctagACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACT
EST: gi|58597274|gb|CK007802.1|CK007802
EST:     ATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAG                         ACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACT
genomic: ATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAGgtaaaaaaaa ... tgtgttctagACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACT
EST: gi|29680245|gb|CB676520.1|CB676520
EST:     ATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAG                         ACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACT
genomic: ATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAGgtaaaaaaaa ... tgtgttctagACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACT
EST: gi|218497579|gb|FG955134.1|FG955134
EST:     ATGCTGAACCTCAGCCAATCA-TTTGGCATACA-TGATCTT-ATCTTCAG                         ACCC-TGCGGCAGCTA-AATGCTGACTCCATCTGGAACTATGGGCCAAACT
genomic: ATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAGgtaaaaaaaa ... tgtgttctagACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACT
EST: gi|88344329|gb|CI655723.1|CI655723
EST:     ATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAG                         ACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAANTATGGGCCAAACT
genomic: ATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAGgtaaaaaaaa ... tgtgttctagACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACT
EST: gi|58677253|gb|CK065940.1|CK065940
EST:     ATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAG                         ACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACT
genomic: ATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAGgtaaaaaaaa ... tgtgttctagACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACT
EST: gi|58667817|gb|CK056503.1|CK056503
EST:     ATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAG                         ACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACT
genomic: ATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAGgtaaaaaaaa ... tgtgttctagACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACT
EST: gi|58690696|gb|CK079383.1|CK079383
EST:     ATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAG                         ACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACT
genomic: ATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAGgtaaaaaaaa ... tgtgttctagACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccacaacaaactgtcatggacatcctttttttaattgatactattgtgttctagACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACTCACTGGGGTGATGCAGGGTCCAATAATCCAAACCCATCAACTCATTCAA
                          tttttttaattgatac  TA-rich tract