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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGTgtaagatctcttacaaaactatgcttcatccccattttccgcacttgtctcatgcaaaaacaatgtatgaagtttctgtcggttttcaattggcag

Basic information

species Oryza sativa
transcript LOC_Os02g10720.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g10720.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G497531_T01 (Zea mays), 5'ss of exon 4
TTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGTgtaagatctcttacaaaactatgcttcatccccattttccgcacttgtctcatgcaaaaacaatgtatgaagtttctgtcggttttcaattggcag
||| ||||||||||| |||||||| || || ||| | ||||||||||||||| ||||||||||||||||||||| ||||  ||| |||  |  ||||  |   ||   ||  ||  || ||   | |||||| ||  | ||||  | | || ||   || |||
TTGTAATGCTACATACGAGAGCCTGCTCGGGAGCTCGAAACCATTTCCACAACCGATCCCTCTTGGTgtaagatatcttgaaaagctacacgacatcttc-catttgacatgtgcgtcctgtttagacaatgcattgattttcc-tggcttgtccgctgtcag

upper sequence: LOC_Os02g10720.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G180967_T02 (Zea mays), 5'ss of exon 4
TTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGTgtaagatctcttacaaaactatgcttcatccccattttccgcacttgtctcatgcaa-aaacaatgtatgaagtttctgtcggttttcaattggcag
||| ||||||||||| || ||||| || |||||| | || || || |||||| ||| ||||||||||||||||| ||||   || |||    |||||  || | |   ||  ||  || |     | ||| || ||  |  |||  | |||| ||   |  |||
TTGTAATGCTACATACGAAAGCCTGCTCGGAAGCTCGAAGCCGTTCCCACAACCGACCCCTCTTGGTgtaagatatcttgagaagctacatgtcatcttcaatctgaacatatgcgtcctattttagacagtgcattga-cttcccttggttgtctgctctcag
















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|3766768|gb|AU030878.1|AU030878
EST:     AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGT                         GAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
genomic: AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGTgtaagatctc ... caattggcagGAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
EST: gi|12622897|gb|AU173110.1|AU173110
EST:     AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGT                         GAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
genomic: AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGTgtaagatctc ... caattggcagGAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
EST: gi|14192160|gb|AU184371.1|AU184371
EST:     AGAGCCTTNTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGT                         GAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
genomic: AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGTgtaagatctc ... caattggcagGAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
EST: gi|88579610|gb|CI688618.1|CI688618
EST:     GGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGT                         GAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
genomic: GGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGTgtaagatctc ... caattggcagGAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
EST: gi|86512046|gb|CI154679.1|CI154679
EST:     AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGT                         GAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
genomic: AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGTgtaagatctc ... caattggcagGAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
EST: gi|29689717|gb|CB685992.1|CB685992
EST:     AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGT                         GAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
genomic: AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGTgtaagatctc ... caattggcagGAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
EST: gi|8324561|gb|AU091706.1|AU091706
EST:     AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGT                         GAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
genomic: AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGTgtaagatctc ... caattggcagGAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
EST: gi|88585027|gb|CI702627.1|CI702627
EST:     GGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGT                         GAAATGGTACATTTCCTCGTGGACGACTGGGAGCAGGAAGGCCTATATGAT
genomic: GGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGTgtaagatctc ... caattggcagGAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
EST: gi|14192107|gb|AU184318.1|AU184318
EST:     AGAGCCTTNTAGGAAGCACAAAACCATTTCCNCAAGCGATCCCTCTTGGT                         GAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
genomic: AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGTgtaagatctc ... caattggcagGAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
EST: gi|88975725|gb|CI023976.1|CI023976
EST:     AGAGCCTTCTAGGAAGCACGAAACCATTTCCACAAGCGATCCCTCTTGGT                         GAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
genomic: AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGTgtaagatctc ... caattggcagGAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
EST: gi|3766735|gb|AU030845.1|AU030845
EST:     AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGT                         GAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
genomic: AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGTgtaagatctc ... caattggcagGAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
EST: gi|88282037|gb|CI403433.1|CI403433
EST:     AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGT                         GAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
genomic: AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGTgtaagatctc ... caattggcagGAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
EST: gi|32947923|gb|BP184495.1|BP184495
EST:     AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGT                         GAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
genomic: AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGTgtaagatctc ... caattggcagGAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
EST: gi|88199489|gb|CI199339.1|CI199339
EST:     AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGT                         GAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
genomic: AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGTgtaagatctc ... caattggcagGAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
EST: gi|88514176|gb|CI441682.1|CI441682
EST:     AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGT                         GAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
genomic: AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGTgtaagatctc ... caattggcagGAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
EST: gi|86853556|gb|CI329014.1|CI329014
EST:     AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGT                         GAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
genomic: AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGTgtaagatctc ... caattggcagGAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
EST: gi|4714360|gb|AU058327.1|AU058327
EST:     AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGT                         GAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
genomic: AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGTgtaagatctc ... caattggcagGAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
EST: gi|88984466|gb|CI015018.1|CI015018
EST:     AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGT                         GAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
genomic: AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGTgtaagatctc ... caattggcagGAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
EST: gi|86882289|gb|CI325747.1|CI325747
EST:     AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGT                         GAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
genomic: AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGTgtaagatctc ... caattggcagGAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
EST: gi|88297617|gb|CI550680.1|CI550680
EST:     AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGT                         GAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
genomic: AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGTgtaagatctc ... caattggcagGAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
EST: gi|86531003|gb|CI171209.1|CI171209
EST:     AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGT                         GAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
genomic: AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGTgtaagatctc ... caattggcagGAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
EST: gi|88297057|gb|CI542769.1|CI542769
EST:     AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGT                         GAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
genomic: AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGTgtaagatctc ... caattggcagGAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
EST: gi|88317636|gb|CI672220.1|CI672220
EST:     GGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGT                         GAAATGGTAGATTTCCTCGTGGACGACTGGGAGCAGGAAGGCCTATATGAT
genomic: GGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGTgtaagatctc ... caattggcagGAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
EST: gi|44678412|gb|CR291846.1|CR291846
EST:     AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGT                         GAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
genomic: AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGTgtaagatctc ... caattggcagGAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
EST: gi|88966152|gb|CI013028.1|CI013028
EST:     AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGT                         GAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT
genomic: AGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGTgtaagatctc ... caattggcagGAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGAT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 31 (upstream exon), 74 (downstream exon)
Score: 9

TTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGTgtaagatctc ... caattggcagGAAATGGTAGATTTCCTCGTGGACGGCTGGGAGCAGGAAGGCCTATATGATTAGTGGGTTAAATGAGTGATGAAGGGTGTTGTTTGTGGGGTCAAATTAT




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