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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTCATCCCCGACGGCATCGACAAGAACGGCAAGCCCCACAAGCTCCGCCTCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagctagtagtgtttttcttgctccatcgatctcaaccacaagacatgagctaactaacatcgacatcgtccctgatcgatcgatcag

Basic information

species Oryza sativa
transcript LOC_Os02g01340.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g01340.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G059083_T02 (Zea mays), 5'ss of exon 2
CGTCATCCCCGACGGCATCGACAAGAACGGCAAGCCCCACAAGCTCCGCCTCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaa-ctagctagtagtgtttttcttgctccatcgatctcaaccacaagacatgagctaactaacatcgacatcgtccctgatcgatcgatcag
||||||| | || |||   ||||||||||||||||| ||||||||| | |||||||||||||||||||||||| |||| || |||| ||||||||||||||| | | |   | || |       ||  |  ||  ||   |   |     ||  |   |  || |   | || | |   |    |  |      
CGTCATCGCGGATGGCGAGGACAAGAACGGCAAGCCGCACAAGCTCAGGCTCTACTCCATCGCCAGCAGCGCCCTCGGAGATTTCGGCGACTCCAAGACGgtgagccaatgattaatacaaa--ttaattaattaattatatgtatgtatcaccattaagatagctatggcaacttttgttgatgtgcag----

upper sequence: LOC_Os02g01340.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G059191_T01 (Zea mays), 5'ss of exon 2
CGTCATCCCCGACGGCATCGACAAGAACGGCAAGCCCCACAAGCTCCGCCTCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagctagtagtgtttttcttgctccatcgatctcaaccacaagacatgagctaactaacatcgacatcgtccctgatcgatcg--atcag--------
| ||||| | || |||   ||||||||||||||||| ||||||||| | || ||||||||||||||||||||| |||| || |||| ||||||||||||||| | |    |    |   || |||||| ||  || |     ||         |  |       ||    || || | | |   |||   ||||         
CATCATCGCTGATGGCGAAGACAAGAACGGCAAGCCGCACAAGCTCAGGCTATACTCCATCGCCAGCAGCGCCCTCGGAGATTTCGGCGACTCCAAGACGgtcagtcatcacc--tagcttgcttgcttcacggaacctttgcatggttttacaaatcctctgtat-attattgttcataaataatccgtatcaaacaaaacg

upper sequence: LOC_Os02g01340.2 (Oryza sativa), 5'ss of exon 1
lower sequence: AT5G66190.2 (Arabidopsis thaliana), 5'ss of exon 3
CGTCATCCCCGACGGCATCGACAAGAACGGCAAGCCCCACAAGCTCCGCCTCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagctagtagtgtttttcttgctccatcgatctcaaccacaagacatgagctaa-ctaacatcgacatcgtccctgatcgatcgatcag
 || || || || || || ||||||||||| ||||| ||||||||| | || ||||| ||||| || || ||||| || ||||| |  ||||||||||| ||||   || | || |   | |        |   |          |  | |||| ||   || |  | || || |  |||  |  |        
AGTGATTCCAGAGGGAATAGACAAGAACGGGAAGCCGCACAAGCTCAGGCTTTACTCTATCGCGAGTAGTGCCATTGGTGACTTTGGAGACTCCAAGACCgtaa---gcaaataatccctctaacaactaactaaataatgatttacaaaatgatcttctcttatctggaaatggatccttttgcag-------

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|38479097|gb|CF963230.1|CF963230
EST:     CTCCATCGCCAGCAGCGCCATCGGGGATTTCGCCGACT-CAAGACG                         GTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATAAGGGAGAGATC
genomic: CTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATC
EST: gi|25798321|gb|CA754282.1|CA754282
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCNAGACG                         GTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATC
EST: gi|33656206|gb|CF278820.1|CF278820
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACG                         GTATCGCTGTGCGTGAAGAGGGCTGGTGTACACCAACGATCAGGGGAGAGA
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGG-CTGGTGTACACCAACGATCAGGG-AGAGA
EST: gi|4880924|gb|AU065223.1|AU065223
EST:     TCTACTCCATCGCCAGCANCGCCATCGGGGACTTCGCCGACTCCAAGACG                         GTATCGCTGTG-GTGAAGAGGCTGGTGTACACCAA
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAA
EST: gi|8956400|gb|BE230203.1|BE230203
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGATTTCGCCGACTCCAAGACG                         GTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATAAGGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATC
EST: gi|58595302|gb|CF993610.1|CF993610
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGATTTCGCCGACTCCAAGACG                         GTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGAT
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGAT
EST: gi|58611960|gb|CK039672.1|CK039672
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGATTTCGCCGACTCCAAGACG                         GTATCGCTGTGCGTGAAGAGGCTGGTGTACAC
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACAC
EST: gi|29676004|gb|CB672279.1|CB672279
EST:     GACTCCAAGACG                         GTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATC
genomic: GACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATC
EST: gi|29676003|gb|CB672278.1|CB672278
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACG                         GTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATC
EST: gi|58594835|gb|CF993143.1|CF993143
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGATTTCGCCGACTCCAAGACG                         GTATCGCTGTGCGTGAAG
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAG
EST: gi|58588294|gb|CF986602.1|CF986602
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGATTTCGCCGACTCCAAGACG                         GTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATAAGGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATC
EST: gi|58662943|gb|CK051629.1|CK051629
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGATTTCGCCGACTCCAAGACG                         GTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATAAGGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATC
EST: gi|38477836|gb|CF961969.1|CF961969
EST:     TCTACTCCAGCGCCAGCAGCGCCATCGGGGATTTCGCCGACTCCAAGACG                         GTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATAAGGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATC
EST: gi|33817858|gb|CF334761.1|CF334761
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACG                         GTATCGCTGTGCGTGAAGAGGCTGGTGTACGCCAACGATC
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATC
EST: gi|58588807|gb|CF987115.1|CF987115
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGATTTCGCCGACTCCAAGACG                         GTATCGCTGTGCGTGAAGA
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGA
EST: gi|33653470|gb|CF276084.1|CF276084
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACG                         GTATTCGCTGTGCGTGA
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTAT-CGCTGTGCGTGA
EST: gi|33661411|gb|CF292378.1|CF292378
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACG                         GTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATC
EST: gi|58607665|gb|CK035698.1|CK035698
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGATTTCGCCGACTCCAAGACG                         GTATCGCTGTGCGTGAAGAGGCTG
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGGCTG
EST: gi|8956756|gb|BE230559.1|BE230559
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGATTTCGCCGACTCCAAGACG                         GTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATAAGGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATC
EST: gi|33661543|gb|CF292510.1|CF292510
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACG                         GTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATC
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATC
EST: gi|33662396|gb|CF293363.1|CF293363
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACG                         GTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATC
EST: gi|29658349|gb|CB654624.1|CB654624
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACG                         GTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATC
EST: gi|44677984|gb|CR291418.1|CR291418
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGATTTCGCCGACTCCAAGACG                         GTATCGCTGTGCGTGAAGA
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGA

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: 74 (upstream exon), 75 (downstream exon)
Score: 106

CGTCATCCCCGACGGCATCGACAAGAACGGCAAGCCCCACAAGCTCCGCCTCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCCTCT




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