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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacggcgccccctgcgcccccaggcctcacctctcccttcactctcgtttcttctcgccatggttgttgttcacctctcgtgctcgacctcgctgacgtgacgtttgttgttgatggcccccgccgctgccgacgccgcagATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTC

Basic information

species Oryza sativa
transcript LOC_Os01g40570.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g40570.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G108144_T01 (Zea mays), 3'ss of exon 1
gtacggcgccccctgcgcccccag-gcctcacctctcccttcactctcgtttcttctcgccatggttgttgttcacctctcgtgctcg---acctcgctgacgtgacgtttgttgttgatggcccccgccgctgccgacgccgcagATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTC
               ||   | ||  |  || |||| || || ||||   ||| |     ||    ||||  |   |||  |||| ||   |||       | |||||| |||| |    |   |||   | |        ||||||| |||| |||| |||||||   |||||||| |||||| |||||||||||||| | ||| | ||| ||
-------------gtcgagtctagcacgccatctctaccctc-ctcttacttcctgatttcagttctgttcatgttctccggtgcccgggaaccgaatgatcctgacgtgtgttatct-cgtttccctttgtt--------cgcagATTTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCGCCCCATGGCATC

upper sequence: LOC_Os01g40570.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G155021_T01 (Zea mays), 3'ss of exon 1
gtacggcgccccctgcgcccccaggcctcacctctcccttcactctcgtttcttctcgccatggttgttgttcacctctcgtgctcgacctcgctgacgtgacgtttgttgttgatggcccccgccgctgccgacgccgcagATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTC
                        | ||  |    |   ||   |    | |||  | || || ||   ||  ||   || || ||  |   ||         ||||  |  ||| |      |   |      ||| ||||||||||| |||| |||||||   |||||||| |||||| |||||||||||||| ||||| | ||||||
------------------------gtcttgcacgccatctctgccctcctccttacctcc-tgatttaagt--actcttcatgttcaccggtgcccggcaactgtttcatcctgacgcgtgttgtttccctttgcgc-gcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTC
















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|88720969|gb|CI744268.1|CI744268
EST:     GGCATCCATGGCGCCAGGGCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCT
genomic: GGCATCCATGGCGCCAGGGCTCTACACCGACATCGGCAAGAAGACCAGAGgtacggcgcc ... gacgccgcagATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCT
EST: gi|88333135|gb|CI640978.1|CI640978
EST:     GGCATCCATGGCGCCAGGGCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCT
genomic: GGCATCCATGGCGCCAGGGCTCTACACCGACATCGGCAAGAAGACCAGAGgtacggcgcc ... gacgccgcagATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCT
EST: gi|84117319|gb|CD151086.1|CD151086
EST:     GGCATGCATGGCGCCAGGGCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCT
genomic: GGCATCCATGGCGCCAGGGCTCTACACCGACATCGGCAAGAAGACCAGAGgtacggcgcc ... gacgccgcagATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCT
EST: gi|88736441|gb|CI759949.1|CI759949
EST:     GGCATCCATGGCGCCAGGGCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCT
genomic: GGCATCCATGGCGCCAGGGCTCTACACCGACATCGGCAAGAAGACCAGAGgtacggcgcc ... gacgccgcagATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCT
EST: gi|8857889|gb|AU095207.1|AU095207
EST:     GGCATCCATGGCGCCAGGGCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCT
genomic: GGCATCCATGGCGCCAGGGCTCTACACCGACATCGGCAAGAAGACCAGAGgtacggcgcc ... gacgccgcagATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCT
EST: gi|88720087|gb|CI745177.1|CI745177
EST:     GGCATTCATGGCGCCAGGGCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCT
genomic: GGCATCCATGGCGCCAGGGCTCTACACCGACATCGGCAAGAAGACCAGAGgtacggcgcc ... gacgccgcagATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCT
EST: gi|88294738|gb|CI604610.1|CI604610
EST:     GGCATCCATGGCGCCAGGGCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCT
genomic: GGCATCCATGGCGCCAGGGCTCTACACCGACATCGGCAAGAAGACCAGAGgtacggcgcc ... gacgccgcagATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCT
EST: gi|11565269|gb|AU165905.1|AU165905
EST:     GGCATCCATGGCGCCAGGGCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCT
genomic: GGCATCCATGGCGCCAGGGCTCTACACCGACATCGGCAAGAAGACCAGAGgtacggcgcc ... gacgccgcagATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCT
EST: gi|88416058|gb|CI594170.1|CI594170
EST:     GGCATCCATGGCGCCAGGGCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCT
genomic: GGCATCCATGGCGCCAGGGCTCTACACCGACATCGGCAAGAAGACCAGAGgtacggcgcc ... gacgccgcagATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCT
EST: gi|88734309|gb|CI757817.1|CI757817
EST:     GGCATCCATGGCGCCAGGGCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCT
genomic: GGCATCCATGGCGCCAGGGCTCTACACCGACATCGGCAAGAAGACCAGAGgtacggcgcc ... gacgccgcagATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCT
EST: gi|88720970|gb|CI744269.1|CI744269
EST:     GGCATCCATGGCGCCAGGGCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCT
genomic: GGCATCCATGGCGCCAGGGCTCTACACCGACATCGGCAAGAAGACCAGAGgtacggcgcc ... gacgccgcagATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCT
EST: gi|33684445|gb|CF312684.1|CF312684
EST:     GGCATCCATGGCGCCAGGGCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCT
genomic: GGCATCCATGGCGCCAGGGCTCTACACCGACATCGGCAAGAAGACCAGAGgtacggcgcc ... gacgccgcagATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCT
EST: gi|88760947|gb|CI770503.1|CI770503
EST:     GGCATCCATGGCGCCAGGGCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCT
genomic: GGCATCCATGGCGCCAGGGCTCTACACCGACATCGGCAAGAAGACCAGAGgtacggcgcc ... gacgccgcagATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCT
EST: gi|33797333|gb|CF324529.1|CF324529
EST:     GGCATCCATGGCGCCAGGGCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCT
genomic: GGCATCCATGGCGCCAGGGCTCTACACCGACATCGGCAAGAAGACCAGAGgtacggcgcc ... gacgccgcagATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCT
EST: gi|117243612|gb|CT843146.1|CT843146
EST:     GGCATCCATGGCGCCAGGGCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCT
genomic: GGCATCCATGGCGCCAGGGCTCTACACCGACATCGGCAAGAAGACCAGAGgtacggcgcc ... gacgccgcagATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCT
EST: gi|86905077|gb|CI289224.1|CI289224
EST:     GGCATCCATGGCGCCAGGGCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCT
genomic: GGCATCCATGGCGCCAGGGCTCTACACCGACATCGGCAAGAAGACCAGAGgtacggcgcc ... gacgccgcagATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCT
EST: gi|58661680|gb|CK050360.1|CK050360
EST:     GGCATCCATGGCGCCAGGGCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCT
genomic: GGCATCCATGGCGCCAGGGCTCTACACCGACATCGGCAAGAAGACCAGAGgtacggcgcc ... gacgccgcagATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCT

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: 68 (upstream exon), 69 (downstream exon)
Score: 41

GCCGCCGCCGCCGCGATATCGATCCCCTCCCTCTCGCCGTCGACGCCGTCGGCATCCATGGCGCCAGGGCTCTACACCGACATCGGCAAGAAGACCAGAGgtacggcgcc ... gacgccgcagATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTC




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