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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGAAGTTATTGATCACTCTCTCGAGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAGgtaaattcaagaaaatgaaaagagaagatttttatgtatcttaatcgtattccttgtgcttgatgtagcccccttttgcatttgctcttatgcag

Basic information

species Oryza sativa
transcript LOC_Os04g56450.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g56450.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G056572_T02 (Zea mays), 5'ss of exon 7
GAGGAAGTTATTGATCACTCTCTCGAGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAGgtaaattcaagaaaatgaaa----ag----agaagatttttatgtatcttaatcgtattccttgtgcttgatg---tag--cccccttttgcatttgctcttatgcag--------------
||||||||| ||||| || | |||||||| || || |||||||||||||||||||||||||| ||  | || ||||||| ||    ||   | |     ||    |||| |||||   |     |    | | || ||||||||  ||   |||  || ||| |||    || |||| | ||               
GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAGgtaatttaggaaatgcggagccggagctccagaatattttgccggtcgcttgctgcactcattgtgcttagtgccttagtaccacctgttggcaatgttctt-tacaatgtttgccatgcag

upper sequence: LOC_Os04g56450.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G056572_T03 (Zea mays), 5'ss of exon 7
GAGGAAGTTATTGATCACTCTCTCGAGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAGgtaaattcaagaaaatgaaa----ag----agaagatttttatgtatcttaatcgtattccttgtgcttgatg---tag--cccccttttgcatttgctcttatgcag--------------
   |||||| ||||| || | |||||||| || || |||||||||||||||||||||||||| ||  | || ||||||| ||    ||   | |     ||    |||| |||||   |     |    | | || ||||||||  ||   |||  || ||| |||    || |||| | ||               
---GAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAGgtaatttaggaaatgcggagccggagctccagaatattttgccggtcgcttgctgcactcattgtgcttagtgccttagtaccacctgttggcaatgttctt-tacaatgtttgccatgcag

upper sequence: LOC_Os04g56450.2 (Oryza sativa), 5'ss of exon 7
lower sequence: AT4G31750.1 (Arabidopsis thaliana), 5'ss of exon 8
GAGGAAGTTATTGATCACTCTCTCGAGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAGgtaa--------attcaag----aaaatgaaaagagaagatttttatgtatcttaatcgtattccttgtgcttgatg--tagcccccttttgcatttgctcttatgcag
||||||    |||||  |||||||||||| |||||||||||||||||||| || ||||| || ||| | || ||||||         |||  |     ||| |     |  ||  ||  | | | |   | ||  | |||| |  ||  |    |   | |  ||   || |    ||  |   
GAGGAAAAAGTTGATAGCTCTCTCGAGTTTCTCATTCTTGCAAGTGATGGTCTCTGGGACGTTGTATCTAACGAGgtaggaagtgtcatttgatttctaaacttccctgttaaacttcctctttttaacattcccaatcctcggactcaaaaactgatctctgttcaaatctttatttcag---

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|86423847|gb|CI062608.1|CI062608
EST:     GTTCCTCATTTCTTGCAAGTGATGGCCTGTGGGATGTAGTAACCAATGAG                         GAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
genomic: GTTCCTCA-TTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAGgtaaattcaa ... tcttatgcagGAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
EST: gi|8858859|gb|AU096177.1|AU096177
EST:     AGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAG                         GAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
genomic: AGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAGgtaaattcaa ... tcttatgcagGAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
EST: gi|27547322|gb|CA765327.2|CA765327
EST:     AGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAG                         GAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
genomic: AGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAGgtaaattcaa ... tcttatgcagGAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
EST: gi|66920381|gb|CX107229.1|CX107229
EST:     AGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAG                         GAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
genomic: AGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAGgtaaattcaa ... tcttatgcagGAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
EST: gi|88844668|gb|CI021243.1|CI021243
EST:     AGTTCCTCATTCTTGCAAGTGATGGGCTTTGGGATGTAGTAACCCATGAG                         GAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
genomic: AGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAGgtaaattcaa ... tcttatgcagGAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
EST: gi|38476736|gb|CF960869.1|CF960869
EST:     TCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAG                         GAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
genomic: TCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAGgtaaattcaa ... tcttatgcagGAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
EST: gi|24208771|gb|AU225798.1|AU225798
EST:     AGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAG                         GAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
genomic: AGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAGgtaaattcaa ... tcttatgcagGAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
EST: gi|86536657|gb|CI176863.1|CI176863
EST:     AGTTCCTCATTCTGGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAG                         GAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
genomic: AGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAGgtaaattcaa ... tcttatgcagGAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
EST: gi|14981649|gb|BI306327.1|BI306327
EST:     AGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAG                         GAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
genomic: AGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAGgtaaattcaa ... tcttatgcagGAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
EST: gi|86423540|gb|CI062301.1|CI062301
EST:     AGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCCATGAG                         GAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
genomic: AGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAGgtaaattcaa ... tcttatgcagGAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
EST: gi|5003298|gb|AU068447.1|AU068447
EST:     AGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAG                         GAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
genomic: AGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAGgtaaattcaa ... tcttatgcagGAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG

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: 75 (upstream exon), 58 (downstream exon)
Score: 9

GAGGAAGTTATTGATCACTCTCTCGAGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAGgtaaattcaa ... tcttatgcagGAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAGAAGCTCTTGCAAGAGGCCTACAAGAGGGAGAGCAGTGACAACATAACTT




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