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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgttgcgttgtggtaatcctgctctgtgagtcagtggtaatattactttctgctatctcttagtaactaaaacgtagaagagatgtgttacttaacttcgcttcttcaggggatgttagctataaatctgataagttacattcaatttctttttggattgttagGTCCGCATGGTTACTGGAGACAACCTTCAAACTGCCAGAGCCATTGCCTTGGAGTGTGGAATTTTATCTGATCCCAATGTGTCAGAGCCAGTCATTATTG

Basic information

species Oryza sativa
transcript LOC_Os04g51610.3
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 23
lower sequence: GRMZM2G140328_T03 (Zea mays), 3'ss of exon 23
gtaatgttgcgttgtggtaatcctgctctgtgagtcagtggtaatattactttctgctatctcttagtaactaaaacgtagaagagatgtgttac--ttaacttcg-cttcttcaggggatgttagctataaatctgataagttacattcaa----tttctttttggattgttagGTCCGCATGGTTACTGGAGACAACCTTCAAACTGCCAGAGCCATTGCCTTGGAGTGTGGAATTTTATCTGATCCCAATGTGTCAGAGCCAGTCATTATTG
                                     ||  |   ||   | |  |  |  | |   | |     |   | ||| |||  ||  |  || |  ||  |||||  |     | |      |   ||||   |  |  | |  |    | | | |||| |||||||||| |||||||||||||| || || ||||||||||| |||||||||||| |||| || || ||  |   ||||||||||||||  ||||| ||||| ||||
-------------------------------------gtattttcatgtttctgcgtcacttttatattagatgcatccaaaagggataggtcgccattcatgtcatcttctataatccgtatctttgcttcgtctggagatgtttacttgaaaattatttgtttgaattgttagGTGCGCATGGTTACTGGTGATAATCTTCAAACTGCGAGAGCCATTGCCCTGGAATGCGGGATACTTGATGATCCCAATGTGTTGGAGCCTGTCATCATTG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 23
lower sequence: GRMZM2G391042_T01 (Zea mays), 3'ss of exon 23
gtaatgttgcgttgtggtaatcctgctctgtgagtcagtggtaatattactttctgctatctcttagtaactaaaacgtagaagagatgtgttacttaacttcgcttcttcaggggatgttagctataaatctgataagttacattcaatttcttt--ttggattgttagGTCCGCATGGTTACTGGAGACAACCTTCAAACTGCCAGAGCCATTGCCTTGGAGTGTGGAATTTTATCTGATCCCAATGTGTCAGAGCCAGTCATTATTG
        |  || |  |  | |||   ||      |  | | ||| ||  | |  | |      |      |  |  ||    |  |    || |  | | |  |   | | |     ||     | | |||      | || ||  | || |||  ||| |||||||||| |||||||||||||| || || ||||||||||| |||||||||||| ||||||| || ||  |   ||||||||||||||||||||| ||||| ||||
--------gtattatcatgtttctgtgttgctttata-cgattatactagatgcatccagaagggacaggtcaccatttatgttatcttccataatcca-tacattcgcttatgtttacttgaaagttattctctgttatcacttttcagttatttatttgaattgttagGTGCGCATGGTTACTGGTGATAATCTTCAAACTGCAAGAGCCATTGCCCTGGAGTGCGGGATACTTGATGATCCCAATGTGTCAGAGCCTGTCATCATTG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 23
lower sequence: GLYMA07G00630.2 (Glycine max), 3'ss of exon 22
gtaatgttgcgttgtggtaatcctgctctgtgagtcagtggtaatattactttctgctatctcttagtaactaaaacgtagaagagatgtgttacttaacttcgcttcttcaggggatgttagctataaatctgataagttacattcaatttctttttggattgttagGTCCGCATGGTTACTGGAGACAACCTTCAAACTGCCAGAGCCATTGCCTTGGAGTGTGGAATTTTATCTG-ATCCCAATGTGTCA--GAGCCAGTCATTATTG
                       |  | || |  | |  ||||   ||  | |||  | | |  || | | |      |      | | |  |||  |  |  |       |    |||| |  |   || || | |  |||||     |    || || |||   |||| ||||||||||||||||||||||||||||| || |  || || || ||||||||||| ||  |  ||  |    ||  ||     ||||||   || |   
----------------------gtaatatgagttttacgggtatagtttgtgtct--tgttttatattgattgtggtttt---tggctttactacg-acatgagtggtcatacaaaatgtaacatgggaacctaacacattacacattctacggttatgaattcacagGTACGCATGGTTACTGGAGACAACCTTCAAACAGCAAAGGCAATAGCTTTGGAGTGTGGCATACTGGCTTCAATTGAAGATGCTGTTGAGCCAAATATAA---

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 23
lower sequence: GLYMA08G23760.1 (Glycine max), 3'ss of exon 25
gtaatgttgcgttgtggtaatcct-gctctgtgagtcagtggtaatattactttctgctatctcttagtaactaaaacgtagaagagatgtgttacttaacttcgcttcttcaggggatgttagctataaatctgataagttacattcaatttctttttggattgttagGTCCGCATGGTTACTGGAGACAACCTTCAAACTGCCAGAGCCATTGCCTTGGAGTGTGGAATTTTATCTG-ATCCCAATGTGTCA--GAGCCAGTCATTATTG
                |||||    | | | ||  | |  ||||   ||    | |  | | || || ||| |     ||      | | |  || |    |  |  |    |    |||| |  |   || |  | |  ||||        |  |  || | |   |||| ||||||||||||||||||||||||||||| || |  || || || ||||||||||| ||  |  ||  |    ||  ||     |||||    || |   
----------------gtaatatgagttgtatgtttaatgggtatagtttacgtgtcttgtttcatattaatt---gtgttttttggctttacta-tggcatgagtgttcatacaaaatgtaacatgggaacccaacacattacgcattccatggtaatgaaatcacagGTACGCATGGTTACTGGAGACAACCTTCAAACAGCAAAGGCAATAGCTTTGGAGTGTGGCATACTGGCTTCAATTGAAGATGCTGTTGAGCCGAATATAA---

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 23
lower sequence: AT5G57110.2 (Arabidopsis thaliana), 3'ss of exon 24
gtaatgttgcgttgtggtaatcctgctctgtgagtcagtggtaatattactttctgctatctcttagtaactaaaacgtagaagagatgtgttacttaacttcgcttcttcaggggatgttagctataaatctgataagttacattcaatttctttttggattgttagGTCCGCATGGTTACTGGAGACAACCTTCAAACTGCCAGAGCCATTGCCTTGGAGTGTGGAATTTTA---TCTGATCCCAATGTGTCAGAGCCAGTCATTATTG
                                        ||| |  |  | |  | | | | ||  | ||  |||   |||| |||   || ||  || ||   |  ||    |  || ||  |  ||  |||     |||| ||||   | ||| | |||  | ||||||| ||||||||||| |||||| | ||||||||||| || ||||||||||| ||||||||  ||   || ||| |  || | || |||||     | |   
----------------------------------------gtacttcttttgttcgatttattttttttacagaaaaacagaaaagacaagtgacagaaatttattgttt---agcctgctaatt--aatgctgcatgattac-ttcatgatatttgttgatgttcagGTCCGTATGGTTACTGGTGACAACGTCCAAACTGCCAGGGCTATTGCCTTGGAATGTGGAATACTAAGTTCAGATGCAGATCTCTCCGAGCCTACTCTCA---

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|58693220|gb|CK081907.1|CK081907
EST:     GCCCGGGTGTTAAAGATTCTGTTCGGTTATGTGCAGCAGCTGGCATTAAG                         GTCCGCATGGTTACTGGAGACAACCTTCAAACTGCCAGAGCCATTGCCTTG
genomic: GCCCGGGTGTTAAAGATTCTGTTCGGTTATGTGCAGCAGCTGGCATTAAGgtaatgttgc ... ggattgttagGTCCGCATGGTTACTGGAGACAACCTTCAAACTGCCAGAGCCATTGCCTTG
EST: gi|702134|gb|D48425.1|D48425
EST:     GCCCGGGTGTTAAAGATTCTGTTCGGTTATGTGCAGCAGCTGGCATTAAG                         GTCCGCATGGTTACTGGAGACAACCTTCAAACTGCCAGAGCCATTGCCTTG
genomic: GCCCGGGTGTTAAAGATTCTGTTCGGTTATGTGCAGCAGCTGGCATTAAGgtaatgttgc ... ggattgttagGTCCGCATGGTTACTGGAGACAACCTTCAAACTGCCAGAGCCATTGCCTTG
EST: gi|29685707|gb|CB681982.1|CB681982
EST:     GCCCGGGTGTTAAAGATTCTGTTCGGTTATGTGCAGCAGCTGGCATTAAG                         GTCCGCATGGTTACTGGAGACAACCTTCAAACTGCCAGAGCCATTGCCTTG
genomic: GCCCGGGTGTTAAAGATTCTGTTCGGTTATGTGCAGCAGCTGGCATTAAGgtaatgttgc ... ggattgttagGTCCGCATGGTTACTGGAGACAACCTTCAAACTGCCAGAGCCATTGCCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggatgttagctataaatctgataagttacattcaatttctttttggattgttagGTCCGCATGGTTACTGGAGACAACCTTCAAACTGCCAGAGCCATTGCCTTGGAGTGTGGAATTTTATCTGATCCCAATGTGTCAGAGCCAGTCATTATTG
                atctgat  putative branch site (score: 4)
                                    tttctttttg  putative PPT
                              attcaatttcttttt  TA-rich tract