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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcacagagtcttatggtataatagttcttccaatatttgattcatgtactactctaattaatattatttgttggctgcagAAAAATCATATATTCACATCTGGTGCTTCTGGGACTAATGCAGCTGTTATCCGGGGTGCTTTAAGGGCTGAAAAGCCAGAGTTGCTCACTGTAATTTTAC

Basic information

species Oryza sativa
transcript LOC_Os01g23680.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g23680.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G081653_T02 (Zea mays), 3'ss of exon 3
------------------------------gtatgtcacagagtcttatggtataatagttcttccaatatttgattcatgtactactctaattaatattatttgttggctgcagAAAAATCATATATTCACATCTGGTGCTTCTGGGACTAATGCAGCTGTTATCCGGGGTGCTTTAAGGGCTGAAAAGCCAGAGTTGCTCACTGTAATTTTAC
                                || || | || |  ||||  |   | |||| |   || |||||| | | ||      |||| |   || | | |    |||||||||||||||||||||||||||| |||||||| || ||||||||||||||  |||| |||||||| |||||||||||||||||||| |||||||||||||
gtaggttcctatgtgccattgtcgttcatatgatctccctgatttatatgccagtgtggttcatattatctttgatccctctagcttgttaataatgtttgtgtataatttgcagAAAAATCATATATTCACATCTGGGGCTTCTGGAACAAATGCAGCTGTTATTAGGGGCGCTTTAAGAGCTGAAAAGCCAGAGTTGCTTACTGTAATTTTAC

upper sequence: LOC_Os01g23680.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G022090_T02 (Zea mays), 3'ss of exon 1
------------------------------gtatgtcacagagtcttatggtataatagttcttccaatatttgattcatgtactactctaattaatatt-atttgttggctgcagAAAAATCATATATTCACATCTGGTGCTTCTGGGACTAATGCAGCTGTTATCCGGGGTGCTTTAAGGGCTGAAAAGCCAGAGTTGCTCACTGTAATTTTAC
                                || || | || |  ||||  |   |  ||  |   || ||  || | | ||  | | | | |||| ||  | | |    ||||||||||||||||||| ||||||||||||||||| || ||||||||||||||| |||||||| |||| |||||||| |||||| |||| |||||||||||||
gtatgttcctatgtgctgttgtcatccatatgatctccctgatttatatgccagtgtgttttatatgatcttatatccttctagcattgttaataatgtttgtgtataatttgcagAAAAATCATATATTTACATCTGGTGCTTCTGGAACAAATGCAGCTGTTATCAGGGGTGCTCTAAGAGCTGAAAAACCAGAGCTGCTTACTGTAATTTTAC

upper sequence: LOC_Os01g23680.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA07G40350.2 (Glycine max), 3'ss of exon 3
-------------------------------------------------------------gtatgtcacaga---gtcttatggtataatagttcttccaatatttgattcatgta-ctac-tctaattaata-ttatttgt-tggctgcagAAAAATCATATATTCACATCTGGTGCTTCTGGGACTAATGCAGCTGTTATCCGGGGTGCTTTAAGGGCTGAAAAGCCAGAGTTGCTCACTGTAATTTTAC
                                                              ||| |     |   ||  |   ||||| |  |  ||    |     ||||   || ||   ||| |  | |  || |   | ||  || ||||||||||||||| ||||||||| || |||||||||||||| ||||||||||| |||||||||||||| || || || |||||||| ||||| || ||||
gtaagtttctgttattttactctatagtatcatatgctttcttgtagtcttgtggaacacaatatatggtgaattggtgatgcagtatagttatgatttttgttaacaattccaatagctgtgtctcacaacttcttgtccatctgtttgtagAAAAATCATATATACACATCTGGAGCATCTGGGACTAATGCTGCTGTTATCCGAGGTGCTTTAAGGGCAGAGAAACCGGAGTTGCTTACTGTTATATTAC

upper sequence: LOC_Os01g23680.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA17G00330.1 (Glycine max), 3'ss of exon 3
--------------------------------------------------------gtatgtcacagagtcttatggtataatagttct-tccaatatttgattcatgt--actactctaattaatat----------tatttgt-----tggctgcagAAAAATCATATATTCACATCTGGTGCTTCTGGGACTAATGCAGCTGTTATCCGGGGTGCTTTAAGGGCTGAAAAGCCAGAGTTGCTCACTGTAATTTTAC
                                                        |||   ||||   | |  ||   |  |  | |  | | |  | |||||  |||  || |||| |||   | |          |  ||||     ||  || |||||||||||||||  |||||||| || |||||||||||||| |||||||| || |||||||||||||| || || ||||||||||| || || || ||||
gtaagttgttattttactcaagagtattatatgcttgcttgaagagtttcagtcttgtagaacacaatatatggtgaattggtgatgcagtactagttatgatttttgttaacaactccaatggctgtgtctcacaacttcttgtccatctgtttgtagAAAAATCATATATATACATCTGGAGCATCTGGGACTAATGCTGCTGTTATTCGAGGTGCTTTAAGGGCAGAGAAACCAGAGTTGCTTACAGTTATATTAC

upper sequence: LOC_Os01g23680.3 (Oryza sativa), 3'ss of exon 2
lower sequence: AT2G43945.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatgtcac-agagtcttatggtataatagttcttccaatatttgattcatgtactactctaattaatattatttgttggctgcagAAAAATCATATATTCACATCTGGTGCTTCTGGGACTAATGCAGCTGTTATCCGGGGTGCTTTAAGGGCTGAAAAGCCAGAGTTGCTCACTGTAATTTTAC
||| ||||  |||   | ||  | |  | |||   |    ||    || |   |   ||| ||| |||    ||| |    |||||||||||||||||| |||||| ||||| ||||| |||||||| || || ||| | ||||| || || || || |  |||||| |||| || |||||| |||
gtaagtcattagaacttcatcctcttgt-gtttgactccgatccatttaaaacatctctcgaat-aattcggtttct----tgcagAAAAATCATATATACACATCAGGTGCATCTGGAACTAATGCTGCAGTCATCAGAGGTGCATTGAGAGCAGAGAGACCAGAGCTGCTTACAGTAATTCTAC

upper sequence: LOC_Os01g23680.3 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv05s0094g01380.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------------------------gtatg-tcacagagtcttatggtataatagttcttccaatatttgattcatgtactactctaattaatattatttgttggctgcagAAAAATCATATATTCACATCTGGTGCTTCTGGGACTAATGCAGCTGTTATCCGGGGTGCTTTAAGGGCTGAAAAGCCAGAGTTGCTCACTGTAATTTTAC
                                              |  || | |  ||| |  |     |  | |  ||  | || ||| ||     | || ||  ||||  ||| |||  ||  || |||||||| || || || ||||| || || ||||| |||||||||||||||||| | |||||  |||| || || || |||||| |||| |||||||| ||||
gtatgatgctgtaacttctatcagtatattttatgtctaacattgtgggtgcttattgagcccaacatgctgctgggactctccat-tttcatattcatgcttctgaaattcctatgatt-atttcctacagAAAAACCACATTTTTACATCAGGAGCATCTGGCACTAATGCAGCTGTTATCAGAGGTGCGCTAAGAGCAGAGAAACCAGAGCTGCTTACTGTAATCTTAC

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|29659908|gb|CB656183.1|CB656183
EST:     TTATGCATCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACG                         AAAAATCATATATTCACATCTGGTGCTTCTGGGACTAATGCAGCTGTTATC
genomic: TTATGCATCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACGgtatgtcaca ... ttggctgcagAAAAATCATATATTCACATCTGGTGCTTCTGGGACTAATGCAGCTGTTATC
EST: gi|29658365|gb|CB654640.1|CB654640
EST:     TTATGCATCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACG                         AAAAATCATATATTCACATCTGGTGCTTCTGGGACTAATGCAGCTGTTATC
genomic: TTATGCATCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACGgtatgtcaca ... ttggctgcagAAAAATCATATATTCACATCTGGTGCTTCTGGGACTAATGCAGCTGTTATC
EST: gi|163923267|gb|EG711076.1|EG711076
EST:     TTATGCATCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACG                         AAAAATCATATATTCACATCTGGTGCTTCTGGGACTAATGCAGCTGTTATC
genomic: TTATGCATCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACGgtatgtcaca ... ttggctgcagAAAAATCATATATTCACATCTGGTGCTTCTGGGACTAATGCAGCTGTTATC
EST: gi|29657705|gb|CB653980.1|CB653980
EST:     TTATGCATCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACG                         AAAAATCATATATTCACATCTGGTGCTTCTGGGACTAATGCAGCTGTTATC
genomic: TTATGCATCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACGgtatgtcaca ... ttggctgcagAAAAATCATATATTCACATCTGGTGCTTCTGGGACTAATGCAGCTGTTATC
EST: gi|29660019|gb|CB656294.1|CB656294
EST:     TTATGCATCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACG                         AAAAATCATATATTCACATCTGGTGCTTCTGGGACTAATGCAGCTGTTATC
genomic: TTATGCATCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACGgtatgtcaca ... ttggctgcagAAAAATCATATATTCACATCTGGTGCTTCTGGGACTAATGCAGCTGTTATC
EST: gi|25807329|gb|CA763290.1|CA763290
EST:     TTATGCATCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACG                         AAAAATCATATATTCACATCTGGTGCTTCTGGGACTAATGCAGCTGTTATC
genomic: TTATGCATCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACGgtatgtcaca ... ttggctgcagAAAAATCATATATTCACATCTGGTGCTTCTGGGACTAATGCAGCTGTTATC
EST: gi|157651885|gb|EX451519.1|EX451519
EST:     TTATGCATCAACAGCTTATTGAGATCCTGAACTATGCTATGGTCATAACG                         AAAAATCATATATTCACATCTGGTGCTTCTGGGACTAATGCAGCTGTTATC
genomic: TTATGCATCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACGgtatgtcaca ... ttggctgcagAAAAATCATATATTCACATCTGGTGCTTCTGGGACTAATGCAGCTGTTATC
EST: gi|86500098|gb|CI142731.1|CI142731
EST:     TTATGCATCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACG                         AAAAATCATATATTCACATCTGGTGCTTCTGGGACTAATGCAGCTGTTATC
genomic: TTATGCATCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACGgtatgtcaca ... ttggctgcagAAAAATCATATATTCACATCTGGTGCTTCTGGGACTAATGCAGCTGTTATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttccaatatttgattcatgtactactctaattaatattatttgttggctgcagAAAAATCATATATTCACATCTGGTGCTTCTGGGACTAATGCAGCTGTTATCCGGGGTGCTTTAAGGGCTGAAAAGCCAGAGTTGCTCACTGTAATTTTAC
                              aattaat  putative branch site (score: 3)
                     tactactctaattaat  TA-rich tract