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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatacagcttgtagctaatgctgcattactaggaaatctgttgctcaggaaaaattcttgtggatattttactgatactttgtttatgtacattttacagGTAAAAATATGGGATCCAAGTTTGCGTGGTTCTGAACTTCGGACAACACTTAAAGGGCACACTAG

Basic information

species Oryza sativa
transcript LOC_Os01g39380.3
intron # 24
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g39380.1 (Oryza sativa), 3'ss of exon 24
lower sequence: GRMZM2G074466_T01 (Zea mays), 3'ss of exon 4
------tatacagcttgtagctaatgctgcattactaggaaatctgttgctcaggaaaaattcttgtggatattttactgatactttgtttatgtacattttacagGTAAAAATATGGGATCCAAGTTTGCGTGGTTCTGAACTTCGGACAACACTTAAAGGGCACACTAG
       ||     ||| ||||| ||||| |||| ||     | | ||  || |      ||  | |||| | |  ||   || |||||||  |||||| | |||||||||||| ||||||||||||||||||||||||||||||||  |||||||||||||||| |||||
tcccctgatttgaattg-agcta-tgctgaattattacatggtatctttatctgtct---ttgatttggacactgaacatttagtttgttt-cgtacatctcacagGTAAAAATTTGGGATCCAAGTTTGCGTGGTTCTGAACTTCGAGCAACACTTAAAGGGCATACTAG

upper sequence: LOC_Os01g39380.1 (Oryza sativa), 3'ss of exon 24
lower sequence: AT1G49040.1 (Arabidopsis thaliana), 3'ss of exon 23
tatacagctt-gtagctaatgctgcattactaggaaatctgttgctcaggaaa--aattcttgtggatattttactgatactttgtttatgtacattttacagGTAAAAATATGGGATCCAAGTTTGCGTGGTTCTGAACTTCGGACAACACTTAAAGGGCACACTAG
   |||  ||  |  ||     |  |   | ||| || |  |    ||| |    |||     |  |   |   ||  |  ||  ||  || |  ||   ||||| ||||| |||||||||||| |||||||||||||||||||  ||||  | ||||| || ||| |
--cacactttcatttcttgaaatttagatcgaggtaaaccttaatacagaatggtaatgacaatctagcatccccttttggttgcttcctgaat-ttgagcagGTTAAAATTTGGGATCCAAGTCTGCGTGGTTCTGAACTTCGAGCAACTTTGAAAGGACATACTGG
















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|29641894|gb|CB646901.1|CB646901
EST:     GTGATCGTGAAGATGCTGGCTTTTTCATCAGTGGAAGCACAGATTGCACG                         GTAAAAATATGGGATCCAAGTTTGCGTGGTTCTGAACTTCGGACAACACTT
genomic: GTGATCGTGAAGATGCTGGCTTTTTCATCAGTGGAAGCACAGATTGCACGgttaggctaa ... cattttacagGTAAAAATATGGGATCCAAGTTTGCGTGGTTCTGAACTTCGGACAACACTT
EST: gi|33690825|gb|CF319064.1|CF319064
EST:     GTGATCGTGAAGATGCTGGCTTTTTCATCAGTGGAAGCACAGATTGCACG                         GTAAAAATATGGGATCCAAGTTTGCGTGGTTCTGAACTTCGGACAACACTT
genomic: GTGATCGTGAAGATGCTGGCTTTTTCATCAGTGGAAGCACAGATTGCACGgttaggctaa ... cattttacagGTAAAAATATGGGATCCAAGTTTGCGTGGTTCTGAACTTCGGACAACACTT
EST: gi|58694147|gb|CK082834.1|CK082834
EST:     GTGATCGTGAAGATGCTGGCTTTTTCATCAGTGGAAGCACAGATTGCACG                         GTAAAAATATGGGATCCAAGTTTGCGTGGTTCTGAACTTCGGACAACACTT
genomic: GTGATCGTGAAGATGCTGGCTTTTTCATCAGTGGAAGCACAGATTGCACGgttaggctaa ... cattttacagGTAAAAATATGGGATCCAAGTTTGCGTGGTTCTGAACTTCGGACAACACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caggaaaaattcttgtggatattttactgatactttgtttatgtacattttacagGTAAAAATATGGGATCCAAGTTTGCGTGGTTCTGAACTTCGGACAACACTTAAAGGGCACACTAG
                        tactgat  putative branch site (score: 2)
                                     tttatgtacatttta  TA-rich tract