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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcgctcgcgcatcccggcctctctctatctcctcgtcctcgtaggatctatgtggctcgccggtggcgttgcgcgctaagctgatgtgaaccaacagGGCGACTCGGAGGCGCACTCGCCGGTGGTCTACGACGATGCCGGGGTCACCTACATGTTCATCCAGCACAACAACGTGTTCCTACTAACCGCCTCCCGCC

Basic information

species Oryza sativa
transcript LOC_Os01g50770.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g50770.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G436835_T01 (Zea mays), 3'ss of exon 2
gtaagcgctcgcgca-tcccggcctctc-tctatctcctcgtcctcgtaggatctatgtggctcgccggtggcgttgcgcgctaagctgatgtgaaccaacagGGCGACTCGGAGGCGCACTCGCCGGTGGTCTACGACGATGCCGGGGTCACCTACATGTTCATCCAGCACAACAACGTGTTCCTACTAACCGCCTCCCGCC
||||| |  |   || |||  ||  |||  ||     || |||||     ||||| || ||| |     ||| | || |  ||      ||| |       ||||||| ||||| | ||||||||| |||||||||||||| || || ||||| ||||||||||||||||||||||| || ||||| || |||||| | ||||
gtaagtggccaatcagtcctcgcgcctcgcctgctctctagtcct---gagatctgtgcggccc-----tggtgctgagttctcgtgcaatggg------tagGGCGATTCGGAAGTGCACTCGCCTGTGGTCTACGACGACGCTGGCGTCACTTACATGTTCATCCAGCACAACAATGTCTTCCTCCTCACCGCCGCTCGCC

upper sequence: LOC_Os01g50770.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G162145_T01 (Zea mays), 3'ss of exon 1
gtaagcgctcgcgcatcccggcctctct--ctatctcctcgtc--ctcgtaggatctatgtggctcgccggtggcgttgcgcgctaagctgatgtgaaccaacagGGCGACTCGGAGGCGCACTCGCCGGTGGTCTACGACGATGCCGGGGTCACCTACATGTTCATCCAGCACAACAACGTGTTCCTACTAACCGCCTCCCGCC
||||| |  ||  |  || |  | |  |  || |   || |||  ||| |  ||||  || ||| |     | | | ||    ||    ||    |||     ||||||||||||| |  |||||||| |||||||||||||| ||||| ||||| ||||||||||||||||||||||| || ||||| || |||||  | ||||
gtaagtggccgatcggcctgctcaccttgcctgttgtcttgtctactcctgagatccgtgcggccc-----tagtgctgaattctcg--tg----gaatgggtagGGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACGTACATGTTCATCCAGCACAACAATGTCTTCCTCCTCACCGCTGCTCGCC
















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|27576432|gb|CA999126.1|CA999126
EST:     TCCAGGCTGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAG                         GGCGACTCGGAGGCGCACTCGCCGGTGGTCTACGACGATGCCGGGGTCACC
genomic: TCCAGGCTGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAGgtaagcgctc ... gaaccaacagGGCGACTCGGAGGCGCACTCGCCGGTGGTCTACGACGATGCCGGGGTCACC
EST: gi|88742515|gb|CI766023.1|CI766023
EST:     TCTCCGCCCTCCAGGCTGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAG                         GGCGANTCGGAG
genomic: TCTCCGCCCTCCAGGCTGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAGgtaagcgctc ... gaaccaacagGGCGACTCGGAG
EST: gi|88376945|gb|CI639270.1|CI639270
EST:     TCTCCGCCCTCCAGGCTGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAG                         GGCGACTCGGAGGCGCACTCGCCGGTGGTCTANGACGATGCCGGGGTCACC
genomic: TCTCCGCCCTCCAGGCTGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAGgtaagcgctc ... gaaccaacagGGCGACTCGGAGGCGCACTCGCCGGTGGTCTACGACGATGCCGGGGTCACC
EST: gi|88390289|gb|CI605742.1|CI605742
EST:     TCTCCGCCCTCCAGGCTGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAG                         GGCGACTCGGAGGCGCACTCGCCGGTGGTCTATGACGATGCCGGGGTCAC
genomic: TCTCCGCCCTCCAGGCTGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAGgtaagcgctc ... gaaccaacagGGCGACTCGGAGGCGCACTCGCCGGTGGTCTACGACGATGCCGGGGTCAC
EST: gi|58665060|gb|CK053746.1|CK053746
EST:     TCTCCGCCCTCCAGGCTGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAG                         GGCGACTCGGAGGCGCACTCGCCGGTGGTCTACGACGATGCCGGGGTCACC
genomic: TCTCCGCCCTCCAGGCTGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAGgtaagcgctc ... gaaccaacagGGCGACTCGGAGGCGCACTCGCCGGTGGTCTACGACGATGCCGGGGTCACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggatctatgtggctcgccggtggcgttgcgcgctaagctgatgtgaaccaacagGGCGACTCGGAGGCGCACTCGCCGGTGGTCTACGACGATGCCGGGGTCACCTACATGTTCATCCAGCACAACAACGTGTTCCTACTAACCGCCTCCCGCC
                                    agctgat  putative branch site (score: 4)