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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGTGGAGGCGTCACCTCCTCGACGGCAACATCTCCCCCACCACCGCGGCGGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAGgtatggaggaggcgcccttccgggcgtccgggaccagccctgaacatcgcccgcgggtgccccccgagggtagatcttagaggtggtttgggttttcgatgcag

Basic information

species Oryza sativa
transcript LOC_Os02g57180.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g57180.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G143651_T01 (Zea mays), 5'ss of exon 1
GCGTGGAGGCGTCACCTCCTCGACGGCAACATCTCCCCCACCACCGCGGCGGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAGgtatggaggaggcgcccttccgggcgtccgggaccagccctgaacatcgcccgcgggtgccccccgag--ggtagatcttagaggtggtttgggttttcgatgcag
||||||||||||||||||||||||  | || |||||||  | ||| |||| || ||| ||||||||||||||||||||||||| | |||||| ||||||||||            |||              ||||   |    | || | |||| |  || ||||    | ||||||| ||||   ||||    ||||       
GCGTGGAGGCGTCACCTCCTCGACCACCACCTCTCCCCTTCAACCTCGGCTGCCATCGCCGCCTTCAGATCCGCCTCCCAGCCCGGGCTCGCTCCCCAAGgta------------cct--------------accatttccctccctctcacgcgtgctcctcccggatagatagatctcagagccagttt--cctttcag-----
















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|58603608|gb|CK014136.1|CK014136
EST:     GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAG                         GATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
genomic: GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAGgtatggagga ... ttcgatgcagGATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
EST: gi|88385402|gb|CI630503.1|CI630503
EST:     GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAG                         GATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGNGAGGGCGCCGGCGG
genomic: GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAGgtatggagga ... ttcgatgcagGATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
EST: gi|88356997|gb|CI620885.1|CI620885
EST:     GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCC-AAG                         GATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
genomic: GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAGgtatggagga ... ttcgatgcagGATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
EST: gi|88383864|gb|CI631754.1|CI631754
EST:     GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAG                         GATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
genomic: GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAGgtatggagga ... ttcgatgcagGATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
EST: gi|88433494|gb|CI594308.1|CI594308
EST:     GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAG                         GATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
genomic: GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAGgtatggagga ... ttcgatgcagGATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
EST: gi|88388115|gb|CI590391.1|CI590391
EST:     GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAG                         GATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
genomic: GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAGgtatggagga ... ttcgatgcagGATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
EST: gi|38565625|gb|CK085078.1|CK085078
EST:     GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAG                         GATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
genomic: GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAGgtatggagga ... ttcgatgcagGATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
EST: gi|29673108|gb|CB669383.1|CB669383
EST:     GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAG                         GATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
genomic: GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAGgtatggagga ... ttcgatgcagGATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
EST: gi|86904270|gb|CI306688.1|CI306688
EST:     GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAG                         GATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
genomic: GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAGgtatggagga ... ttcgatgcagGATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
EST: gi|29671358|gb|CB667633.1|CB667633
EST:     GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAG                         GATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
genomic: GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAGgtatggagga ... ttcgatgcagGATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
EST: gi|88443613|gb|CI591838.1|CI591838
EST:     GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAG                         GATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
genomic: GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAGgtatggagga ... ttcgatgcagGATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
EST: gi|58663529|gb|CK052215.1|CK052215
EST:     GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAG                         GATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
genomic: GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAGgtatggagga ... ttcgatgcagGATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
EST: gi|88377002|gb|CI597786.1|CI597786
EST:     GGCGATCTCCGCCTTCAGATCCGACTCCCAGCCGGCGCTCGCACCCCAAG                         GATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
genomic: GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAGgtatggagga ... ttcgatgcagGATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
EST: gi|88726504|gb|CI750159.1|CI750159
EST:     GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAG                         GATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
genomic: GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAGgtatggagga ... ttcgatgcagGATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
EST: gi|88447774|gb|CI576970.1|CI576970
EST:     GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAG                         GATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
genomic: GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAGgtatggagga ... ttcgatgcagGATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
EST: gi|88362216|gb|CI608607.1|CI608607
EST:     GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAG                         GATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
genomic: GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAGgtatggagga ... ttcgatgcagGATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
EST: gi|88405560|gb|CI588766.1|CI588766
EST:     GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAG                         GATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
genomic: GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAGgtatggagga ... ttcgatgcagGATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
EST: gi|88693529|gb|CI737104.1|CI737104
EST:     GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAG                         GATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
genomic: GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAGgtatggagga ... ttcgatgcagGATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
EST: gi|88362596|gb|CI607354.1|CI607354
EST:     GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAG                         GATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
genomic: GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAGgtatggagga ... ttcgatgcagGATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
EST: gi|88348839|gb|CI631926.1|CI631926
EST:     GNGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCCAAG                         GATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCG
genomic: GCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCA-CCCCAAGgtatggagga ... ttcgatgcagGATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCG
EST: gi|88387570|gb|CI585273.1|CI585273
EST:     GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAG                         GATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
genomic: GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAGgtatggagga ... ttcgatgcagGATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
EST: gi|88721928|gb|CI743440.1|CI743440
EST:     GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAG                         GATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
genomic: GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAGgtatggagga ... ttcgatgcagGATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
EST: gi|58678182|gb|CK066869.1|CK066869
EST:     GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAG                         GATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
genomic: GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAGgtatggagga ... ttcgatgcagGATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
EST: gi|2427794|gb|C72257.1|C72257
EST:     GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAG                         GATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
genomic: GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAGgtatggagga ... ttcgatgcagGATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
EST: gi|6012900|gb|AU078717.1|AU078717
EST:     GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGNGCTCGCACCCCAAG                         GATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
genomic: GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAGgtatggagga ... ttcgatgcagGATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
EST: gi|88449234|gb|CI579918.1|CI579918
EST:     GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAG                         GATTGGGTGGAGCGGATGGCGCGAGGTACATGTCAGCGAGGGCGCCGGCGG
genomic: GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAGgtatggagga ... ttcgatgcagGATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
EST: gi|88730270|gb|CI753884.1|CI753884
EST:     GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAG                         GATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
genomic: GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAGgtatggagga ... ttcgatgcagGATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
EST: gi|33657303|gb|CF279917.1|CF279917
EST:     GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAG                         GATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
genomic: GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAGgtatggagga ... ttcgatgcagGATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
EST: gi|58652884|gb|CK041564.1|CK041564
EST:     GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAG                         GATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
genomic: GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAGgtatggagga ... ttcgatgcagGATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
EST: gi|88356495|gb|CI626110.1|CI626110
EST:     GGCGATCTCCGCCTTCAGATCCGGCTCCCAGCCGGCGCTCGCACCCCAAG                         GATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
genomic: GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAGgtatggagga ... ttcgatgcagGATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
EST: gi|88358531|gb|CI617617.1|CI617617
EST:     GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAG                         GATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG
genomic: GGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAGgtatggagga ... ttcgatgcagGATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGG

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: 51 (upstream exon), 57 (downstream exon)
Score: 2

GCGTGGAGGCGTCACCTCCTCGACGGCAACATCTCCCCCACCACCGCGGCGGCGATCTCCGCCTTCAGATCCGCCTCCCAGCCGGCGCTCGCACCCCAAGgtatggagga ... ttcgatgcagGATTGGGTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGGTCAAGGGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTC




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