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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCGgtaggatttaccattctcctatggattttttccatctttaaactctcacttcggtaatctgcgaatagttgtcatcactagcaataatatttttctttatccaag

Basic information

species Oryza sativa
transcript LOC_Os01g50760.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g50760.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G147721_T01 (Zea mays), 5'ss of exon 6
TCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCGgtaggatttaccattctcctatggattttttcca-tctttaaactctcacttcggtaatctgcgaatagttgtcatcactagcaataatatttttctttatccaag
|| ||||| ||| |||||||||||||||||||| || ||||| || ||||| ||| || |||||| |||   ||  |||  |  || || ||    | | ||     |||| ||   ||   |||  | || ||   |  || |  |||  |      
TCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaagagttaccactct---atatattcctctcagtcatttggatgttaccattctaatttg---atgagtgtggtaacaagt--tcctactcctctcaag-----

upper sequence: LOC_Os01g50760.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G098569_T01 (Zea mays), 5'ss of exon 6
TCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCGgtaggatttaccattctcctatggattttttccatctttaaactctcacttcggtaatctgcgaatagttgtcatcactagcaataatatttttctttatccaag
|||||||||||| |||||||||||||||||||| || |||||||| ||||| ||| || |||    |||   ||  ||| ||  ||       |     |  |  | | |        | ||||      | | |||||  || | ||  || ||||
TCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCTgtaagagttattgctct---atatattcttctcagtc----atctggatgttagcatttca-----atttgttgagtgtggtaataagtttctactccattcaag

upper sequence: LOC_Os01g50760.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv19s0015g01010.t01 (Vitis vinifera), 5'ss of exon 7
TCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCGgtaggatttaccat-tctcctatggattttttccatctttaaactctcacttcggtaatctgcgaatagttgtcatcactagcaataatatttttctttatccaag
|||||||||||||||||||||||| || ||||| |||||||| || ||||| ||| | |   |  | ||| ||| | |   |||   | ||  |  |     ||   | ||       |  |  |  |   ||   |   || ||     |||     
TCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCAgtaagctaagctctctctactaagaacggtttt-gtattccactttattgttaaatcatgctgattttttatttttttttactgaagttacttgaggctat-----

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|27576581|gb|CA999275.1|CA999275
EST:     ACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCG                         GTTGCATGTGCTTTGCTGCTATC
genomic: ACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCGgtaggattta ... tttatccaagGTTGCATGTGCTTTGCTGCTATC
EST: gi|88690724|gb|CI734803.1|CI734803
EST:     ACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCG                         GTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGAT
genomic: ACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCGgtaggattta ... tttatccaagGTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGAT
EST: gi|27577652|gb|CB000347.1|CB000347
EST:     ACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCG                         GTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGAT
genomic: ACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCGgtaggattta ... tttatccaagGTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGAT
EST: gi|27576092|gb|CA998786.1|CA998786
EST:     ACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCG                         GTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGAT
genomic: ACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCGgtaggattta ... tttatccaagGTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGAT
EST: gi|29620886|gb|CB625897.1|CB625897
EST:     ACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCG                         GTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGAT
genomic: ACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCGgtaggattta ... tttatccaagGTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGAT
EST: gi|27576091|gb|CA998785.1|CA998785
EST:     ACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCG                         GTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGAT
genomic: ACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCGgtaggattta ... tttatccaagGTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGAT
EST: gi|29684521|gb|CB680796.1|CB680796
EST:     ACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCG                         GTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGAT
genomic: ACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCGgtaggattta ... tttatccaagGTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGAT
EST: gi|8856728|gb|AU094046.1|AU094046
EST:     ACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCG                         GTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGAT
genomic: ACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCGgtaggattta ... tttatccaagGTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGAT
EST: gi|29688203|gb|CB684478.1|CB684478
EST:     ACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCG                         GTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGAT
genomic: ACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCGgtaggattta ... tttatccaagGTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGAT
EST: gi|27554346|gb|CA998246.1|CA998246
EST:     ACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCG                         GTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGAT
genomic: ACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCGgtaggattta ... tttatccaagGTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGAT
EST: gi|58681411|gb|CK070098.1|CK070098
EST:     TTACTACTCATTCTATCTTCCG                         GTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGAT
genomic: TTACTACTCATTCTATCTTCCGgtaggattta ... tttatccaagGTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGAT
EST: gi|86521107|gb|CI161313.1|CI161313
EST:     GCTTACTACTCATTCTATCTTCCG                         GTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGAT
genomic: GCTTACTACTCATTCTATCTTCCGgtaggattta ... tttatccaagGTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGAT
EST: gi|29684202|gb|CB680477.1|CB680477
EST:     ACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCG                         GTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGAT
genomic: ACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCGgtaggattta ... tttatccaagGTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGAT

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: 52 (upstream exon), 75 (downstream exon)
Score: 114

TCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCGgtaggattta ... tttatccaagGTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGATGTTAAGAACATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAG




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