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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtataaataacatgtttttatcttagaatctgatatgtggcaactctttctctagttttatgcgccttgacaaatctcattccttgataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT

Basic information

species Oryza sativa
transcript LOC_Os02g52860.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g52860.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G152827_T01 (Zea mays), 3'ss of exon 2
gtaagtataaataacatgtttttatcttagaatctgatatgtggcaactctttctctagttttatgcgccttgacaaatctcattccttgataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
       |||  ||  ||  | ||    | ||| |  |   |    |||     ||| |   | ||  |    | |  |||   | ||| ||| |   ||||| |||||||||||||||||||| |||||||| || || ||||
------gtaagcaatttggctcta---aaaaatatcgt---tcaagacttgacttctggccatgtgtcctaatatagctcttgctgcttaatatttttagGCTCTACAAGGGAATTGTTCCTCTCTGGGGTCGTCAGATTCCTT

upper sequence: LOC_Os02g52860.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G015401_T01 (Zea mays), 3'ss of exon 2
gtaagtataaataacatgtttttatcttagaatctgatatgtggcaactctttctctagttttatgcgccttgacaaatctcattccttgataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
       |||  ||  ||  | ||    | ||  |    | |    |||     ||| |   | ||  |    | |  |||   | ||| ||| |   ||||| |||||||||||||||||||| |||||||| || || ||||
------gtaagcaaattggctcta----aaaaaatatcgt-tcaagacttggcttctggccatgtgtcctaatatagctcttgctgcttaatatttttagGCTCTACAAGGGAATTGTTCCTCTCTGGGGTCGTCAGATTCCTT

upper sequence: LOC_Os02g52860.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G060630_T01 (Zea mays), 3'ss of exon 2
gtaagtataaataacatgtttttatcttag-aatctgatatgtggcaactctttctctagttttatgcgccttgacaaatctcattccttgataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
||||| | || |     | |   |  |||   || | ||   | |  |||   | ||| |    ||  ||| | |||  ||||| | ||| |||||   |||||||||||||||||||||||||| |||||||| || || ||||
gtaagca-aattggttagctagaaaattattgatttcatgatttgagacttggtttctggcc--atctgccctaacatctctcactgcttaataattttagGCTTTACAAGGGAATTGTTCCTCTCTGGGGTCGTCAGATTCCTT

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|116875543|gb|EC366051.1|EC366051
EST:     GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGG                         GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
genomic: GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataa ... ataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
EST: gi|218484707|gb|FG949606.1|FG949606
EST:     GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGG                         GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
genomic: GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataa ... ataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
EST: gi|29677043|gb|CB673318.1|CB673318
EST:     GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGG                         GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTTATACTAT
genomic: GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataa ... ataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTTATACTAT
EST: gi|218490441|gb|FG950234.1|FG950234
EST:     GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGG                         GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
genomic: GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataa ... ataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
EST: gi|163928501|gb|EG711386.1|EG711386
EST:     CCCAAGTTCGTCAGATCTGAAGGCGCTCTTGG                         GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
genomic: CCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataa ... ataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
EST: gi|218505349|gb|FG953708.1|FG953708
EST:     GGACTGAGTGATGGGCTCCCCAAGTTCGTTAGATCTGAAGGCGCTCTTGG                         GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
genomic: GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataa ... ataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
EST: gi|58680384|gb|CK069071.1|CK069071
EST:     AGGCGCTCTTGG                         GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
genomic: AGGCGCTCTTGGgtaagtataa ... ataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
EST: gi|66913316|gb|CX100164.1|CX100164
EST:     GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGG                         GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
genomic: GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataa ... ataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
EST: gi|29658502|gb|CB654777.1|CB654777
EST:     GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGG                         GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
genomic: GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataa ... ataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
EST: gi|116874996|gb|EC365504.1|EC365504
EST:     GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGG                         GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
genomic: GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataa ... ataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
EST: gi|14192020|gb|AU184231.1|AU184231
EST:     GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGG                         GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
genomic: GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataa ... ataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
EST: gi|29630079|gb|CB635088.1|CB635088
EST:     GGACTGAGTGATGGGCTCCCCAAGTTCGTTAGATCTGAAGGCGCTCTTGG                         GCTTTACAAGGGAATTGTTCCTCTGAGGGGTCGCCAAATCCCTT
genomic: GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataa ... ataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
EST: gi|29658501|gb|CB654776.1|CB654776
EST:     GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGG                         GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
genomic: GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataa ... ataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
EST: gi|218501146|gb|FG957968.1|FG957968
EST:     GGACTGAGTGATGGGCTCCCCAAGTTCGTTAGATCTGAAGGCGCTCTTGG                         GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
genomic: GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataa ... ataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
EST: gi|163929256|gb|EG713081.1|EG713081
EST:     GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGG                         GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
genomic: GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataa ... ataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
EST: gi|116875503|gb|EC366011.1|EC366011
EST:     GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGG                         GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
genomic: GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataa ... ataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
EST: gi|38470606|gb|CF954737.1|CF954737
EST:     GGACTGAGTGATGGGCTCCCCAAGTTCGTTAGATCTGAAGGCGCTCTTGG                         GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
genomic: GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataa ... ataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT

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: 75 (upstream exon), 75 (downstream exon)
Score: 111

CATTTGAAGCTGTGAAGGTTCGTGTGCAAACCCAACCTGGATTCGCTCGTGGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataa ... ataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactctttctctagttttatgcgccttgacaaatctcattccttgataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
           tagttttat  TA-rich tract