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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGCGACGGACAGCACCGACATCAACGACTCCAGCATCAACCCGGCCATCAAGTGCGACTGCTCCGACCAGAACAACACAGTGTGCCACATCACCGGGCTgtaagtgtacacgcacacgaggtgttcgacggattgcctagcctgcaatgcgcgcaccttcttgcgctagtgtctctgaccattccaactgaaaagtgttgatcgtgtgattcagttatttttcctcttatctgatgagaaggcggagctaacacattacgtgctgacgcag

Basic information

species Oryza sativa
transcript LOC_Os04g52640.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g52640.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G155837_T02 (Zea mays), 5'ss of exon 2
CGGCGACGGACAGCACCGACATC---AACGACTCCAGCATCAACCCGGCCATCAAGTGCGACTGCTCCGACCAGAACAAC---ACAGTGTGCCACATCACCGGGCTgtaagtgtacacgcacacgaggtgttcgacggattgcctagcctgcaatgcgcgcaccttcttgcgctagtgtctctgaccattccaactgaaaagtgttgatcgtgtgattcagttatttttcctcttatctgatgagaaggcggagctaacacattacgtgctgacgcag
      ||||| ||||  |||||   |||||| |||   |||||||||||||||||||||| ||||||| ||||||||||   || || |||||| |||||  ||||||||||       || || || || || | |     | |     | |  ||| | |||   |||   ||     |||     |     ||||      |    |||                                                                 
------CGGACGGCACGAACATCGACAACGACCCCACTTTCAACCCGGCCATCAAGTGCGAGTGCTCCGTCCAGAACAACCGCACCGTCTGCCACGTCACCAAGCTgtaagtgcttctctacgcg-ggcgtgcgtcaggcgctcga-----cgaaacgcccgcctgactgcctgagccctgctg-tgtctgtgcgtgaatgcacgtagctgtg-----------------------------------------------------------------

upper sequence: LOC_Os04g52640.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G126858_T01 (Zea mays), 5'ss of exon 3
CGGCGACGGACAGCACCGACATCAACGACTCCAGCATCAACCCGGCCATCAAGTGCGACTGCTCCGACCAGAACAACACAGTGTGCCACATCACCGGGCTgtaagtgtacacgcacacgaggtgttcgacggattgcctagcctgcaatgcgcgcaccttcttgcgctagtgtctctgaccattccaactga--aaagtgttgatcgtgtgattcagttatttttcctcttatctgatgagaaggcggagctaacacattacgtgctgacgcag
|||| |||||| ||||   |||| ||| |  ||  || ||||||| |||||||||||||||||||||||| ||||||||  | |||||||| |||| |||||||||||   | |   |  |      ||||||   |   |  | | ||||     ||  | | | |  | | |  ||    |||   ||||  ||| |  ||                                                                       
CGGCCACGGACGGCACGTCCATCTACGCCGACAAAATGAACCCGGGCATCAAGTGCGACTGCTCCGACCACAACAACACCATCTGCCACATTACCGAGCTgtaagtgtctgcacg-gcacgtccacggacgga--actgggtattcgatgctttttcccccctcctcctgaggcgttgggtgttcgtgctgagcaaaatcctg-----------------------------------------------------------------------
















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|88410203|gb|CI575801.1|CI575801
EST:     AAGTGCGACTGCTCCGACCAGAACAACACAGTGTGCCACATCACCGGGCT                         GAAGATATATGACAAGGATGCAACTGGCCAGATACCAGGAGAGCTGCGGAA
genomic: AAGTGCGACTGCTCCGACCAGAACAACACAGTGTGCCACATCACCGGGCTgtaagtgtac ... gctgacgcagGAAGATATATGACAAGGATGCAACTGGCCAGATACCAGGAGAGCTGCGGAA
EST: gi|88380887|gb|CI634912.1|CI634912
EST:     AAGTGCGACTGCTCCGACCAGAACAACACAGTGTGCCACATCACCGGGCT                         GAAGATATATGACAAGGATGCAACTGGCCAGATACCAGGAGAGCTGCGGAA
genomic: AAGTGCGACTGCTCCGACCAGAACAACACAGTGTGCCACATCACCGGGCTgtaagtgtac ... gctgacgcagGAAGATATATGACAAGGATGCAACTGGCCAGATACCAGGAGAGCTGCGGAA
EST: gi|88360881|gb|CI625187.1|CI625187
EST:     AAGTGCGACTGCTCCGACCAGAACAACACAGTGTGCCACATCACCGGGCT                         GAAGATATATGACAAGGATGCAACTGGCCAGATACCAGGAGAGCTGGGGAA
genomic: AAGTGCGACTGCTCCGACCAGAACAACACAGTGTGCCACATCACCGGGCTgtaagtgtac ... gctgacgcagGAAGATATATGACAAGGATGCAACTGGCCAGATACCAGGAGAGCTGCGGAA
EST: gi|88507955|gb|CI435461.1|CI435461
EST:     TGCCACATCACCGGGCT                         GAAGATATATGACAAGGATGCAACTGGCCAGATACCAGGAGAGCTGCGGAA
genomic: TGCCACATCACCGGGCTgtaagtgtac ... gctgacgcagGAAGATATATGACAAGGATGCAACTGGCCAGATACCAGGAGAGCTGCGGAA
EST: gi|88368820|gb|CI649411.1|CI649411
EST:     AAGTGCGACTGCTCCGACCAGAACAACACAGTGTGCCACATCACCGGGCT                         GAAGATATATGACAAGGATGCAACTGGCCAGATACCAGGAGAGCTGCGGAA
genomic: AAGTGCGACTGCTCCGACCAGAACAACACAGTGTGCCACATCACCGGGCTgtaagtgtac ... gctgacgcagGAAGATATATGACAAGGATGCAACTGGCCAGATACCAGGAGAGCTGCGGAA
EST: gi|88326454|gb|CI659885.1|CI659885
EST:     AAGTGCGACTGCTCCGACCAGAACAACACAGTGTGCCACATCACCGGGCT                         GAAGATATATGACAAGGATGCAACTGGCCAGATACCAGGAGAGCTGCGGAA
genomic: AAGTGCGACTGCTCCGACCAGAACAACACAGTGTGCCACATCACCGGGCTgtaagtgtac ... gctgacgcagGAAGATATATGACAAGGATGCAACTGGCCAGATACCAGGAGAGCTGCGGAA
EST: gi|88389754|gb|CI626523.1|CI626523
EST:     AAGTGCGACTGCTCCGACCAGAACAACACAGTGTGCCACATCACCGGGCT                         GAAGATATATGAAAAGGATGCAACTGGCCAGATACCAGGAGAGCTGCGGAA
genomic: AAGTGCGACTGCTCCGACCAGAACAACACAGTGTGCCACATCACCGGGCTgtaagtgtac ... gctgacgcagGAAGATATATGACAAGGATGCAACTGGCCAGATACCAGGAGAGCTGCGGAA
EST: gi|88396823|gb|CI577972.1|CI577972
EST:     AAGTGCGACTGCTCCGACCAGAACAACACAGTGTGCCACATCACCGGGCT                         GAAGATATATGACAAGGATGCAACTGGCCAGATAC-AGGAGAGCTGCGGAA
genomic: AAGTGCGACTGCTCCGACCAGAACAACACAGTGTGCCACATCACCGGGCTgtaagtgtac ... gctgacgcagGAAGATATATGACAAGGATGCAACTGGCCAGATACCAGGAGAGCTGCGGAA

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: 71 (upstream exon), 70 (downstream exon)
Score: 14

CGGCGACGGACAGCACCGACATCAACGACTCCAGCATCAACCCGGCCATCAAGTGCGACTGCTCCGACCAGAACAACACAGTGTGCCACATCACCGGGCTgtaagtgtac ... gctgacgcagGAAGATATATGACAAGGATGCAACTGGCCAGATACCAGGAGAGCTGCGGAACCTCACACATTTAACCCATCTGTATGAACTCTCGGATTTCTTACGTGGA




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