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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTTGCGTCATACATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCCATCAATCTCAAGgttagctcttccatccaacctgcgccattgcagactgataggcagcatgataccataatccaaccattccacttttgctaatcaacataccaccatgaaaaatgcag

Basic information

species Oryza sativa
transcript LOC_Os10g35960.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g35960.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G085747_T01 (Zea mays), 5'ss of exon 17
CCTTGCGTCATACATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCCATCAATCTCAAGgttagctct--tccatccaacctgcg----ccattgcagactgataggcagcatgataccata---atccaacc---attccacttttgctaatcaac--ataccaccatgaaaaatgcag----------
||| || ||||||||||||||||| |||||||||||||| |||||||| || ||  |||| ||||  |||||  ||  | |    | |     |||  | |  ||| || |    |  | |||| |   || ||| |   ||    ||||| |   |||||  ||    | || | ||   |            
CCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAGgtgggctctgctctgtgctggattcaacacccaccgaatcctgttacgacttaccacaccacaccgatgcaatcggtatcttcctttttcatttcaactgatggtccaataacaaccaccaaaccctgcag
















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|88228130|gb|CI227610.1|CI227610
EST:     ATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCCATCAATCTCAAG                         TATCAGGCACATCACCGCACGTGTCGGCGCCGCAGTCGTCCGTGCCGCTGT
genomic: ATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCCATCAATCTCAAGgttagctctt ... aaaaatgcagTATCAGGCACATCACCGCACGTGTCGGCGCCGCAGTCGTCCGTGCCGCTGT
EST: gi|58610908|gb|CK038620.1|CK038620
EST:     ATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCCATCAATCTCAAG                         TATCAGGCACATCACCGCACGTGTCGGCGCCGCAGTCGTCCGTGCCGCTGT
genomic: ATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCCATCAATCTCAAGgttagctctt ... aaaaatgcagTATCAGGCACATCACCGCACGTGTCGGCGCCGCAGTCGTCCGTGCCGCTGT
EST: gi|29664102|gb|CB660377.1|CB660377
EST:     ATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCCATCAATCTCAAG                         TATCAGGCACATCACCGCACGTGTCGGCGCCGCAGTCGTCCGTGCCGCTGT
genomic: ATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCCATCAATCTCAAGgttagctctt ... aaaaatgcagTATCAGGCACATCACCGCACGTGTCGGCGCCGCAGTCGTCCGTGCCGCTGT
EST: gi|29615205|gb|CB620218.1|CB620218
EST:     ATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCCATCAATCTCAAG                         TATCAGGCACATCACCGCACGTGTCGGCGCCGCAGTCGTCCGTGCCGCTGT
genomic: ATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCCATCAATCTCAAGgttagctctt ... aaaaatgcagTATCAGGCACATCACCGCACGTGTCGGCGCCGCAGTCGTCCGTGCCGCTGT
EST: gi|29671881|gb|CB668156.1|CB668156
EST:     ATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCCATCAATCTCAAG                         TATCAGGCACATCACCGCACGTGTCGGCGCCGCAGTCGTCCGTGCCGCTGT
genomic: ATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCCATCAATCTCAAGgttagctctt ... aaaaatgcagTATCAGGCACATCACCGCACGTGTCGGCGCCGCAGTCGTCCGTGCCGCTGT
EST: gi|88225783|gb|CI225699.1|CI225699
EST:     ATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCCATCAATCTCAAG                         TATCAGGCACATCACCGCACGTGTCGGCGCCGCAGTCGTCCGTGCCGCTGT
genomic: ATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCCATCAATCTCAAGgttagctctt ... aaaaatgcagTATCAGGCACATCACCGCACGTGTCGGCGCCGCAGTCGTCCGTGCCGCTGT
EST: gi|29662805|gb|CB659080.1|CB659080
EST:     TCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCCATCAATCTNCA-G                         TATCAGGCACATCACCGCACGTGTCGGCGCCGCAGTCGTCCGTGCCGCTG
genomic: TCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCCATCAATCT-CAAGgttagctctt ... aaaaatgcagTATCAGGCACATCACCGCACGTGTCGGCGCCGCAGTCGTCCGTGCCGCTG
EST: gi|88271063|gb|CI386918.1|CI386918
EST:     ATCACAGACGAT-AAATTCGAAAAGGCATCCTCTTTCCATCAATTTCAAA                         TATCAGGCACATCACCGCACGTGTCGGCGCCGCAGTCGTCCGTGCCGCTGT
genomic: ATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCCATCAATCTCAAGgttagctctt ... aaaaatgcagTATCAGGCACATCACCGCACGTGTCGGCGCCGCAGTCGTCCGTGCCGCTGT

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), 72 (downstream exon)
Score: 73

CCTTGCGTCATACATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCCATCAATCTCAAGgttagctctt ... aaaaatgcagTATCAGGCACATCACCGCACGTGTCGGCGCCGCAGTCGTCCGTGCCGCTGTTGATGAAGATCTGGCCGAGGGGCGTTGTGATGTAGACGCTAGGGACCTC




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