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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTGGACTAGAGAATGGCATTCAGGAATTCGGGTCCATAAAGACGGTGCTTACATCTGGTTGGCTGCGGGATGAGAACTCTTTCCAACAGCCTGACAAGgtttgctacatttatttgattcactgaaatttgatttttttttttctgaatgaaaatgcacttccaaatatgagatgatgaatggttctttcgtagctcc...

Basic information

species Oryza sativa
transcript LOC_Os03g20420.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g20420.2 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G180889_T01 (Zea mays), 5'ss of exon 5
AGCTGGACTAGAGAATGGCATTCAGGAATTCGGGTCCATAAAGACGGTGCTTACATCTGGTTGGCTGCGGGATGAGAACTCTTTCCAACAGCCTGACAAGgtttgctac-atttatttgattcactgaaatttgatttttttttttctgaatgaaaatgcacttccaaatatgagatgatgaatggttctttcgtagctcc
| ||||  | || | ||  ||||||  ||| || |||||||||||||| || || || ||||||||||||||||||||||| ||||||||||| ||||||||||| |||  |  | ||||| || || |   ||      |    ||   |||   ||    |    |||  |   || |   || || |           
AACTGGGTTGGAAACTGATATTCAGACATTTGGATCCATAAAGACGGTTCTCACGTCGGGTTGGCTGCGGGATGAGAACTCCTTCCAACAGCCCGACAAGgtttgatactgtggacttgatacagtgca---tggcaaactaagatcaatatggtgattacatcttgaattagttgtgttcg-tgattatag---------

upper sequence: LOC_Os03g20420.2 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G120132_T01 (Zea mays), 5'ss of exon 5
AGCTGGACTAGAGAATGGCATTCAGGAATTCGGGTCCATAAAGACGGTGCTTACATCTGGTTGGCTGCGGGATGAGAACTCTTTCCAACAGCCTGACAAGgtttgctac-atttatttgattcactgaaatttgatttttttttttctgaatgaaaatgcacttccaaata----tgagatgatgaatgg-ttctttcgtagctcc
| || |  | || | ||  ||||||  ||| || || |||||||| || || || || ||||||||||||||||||||||| ||||||||||| ||||||||||| |||  || ||||||| || || |     | |        |  |      | | | | |  || ||    ||   |||||  ||  |||||  |       
AACTAGGTTGGAAACTGATATTCAGACATTTGGATCTATAAAGACAGTTCTCACGTCGGGTTGGCTGCGGGATGAGAACTCCTTCCAACAGCCCGACAAGgtttgatactgttgatttgatacaatgcatggcaactaagagcaatacggtaatgattaccccttgaattagttgtgttgtgatgtctgaattcttgtgctatag-

upper sequence: LOC_Os03g20420.2 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G131440_T01 (Zea mays), 5'ss of exon 8
AGCTGGACTAGAGAATGGCATTCAGGAATTCGGGTCCATAAAGACGGTGCTTACATCTGGTTGGCTGCGGGATGAGAACTCTTTCCAACAGCCTGACAAGgtttgctac-atttatttgattcactgaaatttgatttttttttttctgaatgaaaatgcacttccaaata----tgagatgatgaatggttctttcgtagctcc--
| | ||  | || | ||  ||||||  ||| || |||||||||||||| || |  || ||||||||||||||||||||||| ||||||||||| ||||||||||| ||   |  ||||||| |   | |     | |        |  |      | | | | |  |||||    ||   |||||  ||   || | || |||    
AACAGGGTTGGAAACTGATATTCAGACATTTGGATCCATAAAGACGGTTCTCATGTCGGGTTGGCTGCGGGATGAGAACTCCTTCCAACAGCCCGACAAGgtttgatattgtcgatttgatacgacgcatggcaactaagagcaatacggtaatgattaccccttgaaatagttgtgttgtgatgtctgaa-ctcttgt-gctatag

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|22306425|gb|BQ907647.1|BQ907647
EST:     AACATCTGGTT-GCTCGCGGGATGAGAACTCTTTCCAACAGCCTGACAAG                         GT-GTGCCGGCGGCAAGCCCCATAACCAACGCGGGCGAGCAGATGGGTGTC
genomic: TACATCTGGTTGGCT-GCGGGATGAGAACTCTTTCCAACAGCCTGACAAGgtttgctaca ... aatgctacagGTGGTGCCGGCGGCAAGCCCCATAACCAACGCGGGCGAGAAGATGGGTGTC
EST: gi|55411122|gb|CV723498.1|CV723498
EST:     TTACATCTGGTTGGCTGCGGGATGAGAACTCTTTCCAACAGCCTGACAAG                         GTGGTGCCGGCGGCAAGCCCCATAACCAACGCGGGCGAGAAGATGGGTGTC
genomic: TTACATCTGGTTGGCTGCGGGATGAGAACTCTTTCCAACAGCCTGACAAGgtttgctaca ... aatgctacagGTGGTGCCGGCGGCAAGCCCCATAACCAACGCGGGCGAGAAGATGGGTGTC
EST: gi|86437525|gb|CI119247.1|CI119247
EST:     TTACATCTGGTTGGCTGCGGGATGAGAACTCTTTCCAACAGCCTGACAAG                         GTGGTGCCGGCGGCAAGCCCCATAACCAACGCGGGCGAGAAGATGGGTGTC
genomic: TTACATCTGGTTGGCTGCGGGATGAGAACTCTTTCCAACAGCCTGACAAGgtttgctaca ... aatgctacagGTGGTGCCGGCGGCAAGCCCCATAACCAACGCGGGCGAGAAGATGGGTGTC
EST: gi|29680538|gb|CB676813.1|CB676813
EST:     TTACATCTGGTTGGCTGCGGGATGAGAACTCTTTCCAACAGCCTGACAAG                         GTGGTGCCGGCGGCAAGCCCCATAACCAACGCGGGCGAGAAGATGGGTGTC
genomic: TTACATCTGGTTGGCTGCGGGATGAGAACTCTTTCCAACAGCCTGACAAGgtttgctaca ... aatgctacagGTGGTGCCGGCGGCAAGCCCCATAACCAACGCGGGCGAGAAGATGGGTGTC
EST: gi|86528047|gb|CI168253.1|CI168253
EST:     CAGCCTGACAAG                         GTGGTTCCGGCGGCAAGCCCCATAACCAACGCGGGCGAGAAGATGGGTGTC
genomic: CAGCCTGACAAGgtttgctaca ... aatgctacagGTGGTGCCGGCGGCAAGCCCCATAACCAACGCGGGCGAGAAGATGGGTGTC
EST: gi|29645169|gb|CB650176.1|CB650176
EST:     TTACATCTGGTTGGCTGCGGGATGAGAACTCTTTCCAACAGCCTGACAAG                         GTGGTGCCGGCGGCAAGCCCCATAACCAACGCGGGCGAGAAGATGGGTGTC
genomic: TTACATCTGGTTGGCTGCGGGATGAGAACTCTTTCCAACAGCCTGACAAGgtttgctaca ... aatgctacagGTGGTGCCGGCGGCAAGCCCCATAACCAACGCGGGCGAGAAGATGGGTGTC
EST: gi|29676177|gb|CB672452.1|CB672452
EST:     TTACATCTGGTTGGCTGCGGGATGAGAACTCTTTCCAACAGCCTGACAAG                         GTGGTGCCGGCGGCAAGCCCCATAACCAACGCGGGCGAGAAGATGGGTGTC
genomic: TTACATCTGGTTGGCTGCGGGATGAGAACTCTTTCCAACAGCCTGACAAGgtttgctaca ... aatgctacagGTGGTGCCGGCGGCAAGCCCCATAACCAACGCGGGCGAGAAGATGGGTGTC

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: 69 (upstream exon), 29 (downstream exon)
Score: 5

AGCTGGACTAGAGAATGGCATTCAGGAATTCGGGTCCATAAAGACGGTGCTTACATCTGGTTGGCTGCGGGATGAGAACTCTTTCCAACAGCCTGACAAGgtttgctaca ... aatgctacagGTGGTGCCGGCGGCAAGCCCCATAACCAACGCGGGCGAGAAGATGGGTGTCATTGTGGATCCATACTCCCTCACCTCGTTTGATCTCCTCCTGGACACCA




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