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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctttcagttaaatcgtaacattggtgatttggtgccgatggcaattgaattttggctcaagatttctgttttgtgttgtgcttgtatttgttcagGTACGAGAATCTCATCCTGGTGGCCGGAGGCATCGGCATATCACCGTTCCTGGCGATCCTGAGTGACATAATCCATAGGATCGAGGAAGGCAAACCATGC

Basic information

species Oryza sativa
transcript 13113.m00231
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g36720.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G068557_T01 (Zea mays), 3'ss of exon 6
gtgagctttcagttaaatcgtaacattggtgatttggt-gccgatggcaattgaatt--ttggctcaagatttctgttttgtgttgtgcttg-tatttgttcagGTACGAGAATCTCATCCTGGTGGCCGGAGGCATCGGCATATCACCGTTCCTGGCGATCCTGAGTGACATAATCCATAGGATCGAGGAAGGCAAACCATGC
||||| ||||| ||  ||| ||    |    |     | |  |||  |  ||||     |||| | || |||    |  ||  ||  | ||| ||  |||||||||||||||||||| || |||| || |||||||| || ||||| || ||| |||||||| |||| ||||||||||| ||||||||||| ||||| | ||||
gtgagttttcactttgatcctagttctccctaaccattagttgat--ctgttgatgccgttggataaatattaagttcatgacttcggtttgatacgtgttcagGTACGAGAATCTCGTCTTGGTCGCAGGAGGCATTGGAATATCGCCATTCTTGGCGATCTTGAGCGACATAATCCACAGGATCGAGGAGGGCAAGCAATGC
















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|29689376|gb|CB685651.1|CB685651
EST:     ACCGCCTGCGTGGAAGGGCCTTACGGGCATGAATCGCCATACCACCTGAT                         GTACGAGAATCTCATCCTGGTGGCCGGAGGCATCGGCATATCACCGTTCCT
genomic: ACCGCCTGCGTGGAAGGGCCTTACGGGCATGAATCGCCATACCACCTGATgtgagctttc ... atttgttcagGTACGAGAATCTCATCCTGGTGGCCGGAGGCATCGGCATATCACCGTTCCT
EST: gi|58595574|gb|CK006102.1|CK006102
EST:     ACCGCCTGCGTGGAAGGGCCTTACGGGCATGAATCGCCATACCACCTGAT                         GTACGAGAATCTCATCCTGGTGGCCGGAGGCATCGGCATATCACCGTTCCT
genomic: ACCGCCTGCGTGGAAGGGCCTTACGGGCATGAATCGCCATACCACCTGATgtgagctttc ... atttgttcagGTACGAGAATCTCATCCTGGTGGCCGGAGGCATCGGCATATCACCGTTCCT
EST: gi|29645909|gb|CB650916.1|CB650916
EST:     ACCGCCTGCGTGGAAGGGCCTTACGGGCATGAATCGCCATACCACCTGAT                         GTACGAGAATCTCATCCTGGTGGCCGGAGGCATCGGCATATCACCGTTCCT
genomic: ACCGCCTGCGTGGAAGGGCCTTACGGGCATGAATCGCCATACCACCTGATgtgagctttc ... atttgttcagGTACGAGAATCTCATCCTGGTGGCCGGAGGCATCGGCATATCACCGTTCCT
EST: gi|29685490|gb|CB681765.1|CB681765
EST:     ACCGCCTGCGTGGAAGGGCCTTACGGGCATGAATCGCCATACCACCTGAT                         GTACGAGAATCTCATCCTGGTGGCCGGAGGCATCGGCATATCACCGTTCCT
genomic: ACCGCCTGCGTGGAAGGGCCTTACGGGCATGAATCGCCATACCACCTGATgtgagctttc ... atttgttcagGTACGAGAATCTCATCCTGGTGGCCGGAGGCATCGGCATATCACCGTTCCT
EST: gi|25798304|gb|CA754265.1|CA754265
EST:     ACCGCCTGCGTGGAAGGGCCTTACGGGCATGAATCGCCATACCACCTGAT                         GTACGAGAATCTCATCCTGGTGGCCGGAGGCATCGGCATATCACCTTTCCT
genomic: ACCGCCTGCGTGGAAGGGCCTTACGGGCATGAATCGCCATACCACCTGATgtgagctttc ... atttgttcagGTACGAGAATCTCATCCTGGTGGCCGGAGGCATCGGCATATCACCGTTCCT

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), 71 (downstream exon)
Score: 90

ATGCCCAGGAACAGGGCAGGAATGGCTCTGAGTCAGAGACCGGCCGGATCACCGCCTGCGTGGAAGGGCCTTACGGGCATGAATCGCCATACCACCTGATgtgagctttc ... atttgttcagGTACGAGAATCTCATCCTGGTGGCCGGAGGCATCGGCATATCACCGTTCCTGGCGATCCTGAGTGACATAATCCATAGGATCGAGGAAGGCAAACCATGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaattgaattttggctcaagatttctgttttgtgttgtgcttgtatttgttcagGTACGAGAATCTCATCCTGGTGGCCGGAGGCATCGGCATATCACCGTTCCTGGCGATCCTGAGTGACATAATCCATAGGATCGAGGAAGGCAAACCATGC
                                              tttgttc  CT-rich tract
     tgaatttt  TA-rich tract