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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcgctcacctcactgcttcttcttcttcttcttccctcggtctccgggacttgcttgtctcaccctttctctcttgttttctttcttcttcttcttccagGTGCTCTCCATGTTCTTGGATCGCGGGGCGCCGCCGGACGCGGTGAATCGGCACAAGCAG

Basic information

species Oryza sativa
transcript LOC_Os05g02130.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g02130.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G069162_T03 (Zea mays), 3'ss of exon 1
gtcgctcacct--cactgcttcttcttcttcttcttccctcggtctccgggacttgcttgtctcaccctttctctcttgttttctttcttcttcttcttccagGTGCTCTCCATGTTCTTGGATCGCGGGGCGCCGCCGGACGCGGTGAATCGGCACAAGCAG
||| |||  |   | | || ||| ||||  || |   ||||   ||| ||  ||       |  |||    ||| ||    | | | | ||| |||| | |||||||| || ||| ||||||||| ||||| ||||||||||| |||||||||||||||||||
gtccctccgccgccgccgcctct-cttcagctgcgctcctcatcctcgggacctgagccagccgaccac--ctcgctcacctccctccgtctccttcctgcagGTGCTGTCAATGGTCTTGGATCACGGGGTGCCGCCGGACGTGGTGAATCGGCACAAGCAG

upper sequence: LOC_Os05g02130.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G141922_T01 (Zea mays), 3'ss of exon 1
gtcgctcacctcactgcttcttcttcttcttcttccctcggtctccgggacttgcttgtctcaccctttctctcttgttttctttcttcttcttcttccagGTGCTCTCCATGTTCTTGGATCGCGGGGCGCCGCCGGACGCGGTGAATCGGCACAAGCAG
||  |||  |||||||||   |  || |   |   || | | ||| ||  |        |  |||   || |||  || | |   | ||| |||| | |||||| | |||||| ||||||||| ||||| |||||||||||| ||||| ||||||||||||
gtgcctc--ctcactgct--ctgctcctgacccgtccacagcctctggacc------agccaaccacctcgctcacgtctccc--catctccttcatgcagGTGATGTCCATGATCTTGGATCACGGGGTGCCGCCGGACGCCGTGAACCGGCACAAGCAG
















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|58667172|gb|CK055858.1|CK055858
EST:     GCCG-CGCCAATGGCCGCATCGAG                         GTGCTCTCCATGTTCTTGGATCGCGGGGCGCCGCCGGACGCGGTGAATCGG
genomic: GCCGCCGCCAATGGCCGCATCGAGgtcgctcacc ... cttcttccagGTGCTCTCCATGTTCTTGGATCGCGGGGCGCCGCCGGACGCGGTGAATCGG
EST: gi|88367923|gb|CI572644.1|CI572644
EST:     ACGACCGCCTCTCCGTCCTCCACATCGCCGCCGCCAATGGCCGCATCGAG                         GTGCTCTCCATGTTCTTGGATCGCGGGGCGCCGCCGGACGCGGTGAATCGG
genomic: ACGACCGCCTCTCCGTCCTCCACATCGCCGCCGCCAATGGCCGCATCGAGgtcgctcacc ... cttcttccagGTGCTCTCCATGTTCTTGGATCGCGGGGCGCCGCCGGACGCGGTGAATCGG
EST: gi|88368292|gb|CI577563.1|CI577563
EST:     ACGACCGCCTCTCAGTCCTCCACATCGCCGCCGCCAATGGCCGCATCGAG                         GTGCTCTCCATGTTCTTGGATCGGGGGGCGCCGGCGGACGCGGTGAATCGG
genomic: ACGACCGCCTCTCCGTCCTCCACATCGCCGCCGCCAATGGCCGCATCGAGgtcgctcacc ... cttcttccagGTGCTCTCCATGTTCTTGGATCGCGGGGCGCCGCCGGACGCGGTGAATCGG
EST: gi|86908937|gb|CI302648.1|CI302648
EST:     ACGACCGCCTCTCCGTCCTCCACATCGCCGCCGCCAATGGCCGCATCGAG                         GTGCTCTCCATGTTCTTGGATCGCGGGGCGCCGCCGGACGCGGTGAATCGG
genomic: ACGACCGCCTCTCCGTCCTCCACATCGCCGCCGCCAATGGCCGCATCGAGgtcgctcacc ... cttcttccagGTGCTCTCCATGTTCTTGGATCGCGGGGCGCCGCCGGACGCGGTGAATCGG
EST: gi|87011260|gb|CI289530.1|CI289530
EST:     ACGACCGCCTCTCCGTCCTCCACATCGCCGCCGCCAATGGCCGCATCGAG                         GTGCTCTCCATGTTCTTGGATCGCGGGGCGCCGCCGGACGCGGTGAATCGG
genomic: ACGACCGCCTCTCCGTCCTCCACATCGCCGCCGCCAATGGCCGCATCGAGgtcgctcacc ... cttcttccagGTGCTCTCCATGTTCTTGGATCGCGGGGCGCCGCCGGACGCGGTGAATCGG
EST: gi|87015462|gb|CI303068.1|CI303068
EST:     ACGACCGCCTCTCCGTCCTCCACATCGCCGCCGCCAATGGCCGCATCGAG                         GTGCTCTCCATGTTCTTGGATCGCGGGGCGCCGCCGGACGCGGTGAATCGG
genomic: ACGACCGCCTCTCCGTCCTCCACATCGCCGCCGCCAATGGCCGCATCGAGgtcgctcacc ... cttcttccagGTGCTCTCCATGTTCTTGGATCGCGGGGCGCCGCCGGACGCGGTGAATCGG
EST: gi|88403350|gb|CI573073.1|CI573073
EST:     ACGACCGCCTCTCCGTCCTCCACATCGCCGCCGCCAATGGCCGCATCGAG                         GTGCTCTCCATGTTCTTGGATCGCGGGGCGCCGCCGGACGCGGTGAATTGG
genomic: ACGACCGCCTCTCCGTCCTCCACATCGCCGCCGCCAATGGCCGCATCGAGgtcgctcacc ... cttcttccagGTGCTCTCCATGTTCTTGGATCGCGGGGCGCCGCCGGACGCGGTGAATCGG

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), 75 (downstream exon)
Score: 34

GGCCGCCCTCCTCGCCGCCGACCCTTCCCTCGCTCGCCGCGCCACCCTCTACGACCGCCTCTCCGTCCTCCACATCGCCGCCGCCAATGGCCGCATCGAGgtcgctcacc ... cttcttccagGTGCTCTCCATGTTCTTGGATCGCGGGGCGCCGCCGGACGCGGTGAATCGGCACAAGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggacttgcttgtctcaccctttctctcttgttttctttcttcttcttcttccagGTGCTCTCCATGTTCTTGGATCGCGGGGCGCCGCCGGACGCGGTGAATCGGCACAAGCAG
           gtctcac  putative branch site (score: 34)
            tctcaccctttctctc  CT-rich tract
                               ttttcttt  TA-rich tract