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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgcctcccacccgctaaaaccctagctttcttcttcctcgattcggtttgctccctcgcgctaatcccgctcgatttcgtgtccagCTACGAGTGCAAGCTGTGCCTGACGCTGCACAACAACGAGGGGAACTACCTGGCTCACACGCAGGGGAAGCGGCACCAGACCAACCTCGCCAAGCGTGCC

Basic information

species Oryza sativa
transcript LOC_Os03g15700.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g15700.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G100620_T01 (Zea mays), 3'ss of exon 1
gtactgcctcccacccgctaaaaccct-----agctttcttcttcctcgattcggtttgctccctcgcgctaatcccgctcgatttcgtgtccagCTACGAGTGCAAGCTGTGCCTGACGCTGCACAACAACGAGGGGAACTACCTGGCTCACACGCAGGGGAAGCGGCACCAGACCAACCTCGCCAAGCGTGCC
|||   |  || |  | |||     ||     | ||  |  |   ||||||||| || | ||  | ||||| || | | | |  || ||    ||||| ||||||||||||||||||||||||||||||||||||||||||||||| || |||||||| |||||| ||||||||||||||||||||||||| |||
gtaacccgccctaaaccctagcgtactcttcgaactcgcccccgtctcgattcgcttcgatctat-gcgctgattctgattg--tttgt----agCTATGAGTGCAAGCTGTGCCTGACGCTGCACAACAACGAGGGGAACTACCTAGCCCACACGCAAGGGAAGAGGCACCAGACCAACCTCGCCAAGCGCGCC

upper sequence: LOC_Os03g15700.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G307906_T01 (Zea mays), 3'ss of exon 4
--------------gtactgcctcccacccgctaaaaccctagctttcttcttcctcgattcggtttgctccctcgcgctaatcccgctcgatttcgtgtccagCTACGAGTGCAAGCTGTGCCTGACGCTGCACAACAACGAGGGGAACTACCTGGCTCACACGCAGGGGAAGCGGCACCAGACCAACCTCGCCAAGCGTGCC
                 ||  || ||  |  | ||  | ||  ||  |  |    ||||||||  | | ||  | ||||| || | |||   ||| ||    |||||||||||||||||||||||||||||||||||||| ||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||| |||
gtaacccgccctaaaccctagcttcc-tcttcgaactcgcttactcgcacccggatcgattcgcctcgatctat-gcgctgattctgctt--ttttgt----agCTACGAGTGCAAGCTGTGCCTGACGCTGCACAACAATGAGGGGAACTACCTGGCCCACACGCAGGGGAAGCGGCACCAGACCAACCTCGCCAAGCGCGCC

upper sequence: LOC_Os03g15700.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv08s0007g04710.t01 (Vitis vinifera), 3'ss of exon 1
--gtactgcctcccacccgctaaaaccctagctttcttcttcctcgat---tcggtttgctccctcgcg---ctaatcccgctcgatttcgtg--tccagCTACGAGTGCAAGCTGTGCCTGACGCTGCACAACAACGAGGGGAACTACCTGGCTCACACGCAGGGGAAGCGGCACCAGACCAACCTCGCCAAGCGTGCC
  | |      || |       | || | |   |  ||    |||| |   |   |||  |   | | |    || |       ||||  |    | |||||| ||||| ||||| ||||||||  |||||||||||||||| || ||  |||| ||||| || |||||| |||| ||||| ||  | |||||| | || 
cagaaaataaccctatatatatatactccattctatttggatctcgctattttattttatttttttgtgattttatttttatgtgattgggcaattacagCTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTTGGCCCACACACAAGGGAAGAGGCATCAGACGAATTTGGCCAAGAGAGCT

upper sequence: LOC_Os03g15700.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S318_71V6.1 (Physcomitrella patens), 3'ss of exon 1
-gtactgcctcc-cacccgctaaaaccctagctttcttcttcctcgattcggtttgctccc---tcgcgct-aatcccgctcgattt----cgtgtccagCTACGAGTGCAAGCTGTGCCTGACGCTGCACAACAACGAGGGGAACTACCTGGCTCACACGCAGGGGAAGCGGCACCAGACCAACCTCGCCAAGCGTGCC
  |  | |  |   |   |   | |     | |    |     | ||||  | |   ||     ||  | | |||   |  || |||     |||| ||| || || || ||||| ||  ||||||| |||||||||||||| || || ||||||||||| |||||||| ||||| ||||||||| | || || ||||| 
gatttttctgctgtatgtgtgtagatttgtgatggaatggaaattgattgcgctaagtcgaaaatcttgttgaattttgagcggtttgtgttgtgtgcagTTATGAATGTAAGCTTTGTTTGACGCTCCACAACAACGAGGGTAATTATCTGGCTCACACTCAGGGGAAACGGCATCAGACCAACTTGGCGAAACGTGCA

upper sequence: LOC_Os03g15700.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ15163 (Selaginella moellendorffii), 3'ss of exon 1
-------------gtactgcctcccacccgctaaaaccctagctttcttcttcctcgattcggtttgctccctcgcgctaatcccgctcgatttcgtgtccagCTACGAGTGCAAGCTGTGCCTGACGCTGCACAACAACGAGGGGAACTACCTGGCTCACACGCAGGGGAAGCGGCACCAGACCAACCTCGCCAAGCGTGCC
               | |   | |     |   | |   |    |  || |  |  |||| ||   |      |     ||| ||  | | ||| |    |||||||||||| ||||| ||| |||||||||||||||| ||||| |||||| |||| |||||||| || ||||| |||||||| ||  | |||||||| || 
gtctgtctctctttcatttttttctcttggaggagaatgtccgctgtttttctcgagattgggcgagtgatggcattgaaattcctttggttttgg----cagCTACGAGTGTAAGCTTTGCTTGACGCTGCACAACAATGAGGGAAACTACTTGGCACACACGCAAGGCAAGCGCCACCAGACGAATTTGGCCAAGCGCGCG

upper sequence: LOC_Os03g15700.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ08420 (Selaginella moellendorffii), 3'ss of exon 1
------------gtactgcctcccacccgctaaaaccctagctttcttcttcctcgattcggtttgctccctcgcgct-aatcccgctcgatttcgtgtccagCTACGAGTGCAAGCTGTGCCTGACGCTGCACAACAACGAGGGGAACTACCTGGCTCACACGCAGGGGAAGCGGCACCAGACCAACCTCGCCAAGCGTGCC
             |  ||  |  | |  |  |  |   |  |     | || |||||    |   |     | ||  | ||   |  | | ||| |    |||||||||||| ||||| ||| |||||||||||||||| |||||||||||| |||| |||||||| || ||||| |||||||| ||  | |||||||| || 
gtatgtctctctttcatgtttttctcttgg-aggagaatgtccgctgtttttctcgagattgggcgagtgatggcattgaaattcctttggttttg---gcagCTACGAGTGTAAGCTTTGCTTGACGCTGCACAACAATGAGGGGAACTACTTGGCACACACGCAAGGCAAGCGACACCAGACGAATTTGGCCAAGCGCGCG

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|87022651|gb|CI293541.1|CI293541
EST:     ACCATCGACCTCGCCAAGGACCCCTACTTCATGCGCAACCACCTCGGCAG                         CTACGAGTGCAAGCTGTGCCTGACGCTGCACAACAACGAGGGGAACTACCT
genomic: ACCATCGACCTCGCCAAGGACCCCTACTTCATGCGCAACCACCTCGGCAGgtactgcctc ... tcgtgtccagCTACGAGTGCAAGCTGTGCCTGACGCTGCACAACAACGAGGGGAACTACCT
EST: gi|86899424|gb|CI298202.1|CI298202
EST:     ACCATCGACCTCGCCAAGGACCCCTACTTCATGCGCAACCACCTCGGCAG                         CTACGAGTGCAAGCTGTGCCTGACGCTGCACAACAACGAGGGGAACTACCT
genomic: ACCATCGACCTCGCCAAGGACCCCTACTTCATGCGCAACCACCTCGGCAGgtactgcctc ... tcgtgtccagCTACGAGTGCAAGCTGTGCCTGACGCTGCACAACAACGAGGGGAACTACCT
EST: gi|12622838|gb|AU173051.1|AU173051
EST:     ACCATCGACCTCGCCAAGGACCCCTACTTCATGCGCAACCACCTCGGCAG                         CTACGAGTGCAAGCTGTGCCTGACGCTGCACAACAACGAGGGGAACTACCT
genomic: ACCATCGACCTCGCCAAGGACCCCTACTTCATGCGCAACCACCTCGGCAGgtactgcctc ... tcgtgtccagCTACGAGTGCAAGCTGTGCCTGACGCTGCACAACAACGAGGGGAACTACCT
EST: gi|58676654|gb|CK065341.1|CK065341
EST:     ACCATCGACCTCGCCAAGGACCCCTACTTCATGCGCAACCACCTCGGCAG                         CTACGAGTGCAAGCTGTGCCTGACGCTGCACAACAACGAGGGGAACTACCT
genomic: ACCATCGACCTCGCCAAGGACCCCTACTTCATGCGCAACCACCTCGGCAGgtactgcctc ... tcgtgtccagCTACGAGTGCAAGCTGTGCCTGACGCTGCACAACAACGAGGGGAACTACCT
EST: gi|14191724|gb|AU183935.1|AU183935
EST:     A-NTTTNACCTCGCCAAGGACCCCTACTTCATGCGCAACCACCTCGGCAG                         CTACGAGTGCAAGCTGTGCCTGACGCTGCACAACAACGAGGGGAACTACCT
genomic: ACCATCGACCTCGCCAAGGACCCCTACTTCATGCGCAACCACCTCGGCAGgtactgcctc ... tcgtgtccagCTACGAGTGCAAGCTGTGCCTGACGCTGCACAACAACGAGGGGAACTACCT

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: 54 (upstream exon), 71 (downstream exon)
Score: 44

AGAATGAGGCCATCGACCGGCGGGAGCGCCTCCGCCGCCTCGCCCTCGAGACCATCGACCTCGCCAAGGACCCCTACTTCATGCGCAACCACCTCGGCAGgtactgcctc ... tcgtgtccagCTACGAGTGCAAGCTGTGCCTGACGCTGCACAACAACGAGGGGAACTACCTGGCTCACACGCAGGGGAAGCGGCACCAGACCAACCTCGCCAAGCGTGCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttcctcgattcggtttgctccctcgcgctaatcccgctcgatttcgtgtccagCTACGAGTGCAAGCTGTGCCTGACGCTGCACAACAACGAGGGGAACTACCTGGCTCACACGCAGGGGAAGCGGCACCAGACCAACCTCGCCAAGCGTGCC
                           cgctaat  putative branch site (score: 44)