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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcagcccaaacatacatgacaaaatgattttttttcgctttttaaatgtatttaatggacagtacactcattttattgtgtcttcagCTGCTGTGGGACTATCCTTTTTGCAATTCACCAACATGAACTCAATGCGCAACCTCTTCATTGTTGGTGTCTCCCTCTTTCTTGGCTTATCAATACCAGA

Basic information

species Oryza sativa
transcript LOC_Os09g15170.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g15170.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G100484_T03 (Zea mays), 3'ss of exon 11
gtaagcagcccaaacat-acatgaca-aaatgattttttttcgctttttaa-atgtatttaa-tggacagtacactcattttattgtgtcttcagCTGCTGTGGGACTATCCTTTTTGCAATTCACCAACATGAACTCAATGCGCAACCTCTTCATTGTTGGTGTCTCCCTCTTTCTTGGCTTATCAATACCAGA
|||||||  |||| ||| | |  ||| ||||    |||| | ||  | |   ||   || || || | ||   | |  |    |  ||| ||||||||||||||| || |||||| |||| ||||||||||||||||| |||||||| ||||||||  | |||||||| ||||| || || ||||| ||||||||
gtaagca--ccaagcatcatagtacacaaattgccttttctagcaatgtgttatactttaaactgtagagctaattgctacggtcatgtgttcagCTGCTGTGGGGCTCTCCTTTATGCAGTTCACCAACATGAACTCGATGCGCAATCTCTTCATCATCGGTGTCTCACTCTTCCTGGGTTTATCTATACCAGA

upper sequence: LOC_Os09g15170.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA08G12360.1 (Glycine max), 3'ss of exon 13
------gtaagcagcccaaaca--tacatgacaaaatgatttttttt--------cgctttttaaatgtatttaatggacagt----acactcattt-tattgtgtcttcagCTGCTGTGGGACTATCCTTTTTGCAATTCACCAACATGAACTCAATGCGCAACCTCTTCATTGTTGGTGTCTCCCTCTTTCTTGGCTTATCAATACCAGA
         | || |  ||  |  ||  | || || | |   |||||          || ||| | |   | |  ||    ||    ||| |   |  | |||| | | ||||| ||||||| || || ||||| || ||||| ||||||||||||||| | |||||||| |||  ||| || ||||||||  | || || || || || ||
gtgagtaccaccaactaaactaactaactaactaactaagcctttttattatatatactatttgattccttcttctgccttgttatgacaattgctaattttgtttttgcagCTTCTGTGGGGCTGTCATTTTTACAGTTCACTAACATGAACTCAATGAGGAACCTCTTTATTTGTGGCGTTTCCCTCTTCTTAGGTTTGTCCATTCCTGA

upper sequence: LOC_Os09g15170.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA06G06840.1 (Glycine max), 3'ss of exon 11
gtaagcagcccaaacatac--atgacaaaat---gattttttttcgctttttaaatgtatttaatggacagtacactcattttattgtgtcttcagCTGCTGTGGGACTATCCTTTTTGCAATTCACCAACATGAACTCAATGCGCAACCTCTTCATTGTTGGTGTCTCCCTCTTTCTTGGCTTATCAATACCAGA
|| || | | | |    ||  |||    | |       | | || ||||  |  || | ||| |||           || |||  | | | | ||||| ||||||| ||||| || ||||| ||||| ||||||||||||||| | |||||||| ||| |||||||  |||| ||  | || || ||  | || ||
gtgagtatcaccatttcacctatggtttagtttaagcatgtctttgcttcctctatcttttttatga----------caattttctctatttgcagCTTCTGTGGGGCTATCATTCTTGCAGTTCACTAACATGAACTCAATGAGGAACCTCTTTATTCTTGGTGTAGCCCTTTTCTTAGGTTTTTCTGTTCCTGA

upper sequence: LOC_Os09g15170.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA04G06750.1 (Glycine max), 3'ss of exon 11
gtaagcagcccaaacatacatgacaaaatgattttttttcgcttt-ttaaatgtatttaatggacagtacactcattttattgtgtcttcagCTGCTGTGGGACTATCCTTTTTGCAATTCACCAACATGAACTCAATGCGCAACCTCTTCATTGTTGGTGTCTCCCTCTTTCTTGGCTTATCAATACCAGA
|| || | | | |     | ||       | ||     || ||||  |   | ||| | ||    |  |  || ||||| |||      ||||| ||||||| ||||| || ||||| ||||| ||||||||||||||| | |||||||| |||||||||||  |||| ||  | || || ||  | || ||
gtgagtatcaccacttctcctgtggtttagtttaaacatctctttgcttcctctatcttatttctaacaagcttatttttttg------cagCTTCTGTGGGGCTATCATTCTTGCAGTTCACTAACATGAACTCAATGAGGAACCTCTTTATTGTTGGTGTTGCCCTTTTCTTAGGTTTTTCTGTTCCTGA

upper sequence: LOC_Os09g15170.1 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv10s0003g01460.t01 (Vitis vinifera), 3'ss of exon 12
gtaagcagcccaaacatacatgacaaaatgattttttttcgctttttaaatgtatttaatggacagtacactcattttattgtgtcttcagCTGCTGTGGGACTATCCTTTTTGCAATTCACCAACATGAACTCAATGCGCAACCTCTTCATTGTTGGTGTCTCCCTCTTTCTTGGCTTATCAATACCAGA
|| || |     | ||   ||       |||||  | |    || |||| | |      |||    |  |   ||  | |||    ||||||| ||||||| ||||| ||||||||||| || ||||||||||||||| | |||||||||||    |||||  |  |||| || || || || || || ||
gtgagtattagtatcac-tattttgttttgattcctgt---attcttaactttgcaatttggtggttgaatatatactgttgc--tttcagCTTCTGTGGGGCTATCATTTTTGCAATTTACAAACATGAACTCAATGAGGAACCTCTTCATCACGGGTGTGGCTTTCTTCCTGGGTTTGTCCATTCCTGA

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|58602093|gb|CK012621.1|CK012621
EST:     TCCATTCCCAATATTTGCGGCTATATACTGCGTAATGTTTGGCATTGTCG                         CTGCTGTGGGACTATCCTTTTTGCAATTCACCAACATGAACTCAATGCGCA
genomic: TCCATTCCCAATATTTGCGGCTATATACTGCGTAATGTTTGGCATTGTCGgtaagcagcc ... gtgtcttcagCTGCTGTGGGACTATCCTTTTTGCAATTCACCAACATGAACTCAATGCGCA
EST: gi|112785328|gb|EE590478.1|EE590478
EST:     TCCATTCCCAATATTTGCGGCTATATACTGCGTAATGTTTGGCATTGTCG                         CTGCTGTGGGACTATCCTTTTTGCAATTCACCAACATGAACTCAATGCGCA
genomic: TCCATTCCCAATATTTGCGGCTATATACTGCGTAATGTTTGGCATTGTCGgtaagcagcc ... gtgtcttcagCTGCTGTGGGACTATCCTTTTTGCAATTCACCAACATGAACTCAATGCGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcgctttttaaatgtatttaatggacagtacactcattttattgtgtcttcagCTGCTGTGGGACTATCCTTTTTGCAATTCACCAACATGAACTCAATGCGCAACCTCTTCATTGTTGGTGTCTCCCTCTTTCTTGGCTTATCAATACCAGA
                 atttaat  putative branch site (score: 4)
                                              tgtcttc  putative PPT
      tttttaaatgtattta  TA-rich tract