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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaccaccaactaaactaactaactaactaactaagcctttttattatatatactatttgattccttcttctgccttgttatgacaattgctaattttgtttttgcagCTTCTGTGGGGCTGTCATTTTTACAGTTCACTAACATGAACTCAATGAGGAACCTCTTTATTTGTGGCGTTTCCCTCTTCTTAGGTTTGTCCATTCCTGA

Basic information

species Glycine max
transcript GLYMA08G12360.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


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

upper sequence: GLYMA08G12360.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G437859_T04 (Zea mays), 3'ss of exon 12
gtgagtaccaccaactaaactaactaactaactaactaagcctttttattatatatacta-tttgattccttcttctgccttgttatgacaattgctaattttgtttttgcagCTTCTGTGGGGCTGTCATTTTTACAGTTCACTAACATGAACTCAATGAGGAACCTCTTTATTTGTGGCGTTTCCCTCTTCTTAGGTTTGTCCATTCCTGA
                        |    | |    |   | |  | || || |    |  | | || |  |    |||     |  |   |  |||  | |     |  ||||| | ||||||||||| ||  |||||||||||||||||||||| ||| | |||||||||||    ||||| ||| ||||| | ||  ||||| | || ||
----------------------gttggtcatcctgtttc-cttcctgatgatgtgctttggtgtaatgcaatgcaatgctgc-ctgggctgacggcttttctctgactctcagCTGCGGTGGGGCTGTCCTTCCTACAGTTCACTAACATGAACTCCATGCGCAACCTCTTTATCGTCGGCGTCTCCATCTTCCTTGGCCTGTCCGTCCCGGA

upper sequence: GLYMA08G12360.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv10s0003g01460.t01 (Vitis vinifera), 3'ss of exon 12
gtgagtaccaccaactaaactaactaactaactaactaagcctttttattatatatactatttgattccttcttctgccttgttatgac--aattgctaattttgtttttgcagCTTCTGTGGGGCTGTCATTTTTACAGTTCACTAACATGAACTCAATGAGGAACCTCTTTATTTGTGGCGTTTCCCTCTTCTTAGGTTTGTCCATTCCTGA
                            | | ||       |  | | || | |  | |  |  |||| |   | |||  | |  ||    |||   || | ||| |||  |||||||||||||||| |||||||| || || || |||||||||||||||||||||||||| ||    || ||  |  ||||| | |||||||||||||||||
---------------------------gtgagtattagtatcactattttgttttgattcctgtattcttaactttgcaatttggtggttgaatatatactgttgcttt--cagCTTCTGTGGGGCTATCATTTTTGCAATTTACAAACATGAACTCAATGAGGAACCTCTTCATCACGGGTGTGGCTTTCTTCCTGGGTTTGTCCATTCCTGA

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|193585013|gb|FK542416.1|FK542416
EST:     ACCATTCCCCATGTTTGCTGCTGTGTATTGTGTTTTGTTTGGTATTGTGG                         CTTCTGTGGGGCTGTCATTTTTACAGTTCACTAACATGAACTCAATGAGGA
genomic: ACCATTCCCCATGTTTGCTGCTGTGTATTGTGTTTTGTTTGGTATTGTGGgtgagtacca ... gtttttgcagCTTCTGTGGGGCTGTCATTTTTACAGTTCACTAACATGAACTCAATGAGGA
EST: gi|58017520|gb|CX704262.1|CX704262
EST:     ACCATTCCCCATGTTTGCTGCTGTGTATTGTGTTTTGTTTGGTATTGTGG                         CTTCTGTGGGGCTGTCATTTTTACAGTTCACTAACATGAACTCAATGAGGA
genomic: ACCATTCCCCATGTTTGCTGCTGTGTATTGTGTTTTGTTTGGTATTGTGGgtgagtacca ... gtttttgcagCTTCTGTGGGGCTGTCATTTTTACAGTTCACTAACATGAACTCAATGAGGA
EST: gi|58014211|gb|CX700953.1|CX700953
EST:     ACCATTCCCCATGTTTGCTGCTGTGTATTGTGTTTTGTTTGGTATTGTGG                         CTTCTGTGGGGCTGTCATTTTTACAGTTCACTAACATGAACTCAATGAGGA
genomic: ACCATTCCCCATGTTTGCTGCTGTGTATTGTGTTTTGTTTGGTATTGTGGgtgagtacca ... gtttttgcagCTTCTGTGGGGCTGTCATTTTTACAGTTCACTAACATGAACTCAATGAGGA
EST: gi|31473755|gb|CD415783.1|CD415783
EST:     ACCATTCCCCATGTTTGCTGCTGTGTATTGTGTTTTGTTTGGTATTGTGG                         CTTCTGTGGGGCTATCATTTTTACAGTTCACTAACATGAACTCAATGAGGA
genomic: ACCATTCCCCATGTTTGCTGCTGTGTATTGTGTTTTGTTTGGTATTGTGGgtgagtacca ... gtttttgcagCTTCTGTGGGGCTGTCATTTTTACAGTTCACTAACATGAACTCAATGAGGA
EST: gi|58024713|gb|CX711454.1|CX711454
EST:     ACCATTCCCCATGTTTGCTGCTGTGTATTGTGTTTTGTTTGGTATTGTGG                         CTTCTGTGGGGCTGTCATTTTTACAGTTCACTAACATGAACTCAATGAGGA
genomic: ACCATTCCCCATGTTTGCTGCTGTGTATTGTGTTTTGTTTGGTATTGTGGgtgagtacca ... gtttttgcagCTTCTGTGGGGCTGTCATTTTTACAGTTCACTAACATGAACTCAATGAGGA
EST: gi|58018670|gb|CX705412.1|CX705412
EST:     ACCATTCCCCATGTTTGCTGCTGTGTATTGTGTTTTGTTTGGTATTGTGG                         CTTCTGTGGGGCTGTCATTTTTACAGTTCACTAACATGAACTCAATGAGGA
genomic: ACCATTCCCCATGTTTGCTGCTGTGTATTGTGTTTTGTTTGGTATTGTGGgtgagtacca ... gtttttgcagCTTCTGTGGGGCTGTCATTTTTACAGTTCACTAACATGAACTCAATGAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatttgattccttcttctgccttgttatgacaattgctaattttgtttttgcagCTTCTGTGGGGCTGTCATTTTTACAGTTCACTAACATGAACTCAATGAGGAACCTCTTTATTTGTGGCGTTTCCCTCTTCTTAGGTTTGTCCATTCCTGA
                                   tgctaat  putative branch site (score: 2)
                                         ttttgttttt  CT-rich tract
                                      taattttgttttt  TA-rich tract