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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtatcaccacttctcctgtggtttagtttaaacatctctttgcttcctctatcttatttctaacaagcttatttttttgcagCTTCTGTGGGGCTATCATTCTTGCAGTTCACTAACATGAACTCAATGAGGAACCTCTTTATTGTTGGTGTTGCCCTTTTCTTAGGTTTTTCTGTTCCTGA

Basic information

species Glycine max
transcript GLYMA04G06750.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


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

upper sequence: GLYMA04G06750.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os01g55500.2 (Oryza sativa), 3'ss of exon 11
gtgagtatcaccacttctcctgtggtttagtttaaacatctctttgcttcctctatcttatttctaacaagcttatttt--tttgcagCTTCTGTGGGGCTATCATTCTTGCAGTTCACTAACATGAACTCAATGAGGAACCTCTTTATTGTTGGTGTTGCCCTTTTCTTAGGTTTTTCTGTTCCTGA
||  ||  | |  |  |  |||  |    |  |||| |   |  || ||    | |  | |  |  |   ||||  |||   || ||||  | |||||||| || ||||||||||| |||||||||||||| ||| | ||||||||||| || |||||  || | ||  | ||  | ||||| || ||
gttggttaccctgcgccatctgatgc---gagtaaatacgccactgtttttgttcttgtctcacacatttgctttgtttgactttcagCGGCAGTGGGGCTCTCCTTCTTGCAGTTTACTAACATGAACTCCATGCGCAACCTCTTTATCGTCGGTGTCTCCATCTTTCTTGGCCTATCTGTGCCCGA

upper sequence: GLYMA04G06750.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G437859_T04 (Zea mays), 3'ss of exon 12
gtgagtatcaccacttc--tcctgtggtttagtttaaacatctctttgcttcctctatcttatttctaacaagcttatttt--tttgcagCTTCTGTGGGGCTATCATTCTTGCAGTTCACTAACATGAACTCAATGAGGAACCTCTTTATTGTTGGTGTTGCCCTTTTCTTAGGTTTTTCTGTTCCTGA
||  ||    |   |||  |||||  | |  | ||     |            |    | |    || ||    ||  | |   |  ||||| | |||||||| || ||| | |||||||||||||||||||| ||| | ||||||||||| || || ||  || | ||| | ||  | || || || ||
gttggtcatcctgtttccttcctgatgatgtgctttggtgtaatgcaatgcaatgctgcctggg-ctgacggcttttctctgactctcagCTGCGGTGGGGCTGTCCTTCCTACAGTTCACTAACATGAACTCCATGCGCAACCTCTTTATCGTCGGCGTCTCCATCTTCCTTGGCCTGTCCGTCCCGGA

upper sequence: GLYMA04G06750.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv10s0003g01460.t01 (Vitis vinifera), 3'ss of exon 12
gtgagtatcaccacttctcctgtggtttagtttaaacatctctttgcttcctctatcttatttct-aacaagcttatttttttgcagCTTCTGTGGGGCTATCATTCTTGCAGTTCACTAACATGAACTCAATGAGGAACCTCTTTATTGTTGGTGTTGCCCTTTTCTTAGGTTTTTCTGTTCCTGA
|||||||| |  |   ||  | || |||  ||     || ||||  |||   | || |  |   | || |       ||  || |||||||||||||||||||||| ||||| || || |||||||||||||||||||||||||| ||    ||||| ||  | ||| | ||||| ||  |||||||
gtgagtattagtatcactattttgttttgattcctgtat-tcttaactttg-caatttggtggttgaatatatactgttgctttcagCTTCTGTGGGGCTATCATTTTTGCAATTTACAAACATGAACTCAATGAGGAACCTCTTCATCACGGGTGTGGCTTTCTTCCTGGGTTTGTCCATTCCTGA

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|9564090|gb|BE473599.1|BE473599
EST:     ACCATTCCCCATTTTTGCAGCTGTATACTGTGTTCTGTTTGGCCTTGTGG                         CTTCTGTGGGGCTATCATTCTTGCAGTTCACTAACATGAACTCAATGAGGA
genomic: ACCATTCCCCATTTTTGCAGCTGTATACTGTGTTCTGTTTGGCCTTGTGGgtgagtatca ... ttttttgcagCTTCTGTGGGGCTATCATTCTTGCAGTTCACTAACATGAACTCAATGAGGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaacatctctttgcttcctctatcttatttctaacaagcttatttttttgcagCTTCTGTGGGGCTATCATTCTTGCAGTTCACTAACATGAACTCAATGAGGAACCTCTTTATTGTTGGTGTTGCCCTTTTCTTAGGTTTTTCTGTTCCTGA
                              ttctaac  putative branch site (score: 1)
                                        cttattttttt  putative PPT
                      tatcttatttctaa  TA-rich tract