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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcttatctattcctttcatgcatttttgttgcagtgctgttgcagttaccgcttaccatttatgtctattatgttttgttgcagGCACGCTTCTTCTTCCAACAACTTATATCAGGGGTTAGCTACTGTCATGCAATG

Basic information

species Glycine max
transcript GLYMA20G01240.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G01240.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G081915_T01 (Zea mays), 3'ss of exon 2
-----------------------------------gttcttatctattcc-tttcatgcattt-ttgttg-cagtgctgttgcagttaccgcttaccattta---tgtcta---ttatgttttgttgcagGCACGCTTCTTCTTCCAACAACTTATATCAGGGGTTAGCTACTGTCATGCAATG
                                    ||  |     | |  | |  |||| |  ||| |  | | ||   | | | | |     || | | |   |||| |      | |||  || ||||| || ||||| ||||||||||| ||||||||||| |||||||| ||| | |||
gtccgtctttctctcgctatcatcgaccctgcttgcttgctgctcgtgctgtcttgtgcactaattgctatctgcgccactcctgcttcactggactaatcaaactgtcaaagcccctttttcatttcagGCGCGTTTCTTTTTCCAACAACTCATATCAGGGGTCAGCTACTGCCATTCCATG

upper sequence: GLYMA20G01240.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G171435_T02 (Zea mays), 3'ss of exon 3
gttcttatctattcctttcatgcatttttgttgcagtgctgttgcagttaccg-cttaccatttatgtctat-tatgttttgttgcagGCACGCTTCTTCTTCCAACAACTTATATCAGGGGTTAGCTACTGTCATGCAATG
|||  |   |    |||   | ||| ||| ||   |        |  ||     | |||||  | ||  | | ||| | |  || ||||| |||| ||||||||||||||| || ||||| || |||||||| ||| |||||
gtttgtgcttgccacttg-gttcatctttcttcttgacacacctcgttttttatcctaccaaatgtgcgtgtatatatatctttccagGCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCAATG

upper sequence: GLYMA20G01240.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv03s0063g01080.t01 (Vitis vinifera), 3'ss of exon 3
gttcttatctattcctttcatgcatttttgttgcagtgctgttgcagttaccgcttaccatttatgtctattatgttttgttgcagGCACGCTTCTTCTTCCAACAACTTATATCAGGGGTTAGCTACTGTCATGCAATG
||||||||  |      ||||    |||| |   | |    | ||| |   || |||    |||  |    ||  || |  |||||||||| |||||||||||||||||| ||||||| || |||||||||||||| |||
gttcttatgcaacttgctcatttggttttctgttactctcctcgcact---cgtttatggcttaccttctctagcttgtactgcagGCACGTTTCTTCTTCCAACAACTTGTATCAGGAGTCAGCTACTGTCATGCGATG

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|18041406|gb|BM309700.1|BM309700
EST:     GAGAGTTATTTGAGCGGATATGCAATGCAGGACGGTTTAGTGAGGATGAG                         GCACGCTTCTTCTTCCAACAACTTATATCAGGGGTTAGCTACTGTCATGCA
genomic: GAGAGTTATTTGAGCGGATATGCAATGCAGGACGGTTTAGTGAGGATGAGgttcttatct ... tttgttgcagGCACGCTTCTTCTTCCAACAACTTATATCAGGGGTTAGCTACTGTCATGCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcagtgctgttgcagttaccgcttaccatttatgtctattatgttttgttgcagGCACGCTTCTTCTTCCAACAACTTATATCAGGGGTTAGCTACTGTCATGCAATG
                    cgcttac  putative branch site (score: 3)
                                            ttttgtt  putative PPT
                            atttatgtctattat  TA-rich tract