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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatgccagttaaactttttctcctggagtattttggcatatagggatagcataacctttccagctcacttgcttttttcttctgatttcccaaattttaacagGCAAATGGTGGATTTATTATGAGTGCAAGCCATAATCCTGGCGGACCTGAATATGATTGGGGTATTAAG

Basic information

species Glycine max
transcript GLYMA20G29230.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G29230.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os10g11140.2 (Oryza sativa), 3'ss of exon 6
gcatgccagttaaactttttctcctggagtattttggcatatagggatagcataacctttccagctcacttgcttttttcttctgatttcccaaattttaacagGCAAATGGTGGATTTATTATGAGTGCAAGCCATAATCCTGGCGGACCTGAATATGATTGGGGTATTAAG
                 | | |  |  |   ||||  |||  |  |   || | ||  |      | | || ||  ||  ||    ||| |  |||| |   |||| |||||||| || || |||||||||||||||||||| || || || ||  ||||||||||||| |||
----------------gtatgttttacacctttttt-cattcattgtgtgcttcactatcttttttaattttctaattcattgcagttttc--aattctgttagGCCAATGGTGGCTTCATCATGAGTGCAAGCCATAATCCAGGTGGGCCAGATAATGATTGGGGTATCAAG

upper sequence: GLYMA20G29230.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G025854_T02 (Zea mays), 3'ss of exon 6
gcatgccagttaaactttttctcctggagtattttggcatatagggatagcataacctttccagctcacttgcttttttcttctgatttcccaaattttaacagGCAAATGGTGGATTTATTATGAGTGCAAGCCATAATCCTGGCGGACCTGAATATGATTGGGGTATTAAG
          ||  ||||   || |  |  | ||    || | |          || ||  |   |   ||  | ||||  | || ||||   | ||||   |||| ||||| || ||||| |||||||||||||||||||| || ||||| ||  |||| ||||||||||||
---------gtatgctttggatcttctataaattaattatgtggatgactatccactttgtccattttttttttatttttgtatggtttctatattttt--tagGCCAATGGCGGCTTTATCATGAGTGCAAGCCATAATCCAGGTGGACCAGACAATGACTGGGGTATTAAG

upper sequence: GLYMA20G29230.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 6
gcatgccagttaaactttttctcctggagtattttggcatatagggatagcataacctttccagctcacttgcttttttcttctgatttcccaa-attttaacagGCAAATGGTGGATTTATTATGAGTGCAAGCCATAATCCTGGCGGACCTGAATATGATTGGGGTATTAAG
                           ||  ||||    ||||    |   | ||  || | || ||  ||  ||  ||  |||  ||    |  ||| | |||||||||||| ||||| |||||||||||||||||||||||||| |||||||||||||| |||||||| |||
------------------------gcaagctttttaatttatatct-tcttacaaagtt-caagatcgtttttttcattactcttgttgataattattctcacagGCAAATGGAGGATTCATTATGAGTGCAAGCCATAATCCTGGTGGACCTGAATATGACTGGGGTATCAAG

upper sequence: GLYMA20G29230.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv16s0022g02320.t01 (Vitis vinifera), 3'ss of exon 6
gcatgccagttaaactttttctcctggagtattttggcatatagggatagcataacctttcca-gctcacttgcttttttcttctg------atttc---ccaaat--tttaacagGCAAATGGTGGATTTATTATGAGTGCAAGCCATAATCCTGGCGGACCTGAATATGATTGGGGTATTAAG
|||   ||  |     |  |       ||  |||  |||| | || |    ||      ||||  ||||  ||| || ||||| |       | ||    ||||||  | |  ||||| ||||| || ||||| ||||||||||||||||||||||| || ||||||||||||||||| || |||
gcaaagcatattcctctccttgttcctagc-tttctgcatct-ggcaccttattttaaatccatactcatctgccttgttcttttataacacaattaaaaccaaataatgtttcagGCCAATGGAGGTTTTATAATGAGTGCAAGCCATAATCCTGGTGGGCCTGAATATGATTGGGGCATCAAG

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|15000098|gb|BI320912.1|BI320912
EST:     AAGGTATTTTGTCAACACCAGCCGTTTCTGCTGTAATAAGAAAGAGAAAG                         GCAAATGGTGGATTTATTATGAGTGCAAGCCATAATCCTGGCGGACCTGAA
genomic: AAGGTATTTTGTCAACACCAGCCGTTTCTGCTGTAATAAGAAAGAGAAAGgcatgccagt ... attttaacagGCAAATGGTGGATTTATTATGAGTGCAAGCCATAATCCTGGCGGACCTGAA
EST: gi|19348237|gb|BM892769.1|BM892769
EST:     AAGGTATTTTGTCAACACCAGCCGTTTCTGCTGTAATAAGAAAGAGAAAG                         GCAAATGGTGGATTTATTATGAGTGCAAGCCATAATCCTGGCGGACCTGAA
genomic: AAGGTATTTTGTCAACACCAGCCGTTTCTGCTGTAATAAGAAAGAGAAAGgcatgccagt ... attttaacagGCAAATGGTGGATTTATTATGAGTGCAAGCCATAATCCTGGCGGACCTGAA
EST: gi|7796595|gb|AW781992.1|AW781992
EST:     AAGGTATTTTGTCAACACCAGCCGTTTCTGCTGTAATAAGAAAGAGAAAG                         GCAAATGGTGGATTTATTATGAGTGCAAGCCATAATCCTGGCGGACCTGAA
genomic: AAGGTATTTTGTCAACACCAGCCGTTTCTGCTGTAATAAGAAAGAGAAAGgcatgccagt ... attttaacagGCAAATGGTGGATTTATTATGAGTGCAAGCCATAATCCTGGCGGACCTGAA
EST: gi|17021716|gb|BM092750.1|BM092750
EST:     AAGGTATTTTGTCAACACCAGCCGTTTCTGCTGTAATAAGAAAGAGAAAG                         GCAAATGGTGGATTTATTATGAGTGCAAGCCATAATCCTGGCGGACCTGAA
genomic: AAGGTATTTTGTCAACACCAGCCGTTTCTGCTGTAATAAGAAAGAGAAAGgcatgccagt ... attttaacagGCAAATGGTGGATTTATTATGAGTGCAAGCCATAATCCTGGCGGACCTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcataacctttccagctcacttgcttttttcttctgatttcccaaattttaacagGCAAATGGTGGATTTATTATGAGTGCAAGCCATAATCCTGGCGGACCTGAATATGATTGGGGTATTAAG
                               ttctgat  putative branch site (score: 3)
                                           aaattttaaca  TA-rich tract