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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcatgtatgttttttttgcacccttactttttttgtctatcatacttttctgaaatctgatcaaatttggactatggtatgtttcaaatatctgctagCGATGGCGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA

Basic information

species Glycine max
transcript GLYMA08G20830.3
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 6
tttcatgtatgttttttttgcacccttactttttttgtctatcatacttttctgaaatctga---tcaaatttggactatggtat-gtttcaaatatctgctagCGATGGCGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
     ||| ||  || | || |||  || |  |     ||    ||  |||   ||   |||   | ||  |   || ||| | |  | |    |  |  | || || || || || | ||||||||| |||||| | |||||||||||||||||||||||||||||||| ||||| ||||||||||||||||| |||||||||
----ctgtgtgagttctctgaacctataatactacctgcttctgtatattttcaaatcatgagcatgaagctaataccatgttctcatattgttttacacccagTGACGGGGAGACATACATATCAGCAGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAACCAAAGCTTTAATATTGTTGATGTGAAGCCTGCA

upper sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 6
tttcatgtatgttttttttgcacccttactttttttgtctatcatacttttctgaaatctgatcaaatttggactatggtatgt--ttcaaatatctgctagCGATGGCGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
 ||     ||||   | |   |  | | |  ||    | ||   |||  ||  ||  | |    |       | | | |  ||   ||    | |  |  || ||||| || |||||||||||||| |||||||| || ||||||||||||||  ||||||||||||| ||||||||||| ||| ||||||| || ||| ||
-tttgctgatgtgcatctcatatacattcgattag-atgtaatgtaccctttcgagttttatgtagtgacatattgttgcctgctcttttttttttcgacagTGATGGTGAGACTTTCATATCAGCAGATGATTTGCGGATAAATCTTTGGAATTTGGAAATTAGCAACCAAAGTTTTAACATTATTGATGTTAAACCTACA

upper sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 6
----tttcatgtatgttttttttgcacccttactttttttgtctatcatacttttctgaaatctgatcaaatttggactatggtatgtttcaaatatctgctagCGATGGCGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
    || |   | ||    |  || |   |  |||   |   || |   | |||| || | |  |    ||| |    |||  | |       || ||  | || ||||| || || || ||||||||||||||||| || ||||||||||||||  ||||||| |||||||||||||| |||||| ||||||| |||||| ||
tatgttgctgatttgcccctcatgtattgtagcttaactgtactttgccatttttttgtattgggtagtaatata---tatattgtaacctctatttccac-agTGATGGTGAGACATTTATATCAGCTGATGATTTGCGGATAAATCTTTGGAATTTGGAAATCAGCAATCAAAGTTTCAATATTATTGATGTTAAGCCTACA

upper sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 6
tttcatgtatgttttttttgcacccttactttttttgtctatcatacttttctg---aaatctg--atcaaatttggactatggtat-gtttcaaatatctgctagCGATGGCGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
     || |||  ||  | |   |     ||||||||  | | ||| ||| |||      | |   |  |   |   || |||   |   ||    |   |   |||||||| ||||| ||||||||||| |||||| | |||||||| ||||||||  | |||||||||||||| || ||||| ||||||||||| || ||||||
-----tgaatgagttaat-gtggctgagttttttttggatcttatattttgctgcctgggtttattactatggtgataccatgtcctcactttgttttgttcacagCGATGGAGAAACGTTCATATCAGCAGATGATCTGCGAATAAACCTTTGGAATTTAGAAATTAGCAATCAGAGCTTTAACATTGTTGATGTGAAACCTGCA

upper sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 6
tttcatgtatgttttttttgcacccttactttttttgtctatcatacttttctgaaatctgatcaaatttggactatggtatgtttcaaatatctgct-----agCGATGGCGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
|| |   | ||    | ||  | | | | | | |    ||  |||  |||| |    ||  ||    |   || |||    | |||  ||| | |  |     || ||||| || || || ||||||||||||||||| || |||||||| |||||  ||||||| |||||||||||||| |||||| ||||||| |||||| ||
ttgctgatttgcacctcttatatcttaaatgtatg---ctgccat-tttttgtattgtcctattgggtagtga-tatatattatttgtaatctttatttcaacagTGATGGTGAGACATTTATATCAGCTGATGATTTGCGGATAAATCTATGGAATTTGGAAATCAGCAATCAAAGTTTCAATATTATTGATGTTAAGCCTACA

upper sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G165418_T04 (Zea mays), 3'ss of exon 6
tttcatgtatgttttttttgcaccctt-actttttttgtctatcata-cttttctgaaatctgatcaaatttggactatggtatgtttcaaatatctgctagCGATGGCGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
 || || |   |      ||||   |  |  |  ||  || || ||| | ||| ||     ||     ||    | | | ||||  ||     |||  | || ||||| || || ||||||||||| |||||| | ||||||||| | |||||| ||||||| | ||  || || ||||| ||||||||||| |||||| ||
-ttaatattcctgcagggtgcagattccaaatacttcttcaatgataacatttgtgggcattgtattgatacatattcttgtattatttgttaatcgac-agTGATGGTGAGACATTCATATCAGCAGATGATCTCCGAATAAATTTATGGAACTTGGAAATAAACAGCCAGAGCTTTAACATTGTTGATGTGAAGCCTACA

upper sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 6
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 6
tttcatgtatgttttttttgcacccttactttttttgtctatcatacttttc--tgaaatctgatcaaatttggactatggtatgtttcaaatatctgcta--gCGATGGCGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
     | |    ||| |    |  |||  |  |  |   | ||| |  ||    || | | |  |     |||   ||  | ||  |||   ||  || ||  | || || ||||| || || || ||||||||| | ||| ||||||| |||||  ||||||||||||| || ||||| |||||||||||||| |||||  ||
----ttattctctttgtcgaaaatcttgttgatcctaaatttcacaacttgtattgcattgttttgttccttgtggtaatgaatcgttcccttaattgttacagTGACGGAGAAACCTTTATTTCGGCTGATGATCTGCGAGTAAATCTCTGGAATTTGGAAATTAGCAACCAGAGTTTCAATATTGTTGATGTTAAGCCCACA

upper sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 6
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 8
tttcatgtatgttttttt-tgcac-ccttactttttttgtctatcatacttttctgaaatctgatcaaatttggactatggtatgtttcaaatatctgctagCGATGGCGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
 |||| ||   | |      | || ||||  |  | ||  ||    | || | ||   || |||| |  ||  |    |  ||  |||    |      |||||| |||||||| || || || ||||||||||| ||||| ||||||||||| ||||||||||||||||||||||| |||||||||||||| |||||||| 
-ttcaagttcctatccaaacggacaccttgttgatattagctcgagttctatactttcat-tgataatgttctgctcctaataatttttctcttataattagCGACGGCGAAACATTTATTTCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCG

upper sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 6
-------tttcatgtatgttttttttgcacccttactttttttgtctatcatacttttctgaaatctgatcaaatttggactatggtatgtttcaaatatctgctagCGATGGCGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
       | | ||| |     |  |   |    ||  || ||| | | || || ||   |   || |  | |||||| |   || || | | ||   | ||| | || ||||| ||||| || ||||||||||||||| | |||||||| ||||||||| ||||||||||||| ||||| || |||||||||||||| |||||||||
gaaagactattatggaaacaatgct---aatggtaacttgtttatttctcttatttgggtacgatttagtgaaattttgctgattgtttctctc---tctct-ccagTGATGGTGAAACATTTATATCAGCTGATGATCTGCGAATAAACCTTTGGAACTTGGAAATTAGCAACCAAAGCTTCAATATTGTTGATGTGAAGCCTGCA

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|193511886|gb|FK469995.1|FK469995
EST:     GTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG                         CGATGGCGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAA
genomic: GTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAGgtgatttgaa ... tatctgctagCGATGGCGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAA
EST: gi|7796415|gb|AW781812.1|AW781812
EST:     GTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG                         CGATGGCGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAA
genomic: GTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAGgtgatttgaa ... tatctgctagCGATGGCGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttttctgaaatctgatcaaatttggactatggtatgtttcaaatatctgctagCGATGGCGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
           atctgat  putative branch site (score: 4)
                                  tatgtttcaaatat  TA-rich tract