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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttcttttaatatctggaccagtatctattatacattttcatgcacatttgtagggttgtggtccagcgtatgataatacaagtgtattgtaacttgcagTGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTATTTCCTGGTCTTCCACATATATTTCTTCTCTTATGCTTATG

Basic information

species Glycine max
transcript GLYMA08G19970.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G19970.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os03g45770.2 (Oryza sativa), 3'ss of exon 10
gttcttttaatatctggaccagtatctattatacattttcatgcacatttgtagggttgt--ggtccagcgtatgataataca---agtgtattgtaacttgcagTGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTATTTCCTGGTCTTCCACATATATTTCTTCTCTTATGCTTATG
   | ||||| || || | |  | || |  || |||| |||      ||   | |  |      | | |  | |   |||  |   | | |  |||   |||||||||  | ||| | ||||||||| ||||||| || ||||| || |||||||||||| |||| |||||||| || |||||||| ||  | ||||
---catttaacatttgcaac--tttcaagcatgcattatcagaattgttgtcatgcatagcaaattcggtctgtctgaatttactgaattttgtgtcctttgcagTGTGAGGACATCTATATCAATGCAGTTCTTCCCGCGCTTTTTCTTGCTGTATTTCTTGGTTTTCCACATTTACTTCTTCTCGTACACATATG

upper sequence: GLYMA08G19970.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM5G814310_T02 (Zea mays), 3'ss of exon 2
----gttcttttaatatctggaccagtatctattatacattttcatgcacatttgtagggttgtggtccagcgtatgataatacaagtgtattgtaacttgcagTGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTATTTCCTGGTCTTCCACATATATTTCTTCTCTTATGCTTATG--------
    ||    | |||   |  | ||| |   ||  |   |    | | | ||||  | | |  |  | |     ||  | || |     | || |   || |||||| || ||| | ||||| ||| |||||||||| |||||||| |||||||||||  |||| ||||| || || |||||||| ||| | ||||        
gcgggtagcatgaatgcatctatcagaaatgatcttgtgtagg-acgaa-attttcaagctaatcattct-taaatacttatccttaaatctt-tgcttttcagTGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATGGTATGTGT

upper sequence: GLYMA08G19970.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM5G814310_T01 (Zea mays), 3'ss of exon 2
----gttcttttaatatctggaccagtatctattatacattttcatgcacatttgtagggttgtggtccagcgtatgataatacaagtgtattgtaacttgcagTGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTATTTCCTGGTCTTCCACATATATTTCTTCTCTTATGCTTATG
    ||    | |||   |  | ||| |   ||  |   |    | | | ||||  | | |  |  | |     ||  | || |     | || |   || |||||| || ||| | ||||| ||| |||||||||| |||||||| |||||||||||  |||| ||||| || || |||||||| ||| | ||||
gcgggtagcatgaatgcatctatcagaaatgatcttgtgtagg-acgaa-attttcaagctaatcattct-taaatacttatccttaaatctt-tgcttttcagTGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATG

upper sequence: GLYMA08G19970.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G60995.1 (Arabidopsis thaliana), 3'ss of exon 12
-------------------------------gttcttttaatatctggaccagtatct-attata----cattttcatgc--acatttgtagggttgtggtccagcgta-tgataatacaagtgtatt----gtaacttgcagTGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTATTTCCTGGTCTTCCACATATATTTCTTCTCTTATGCTTATG
                               ||  ||  | |||   |  |  |  ||  | |||    || |  || |   |  ||| |   || |  || ||  | | | |||| | |    |||      ||  |||||||||| | ||||||||||| ||||||||||| || || ||||| |||||||| ||| |||| ||||| || ||||||||||| ||||| ||||
gttttggtctcctcttttgcctcagtcacctgtatttccactatgaagctcttttgctcgtgataatctcactgccaagttaaagttttttttgtagctgttcaatggaataataacaaactcttatcctccatatattgcagTGTCAGGACACCAATATCGATGAAGTTCTTCCCGCGTTTCTTCTTGCTGTACTTCTTGGTGTTCCATATTTATTTCTTCTCATATGCATATG

upper sequence: GLYMA08G19970.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S96_202V6.1 (Physcomitrella patens), 3'ss of exon 12
---gttcttttaatatctggaccagtatctattatacattttcatgcacatttgtagggttgtggtccagcgtatgataatacaagtgtattgtaacttgcagTGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTATTTCCTGGTCTTCCACATATATTTCTTCTCTTATGCTTATG
    || |||   ||   ||     ||| |  | |  | ||  | ||    ||  | || | | |||  |||      |      ||   |   |  |||||| ||  | || ||  |||| ||| |||||||||||||||||||||| || |||||| |||  |||||||| || |||||||||||| | || |
gaatttttttctgtaagcggttgtttatttcatttggaattataagcttcctttgacggatattgtcacgcg---agcaccctttgtacttgccattttgcagCGTGAGGACGCCCCTATCGATGCAGTTCTTTCCTCGCTTCTTTTTTCTCTATTTCATGGCTTTCCACATTTACTTCTTCTCTTATACCTACG

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|7589379|gb|AW705154.1|AW705154
EST:     TTCATGGTCTTGATTCTTGTCTGGTTGTGTGAACTTTTTACTCTCATTAG                         TGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTA
genomic: TTCATGGTCTTGATTCTTGTCTGGTTGTGTGAACTTTTTACTCTCATTAGgtctgtttct ... taacttgcagTGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTA
EST: gi|5606329|gb|AI900427.1|AI900427
EST:     TTCATGGTCTTGATTCTTGTCTGGTTGTGTGAACTTTTTACTCTCATTAG                         TGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTNTGCTGTA
genomic: TTCATGGTCTTGATTCTTGTCTGGTTGTGTGAACTTTTTACTCTCATTAGgtctgtttct ... taacttgcagTGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttgtagggttgtggtccagcgtatgataatacaagtgtattgtaacttgcagTGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTATTTCCTGGTCTTCCACATATATTTCTTCTCTTATGCTTATG
                                          ttgtaac  putative branch site (score: 2)
                        tatgataata  TA-rich tract