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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataaccgttttgatatcttggttttgccggttcgatttctttttgttgcaaaattgtgtaagtttgaaaacttatttatttatttattttatgtttgcagAGTACAAGGTGCACACATACAACAGGAATGGTCTTTGCGCGTTGGGATTTATGGATGATCATTACCCGATTCGGAGTGCGTTTTCTCTTCTCAATCAG

Basic information

species Glycine max
transcript GLYMA09G13840.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G13840.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 1
-----ataaccgttttgatatcttggttttgccggttcgatttctttttgttgcaaaattgtgtaagtttgaaaacttatttatttatttattttatgtttgcagAGTACAAGGTGCACACATACAACAGGAATGGTCTTTGCGCGTTGGGATTTATGGATGATCATTACCCGATTCGGAGTGCGTTTTCTCTTCTCAATCAG
       |  || | |   || || | | |   | |  |     ||    ||||    |  ||| | |       | | |  |    ||    | || |||||||| |||||||| ||| || ||||||||||||||||||||||  | | ||||||||||||||| || ||  | || ||||| ||||||||||| ||| ||
aatctgcagtcgatgtt-cattttcggtctagtgatcaggagaattcagtttgc----tgttgttaatgaacggtcatgtaaacaagttgtcctgatatttgcagAATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAG

upper sequence: GLYMA09G13840.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G387076_T02 (Zea mays), 3'ss of exon 2
ataaccgttttgatatc----ttggttttgccggttcg--atttctttttgttgcaaaattgtgtaagtttgaaaacttatttatttatttattttatgtttgcagAGTACAAGGTGCACACATACAACAGGAATGGTCTTTGCGCGTTGGGATTTATGGATGATCATTACCCGATTCGGAGTGCGTTTTCTCTTCTCAATCAG
|||||  | | | |  |    || | |||   | |  |  ||   |||||| ||   | ||      | |       || |    |    | | || |  || |||| |||||||| ||| |  |||| || ||||| ||||| ||| | | ||| |||||||||||||| ||| | |||||||| ||||||||||| ||||||
ataacattatggctgaccctgtttgctttagagatatggaatacatttttgctgttcatttccactcgctg------ttgtgacgtacaatgtcttttcatttcagAATACAAGGTCCACTCCCACAATAGAAATGGGCTTTGTGCGGTTGCATTCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAG

upper sequence: GLYMA09G13840.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G178244_T01 (Zea mays), 3'ss of exon 1
----ataaccgttttgatatcttggttttgccggttcg--atttctttttgttgcaaaattgtgtaagtttgaaaacttatttatttatttattttatgtttgcagAGTACAAGGTGCACACATACAACAGGAATGGTCTTTGCGCGTTGGGATTTATGGATGATCATTACCCGATTCGGAGTGCGTTTTCTCTTCTCAATCAG
    | |   |  |     | || | ||||  | || |  ||   |||||||||   | ||  | | | |       ||    ||  | |   ||    ||| |||| || ||||| ||| |  ||||||| ||||| ||||| ||| ||| ||||||||||||||| || ||  | || ||||| ||||||||||| ||||||
cataacatatggctgaccctgtttgctttggagatttggaatacatttttgttgtccatttccgcatgct-----gttttgacatacaatctcttcccattt-cagAATATAAGGTTCACTCCCACAACAGAAATGGGCTTTGTGCGGTGGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATCAG

upper sequence: GLYMA09G13840.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G58060.1 (Arabidopsis thaliana), 3'ss of exon 1
---ataacc--gttttgatatcttggttttgccggttcgatttctttttgttgcaaaattgtgtaagtttgaaaacttatttatttatttattttatgtttgcagAGTACAAGGTGCACACATACAACAGGAATGGTCTTTGCGCGTTGGGATTTATGGATGATCATTACCCGATTCGGAGTGCGTTTTCTCTTCTCAATCAG
   ||  ||  | ||| || |||||   ||  |  |   |||  | |      | || ||| |  | ||  |    |  | | |||||||  ||| || ||  |||||||||||| ||| | ||||| || ||||| ||||||||| |||| || ||||| |||||||||||  |||| ||||| || |||||||||||||||
actatgccccggctttaatttcttgcgatt--ctatcttattgttctagtcctcgaatttgggataatt--agggttcgtgtttttattttgtttttggtt-tagAGTACAAGGTTCACGCTTACAATAGAAATGGCCTTTGCGCGGTGGGTTTCATGGACGATCATTACCCTGTTCGAAGTGCTTTCTCTCTTCTCAATCAG

upper sequence: GLYMA09G13840.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G58060.2 (Arabidopsis thaliana), 3'ss of exon 2
ataaccgttttgatatcttggttttgccggttcgatttctttttgttgcaaaattgtgtaagtttgaaaacttatttatttatttattttatgtttgcagAGTACAAGGTGCACACATACAACAGGAATGGTCTTTGCGCGTTGGGATTTATGGATGATCATTACCCGATTCGGAGTGCGTTTTCTCTTCTCAATCAG
                                       || | ||     |||| ||  |   | |    |  | | |||||||  ||| || ||  |||||||||||| ||| | ||||| || ||||| ||||||||| |||| || ||||| |||||||||||  |||| ||||| || |||||||||||||||
--------------------------------------gttctagtcctcgaatt-tgggataattagggttcgtgtttttattttgtttttggtt-tagagtacaagGTTCACGCTTACAATAGAAATGGCCTTTGCGCGGTGGGTTTCATGGACGATCATTACCCTGTTCGAAGTGCTTTCTCTCTTCTCAATCAG

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|298197641|gb|HO045120.1|HO045120
EST:     AGTCGCCAGTCGCACTCCTCAGGGCCAACGCCAATCCGTACAACACGAAG                         AGTACAAGGTGCACACATACAACAGGAATGGTCTTTGCGCGTTGGGATTTA
genomic: AGTCGCCAGTCGCACTCCTCAGGGCCAACGCCAATCCGTACAACACGAAGgtccttcttt ... atgtttgcagAGTACAAGGTGCACACATACAACAGGAATGGTCTTTGCGCGTTGGGATTTA
EST: gi|192313879|gb|FK011083.1|FK011083
EST:     AGTCGCCAGTCGCACTCCTCAGGGCCAACGCCAATCCGTACAACACGAAG                         AGTACAAGGTGCACACATACAACAGGAATGGTCTTTGCGCGTTGGGATTTA
genomic: AGTCGCCAGTCGCACTCCTCAGGGCCAACGCCAATCCGTACAACACGAAGgtccttcttt ... atgtttgcagAGTACAAGGTGCACACATACAACAGGAATGGTCTTTGCGCGTTGGGATTTA
EST: gi|6341489|gb|AW164313.1|AW164313
EST:     GTCGCCAGTNCGCACTCCTCAGGGCCAACGCCAATCCGTACAACACGAAG                         AGTACAAGGTGCACACAT
genomic: GTCGCCAGT-CGCACTCCTCAGGGCCAACGCCAATCCGTACAACACGAAGgtccttcttt ... atgtttgcagAGTACAAGGTGCACACAT
EST: gi|298168934|gb|HO009864.1|HO009864
EST:     AGTCGCCAGTCGCACTCCTCAGGGCCAACGCCAATCCGTACAACACGAAG                         AGTACAAGGTGCACACATACAACAGGAATGGTCTTTGCGCGTTGGGATTTA
genomic: AGTCGCCAGTCGCACTCCTCAGGGCCAACGCCAATCCGTACAACACGAAGgtccttcttt ... atgtttgcagAGTACAAGGTGCACACATACAACAGGAATGGTCTTTGCGCGTTGGGATTTA
EST: gi|298164125|gb|HO013770.1|HO013770
EST:     AGTCGCCAGTCGCACTCCTCAGGGCCAACGCCGATCCGTACAACACGAAG                         AGTACAAGGTGCACACATACAACAGGAATGGTCTTTGCGCGTTGGGATTTA
genomic: AGTCGCCAGTCGCACTCCTCAGGGCCAACGCCAATCCGTACAACACGAAGgtccttcttt ... atgtttgcagAGTACAAGGTGCACACATACAACAGGAATGGTCTTTGCGCGTTGGGATTTA
EST: gi|298163467|gb|HO012200.1|HO012200
EST:     AGTCGCCAGTCGCACTCCTCAGGGCCAACGCCAATCCGTACAACACGAAG                         AGTACAAGGTGCACACATACAACAGGAATGGTCTTTGCGCGTTGGGATTTA
genomic: AGTCGCCAGTCGCACTCCTCAGGGCCAACGCCAATCCGTACAACACGAAGgtccttcttt ... atgtttgcagAGTACAAGGTGCACACATACAACAGGAATGGTCTTTGCGCGTTGGGATTTA
EST: gi|192333542|gb|FK025737.1|FK025737
EST:     AGTCGCCAGTCGCACTCCTCAGGGCCAACGCCAATCCGTACAACACGAAG                         AGTACAAGGTGCACACATACAACAGGAATGGTCTTTGCGCGTTGGGATTTA
genomic: AGTCGCCAGTCGCACTCCTCAGGGCCAACGCCAATCCGTACAACACGAAGgtccttcttt ... atgtttgcagAGTACAAGGTGCACACATACAACAGGAATGGTCTTTGCGCGTTGGGATTTA
EST: gi|298172019|gb|HO021611.1|HO021611
EST:     AGTCGCCAGTCGCACTCCTCAGGGCCAACGCCAATCCGTACAACACGAAG                         AGTACAAGGTGCACACATACAACAGGAATGGTCTTTGCGCGTTGGGATTTA
genomic: AGTCGCCAGTCGCACTCCTCAGGGCCAACGCCAATCCGTACAACACGAAGgtccttcttt ... atgtttgcagAGTACAAGGTGCACACATACAACAGGAATGGTCTTTGCGCGTTGGGATTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcaaaattgtgtaagtttgaaaacttatttatttatttattttatgtttgcagAGTACAAGGTGCACACATACAACAGGAATGGTCTTTGCGCGTTGGGATTTATGGATGATCATTACCCGATTCGGAGTGCGTTTTCTCTTCTCAATCAG
             taagtttgaaaactta  TA-rich tract