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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaaaatttgctaagagtatatgtgatcttcaacacaccctctgatacatatgtattattttagtccaacatttgttgtttctataatgttgcagGTCCCTATTAAGTGGCCACAAAGCAGAGATGAGGTATGGAAAGCAAATATCCCACATACTCACCTTGCACACGAGAAATCTGACCAGAATTGGATGGTTG

Basic information

species Glycine max
transcript GLYMA10G32470.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G32470.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 3
gtgaaaatttgctaagagtatatgtgatcttcaacacaccctctgatacatatgtattatt-ttagtccaacatttgttgtttcta-----taatgttgcagGTCCCTATTAAGTGGCCACAAAGCAGAGATGAGGTATGGAAAGCAAATATCCCACATACTCACCTTGCACACGAGAAATCTGACCAGAATTGGATGGTTG
       |  |   |   |||   |       || |     ||   | |  ||||  |||  ||| | || |   |     |  ||     | |  |||||||| || || || |||||| ||||  | |||   || |||||||||||||| || || |||||||||||||| ||||| || ||||||||||||||| |||
--tctgttccgtccaatctatgcctttcaaaaaaaatgttttcaagtgctaatgtcctatccttactacacctcattggactcataaaaattgactttgcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATTCCGCACACTCACCTTGCACATGAGAAGTCAGACCAGAATTGGATGATTG

upper sequence: GLYMA10G32470.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G107629_T03 (Zea mays), 3'ss of exon 4
-gtgaaaatttgct----aagagtatatgtgatcttcaacacaccctctgatacatatgtattattttagtccaacatttgttgtttctataatgttgcagGTCCCTATTAAGTGGCCACAAAGCAGAGATGAGGTATGGAAAGCAAATATCCCACATACTCACCTTGCACACGAGAAATCTGACCAGAATTGGATGGTTG
    || |  |||      ||| |     |  | |   | |     |||| |  || || ||  ||   |  |   ||  |         |  | || ||||||||||| || |||||| ||||  | ||||  |||||||||||||| || ||||| |||||||||||| | ||||| || |||||||| ||||||||||
taataacacgtgccctgacagactgaccttcctatctgaaattagttctgtttgat-tgcatccttgctgagctgtatccgacccacaattttttttccagGTCCCTATAAAATGGCCAAAAAGTCGTGATGTAGTATGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG

upper sequence: GLYMA10G32470.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G575696_T01 (Zea mays), 3'ss of exon 1
--gtga-aaatttgctaagagtatatgtgatc--ttcaacacaccctctgatacatatgtattattttagtccaacatttgttgtttctataatgttgcagGTCCCTATTAAGTGGCCACAAAGCAGAGATGAGGTATGGAAAGCAAATATCCCACATACTCACCTTGCACACGAGAAATCTGACCAGAATTGGATGGTTG
   | | |  |   || | ||  |       |  |  || |     |||| |  || || ||  ||   |  |   ||  | |     | |  | || |||||||| || || |||||| ||||  | ||||  |||||||||||||| || ||||| |||||||||||| | ||||| || |||||||| ||||||||||
taataacacgtgccctgacagactgaccttccaatctaaaattagttctgtttgat-tgcatccttgctgagctgtatccgatccacatttttttttccagGTCCCCATAAAATGGCCAAAAAGTCGTGATGTAGTATGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG

upper sequence: GLYMA10G32470.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G067764_T02 (Zea mays), 3'ss of exon 3
---gtgaaa-atttgctaagagtatatgtgatcttcaacacaccctctgatacatatgtattattttagtccaacatttgttgtttcta-taatgttgcagGTCCCTATTAAGTGGCCACAAAGCAGAGATGAGGTATGGAAAGCAAATATCCCACATACTCACCTTGCACACGAGAAATCTGACCAGAATTGGATGGTTG
    | | |  |   || |   |  |    ||  ||| |  |   |  | |   | || ||   |     |  |  | | |    || | || | || ||||| ||||| || |||||| ||||  | ||||  || ||||||||||| || ||||| |||||||||||| | ||||| || |||||||| ||||||||||
ggtttaacacgtccactgaccttccactatatactcatctgaaatta-gttctgtttgaatggatccttgctgagttgtatcagatccactattttttcagGTTCCTATAAAATGGCCAAAAAGTCGTGATGTAGTGTGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG

upper sequence: GLYMA10G32470.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G14360.2 (Arabidopsis thaliana), 3'ss of exon 3
gtgaaaatttgctaagagtatatgtgatcttcaacacaccctctgatacatatgta-ttattttagtccaacatttgttgtttctataatgttgcagGTCCCTATTAAGTGGCCACAAAGCAGAGATGAGGTATGGAAAGCAAATATCCCACATACTCACCTTGCACACGAGAAATCTGACCAGAATTGGATGGTTG
               | || |||  ||| |   | |||   |     | ||   || |||   |     |||  || |   ||| |  |||||  |||| || ||||| |||||| ||||||||||||| || |||||||  || || || |||||||| |||||||| ||||| |||||||| || ||||||||||
---------------gtgtctat-cgatatgttatacagttttatcgatatgattagttacgatgacataactgttttctcttccaatatgttttagGTTCCGATTAAATGGCCAAAAAGCAGAGATGAAGTGTGGAAAGTGAACATACCTCATACTCATCTTGCACATGAGAAGTCTGACCAAAACTGGATGGTTG

upper sequence: GLYMA10G32470.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G04430.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgaaa-atttgctaagagtatatg---tgatcttcaacacaccctctgatacatatgtattattttagtccaacatttgttgtttctataatgttgcagGTCCCTATTAAGTGGCCACAAAGCAGAGATGAGGTATGGAAAGCAAATATCCCACATACTCACCTTGCACACGAGAAATCTGACCAGAATTGGATGGTTG
|||  | |||||||       | ||   |||| |   |      |   | ||||| ||| ||  | | ||      ||  |||| |  ||     |  |||| ||||||||||||||  | || |||||||| || ||||||||||| || || || |||||||||||| | ||||| ||||| ||||| ||||||||||
gtgctatatttgctttcttgttttgctttgatttgtgattggttcctggttacat-tgtcttgatattgttt--tgttctttgtattgatttgcgtttagGTTCCTATTAAGTGGCCTAAGAGTAGAGATGAAGTGTGGAAAGCAAACATACCTCACACTCACCTTGCAAAAGAGAAGTCTGATCAGAACTGGATGGTTG

upper sequence: GLYMA10G32470.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 3
gtgaaaatttgctaagagtatatgtgatcttcaacacaccctctgatacatatgtattattttagtccaacatttgt-tgtttctataatgttgcagGTCCCTATTAAGTGGCCACAAAGCAGAGATGAGGTATGGAAAGCAAATATCCCACATACTCACCTTGCACACGAGAAATCTGACCAGAATTGGATGGTTG
            | ||| | |  || | ||| |    |         |||   || ||    |  ||  |  ||||| ||| ||| |    |||||| |||| || ||||||||| ||||||||||||| |||||||||||||| || || ||||||||||||||||| ||||||||||||||||||||||||||||
-----------gtgagaatgtgcgtaagcttaatagta---------acaagggtgttgaagttttcttatttttgtgtgtgtctcttcccttgcagATCCCAATCAAGTGGCCAAAAAGCAGAGATGAAGTATGGAAAGCAAACATACCTCATACTCACCTTGCACATGAGAAATCTGACCAGAATTGGATGGTTG

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|193332782|gb|FK299100.1|FK299100
EST:     CTGCAGAAAGGCGGTACAATTGCTTGATTCCTCCTCCATCTGGATACAAG                         GTCCCTATTAAGTGGCCACAAAGCAGAGATGAGGTATGGAAAGCAAATATC
genomic: CTGCAGAAAGGCGGTACAATTGCTTGATTCCTCCTCCATCTGGATACAAGgtgaaaattt ... aatgttgcagGTCCCTATTAAGTGGCCACAAAGCAGAGATGAGGTATGGAAAGCAAATATC
EST: gi|151395442|gb|EV265319.1|EV265319
EST:     CTGCAGAAAGGCGGTACAATTGCTTGATTCCTCCTCCATCTGGATACAAG                         GTCCCTATTAAGTGGCCACAAAGCAGAGATGAGGTATGGAAAGCAAATATC
genomic: CTGCAGAAAGGCGGTACAATTGCTTGATTCCTCCTCCATCTGGATACAAGgtgaaaattt ... aatgttgcagGTCCCTATTAAGTGGCCACAAAGCAGAGATGAGGTATGGAAAGCAAATATC
EST: gi|8284424|gb|BE021983.1|BE021983
EST:     CTGCAGAAAGGCGGTACAATTGCTTGATTCCTCCTCCATCTGGATACAAG                         GTCCCTATTAAGTGGCCACAAAGCAGAGATGAGGTATGGAAAGCAAATATC
genomic: CTGCAGAAAGGCGGTACAATTGCTTGATTCCTCCTCCATCTGGATACAAGgtgaaaattt ... aatgttgcagGTCCCTATTAAGTGGCCACAAAGCAGAGATGAGGTATGGAAAGCAAATATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgatacatatgtattattttagtccaacatttgttgtttctataatgttgcagGTCCCTATTAAGTGGCCACAAAGCAGAGATGAGGTATGGAAAGCAAATATCCCACATACTCACCTTGCACACGAGAAATCTGACCAGAATTGGATGGTTG
 ctctgat  putative branch site (score: 4)
     tacatatgtattattt  TA-rich tract