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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcctaaattactgttgtgtttagattgtttcttttcctagttttgttaatttcaagaagaaatatctattatctaacatttagttcttcaatttcctcttttgataagGTAAATGAGTCTAAAAATGTTTTGAAGCTTTGTGACTTTGGCAATGCCATGTTTGCTGGTAAAAATGAAGTTACACCATATCTTGTGAGTCGTTTTTATC

Basic information

species Glycine max
transcript GLYMA10G42220.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G42220.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os12g44330.2 (Oryza sativa), 3'ss of exon 8
----gtatgcctaaattactgttgtgtttagattgtttcttttcctagttttgttaatttcaagaagaaatatctattatctaacatttagttcttcaatttcctcttttgataagGTAAATGAGTCTAAAAATGTTTTGAAGCTTTGTGACTTTGGCAATGCCATGTTTGCTGGTAAAAATGAAGTTACACCATATCTTGTGAGTCGTTTTTATC
      |||| | ||| | | || | | | | |||||   |     |||  |  ||   || | |  ||| |||  ||         ||| || ||    ||  | || |  | |||| |||||| |||| |||||  ||||||| ||||| ||||||||||| ||| ||||||| |  || || |||||||| ||||||||||| ||||| ||||
ttgaacatgcttgaat-atttttatttat-gcttgttatatactacagtcattgta---tctacagtaaacatccttt---------ttaattttttgtcttgatattct--ttagGTGAATGAGGCTAAGAATGTGCTGAAGCTCTGTGATTTTGGCAATGCAATGCTTGCTGGAATGAACGAGGTTACACCTTATCTTGTGAGCCGTTTCTATC

upper sequence: GLYMA10G42220.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G151236_T03 (Zea mays), 3'ss of exon 7
gtatgcctaaattactgttgtgtttagattgtttcttttcctagttttgttaatttcaagaagaaatatctattatctaacatttagttcttcaatttcctcttttgataagGTAAATGAGTCTAAAAATGTTTTGAAGCTTTGTGACTTTGGCAATGCCATGTTTGCTGGTAAAAATGAAGTTACACCATATCTTGTGAGTCGTTTTTATC
   | | |||  ||   | | |    |  ||| |     ||     | |    |||       ||||    |   | ||  | |  || | |   ||    | |      |||| |||||| |||| |||||  | ||||| ||||| ||||| ||||| ||| |||||||||  ||||||||||| || |||||||| || ||||| ||||
--cttcttaatataagctcggg----ggctgtcttacccccgcaggtcgagttttttttttttaaattaacaccgtttattactgtgtccattgcttgtaccct------agGTGAATGAGGCTAAGAATGTGCTCAAGCTATGTGATTTTGGGAATGCTATGCTTGCTGGTATGAATGAAGTTACGCCTTATCTTGTTAGCCGTTTCTATC

upper sequence: GLYMA10G42220.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G147811_T01 (Zea mays), 3'ss of exon 8
------------------------------------------------------------------------gtatgcctaaattactgttgtgtttagattgtttcttttcctagttttgttaatttcaagaaga--aatatctattatctaacatttagttcttcaatttcctcttttgataagGTAAATGAGTCTAAAAATGTTTTGAAGCTTTGTGACTTTGGCAATGCCATGTTTGCTGGTAAAAATGAAGTTACACCATATCTTGTGAGTCGTTTTTATC
                                                                         | |   || || |    | | ||| |  | |    |    |  || | |||    ||| | |   |||| | |||    | ||||||  | | || || | | | ||    |||| |||||| |||| |||||  | ||| | ||||| |||||||| || ||| |||||||||  ||||||||||| || |||||||| || ||||| ||||
gtacgccatctttgcttgtcatcatttttaattatagtattattgcaagttctctttctcaacaggaattgcatcttaatacataaaaactattttttggatatgctgtcatttcattcttttacgcacaaaatgcacaataccaatttaacaccatttatgtgtcca-ttgcttgtatt--ctagGTGAATGAGGCTAAGAATGTGCTCAAGGTATGTGATTTTGGCAACGCTATGCTTGCTGGTATGAATGAAGTTACGCCTTATCTTGTCAGCCGTTTCTATC

upper sequence: GLYMA10G42220.1 (Glycine max), 3'ss of exon 13
lower sequence: AT3G25840.1 (Arabidopsis thaliana), 3'ss of exon 8
gtatgcctaaattactgttgtgtttagattgtttcttttcctagttttgttaatttcaagaagaaatatctattatctaacatttagttcttcaatttcctcttttgataagGTAAATGAGTCTAAAAATGTTTTGAAGCTTTGTGACTTTGGCAATGCCATGTTTGCTGGTAAAAATGAAGTTACACCATATCTTGTGAGTCGTTTTTATC
                        |   |      |||   | ||||| |     | ||    | |       | ||||||  || | ||||  |||  |          |||| ||||||   |||||||| || ||||||||||| ||||| ||||| |||||||| || ||||| ||||||||||| |||||||| ||||| |||||  
-----------------------gtcagtcacacttttcattggttttctcctacttaattcaata-----gctttctaactgttgggtctttgattgtcc---------agGTCAATGAGGGGAAAAATGTCTTAAAGCTTTGTGATTTTGGTAATGCAATGTTTGCAGGCAAAAACGAAGTTACACCGTATCTTGTTAGTCGCTTTTACA

upper sequence: GLYMA10G42220.1 (Glycine max), 3'ss of exon 13
lower sequence: AT1G13350.1 (Arabidopsis thaliana), 3'ss of exon 8
gtatgcctaaattactgttgtgtttagattgtttcttttcctagttttgttaatttcaagaagaaatatctattatctaacatttagttcttcaatttcctcttttgataagGTAAATGAGTCTAAAAATGTTTTGAAGCTTTGTGACTTTGGCAATGCCATGTTTGCTGGTAAAAATGAAGTTACACCATATCTTGTGAGTCGTTTTTATC
                        ||   | |   | |   |  ||||      | |     ||   |  ||   | |||| | | ||  |||      ||   ||    |||| ||||||   | |||    || ||||||||||||||||| | ||| ||||||||||||| ||| |||||||||||||||||||| ||||| || ||  
-----------------------gtaagctatacttgtctgtgttttt-----ctcctgcttgatgcacataaattttaacttctggtcgttc------cttgattatccagGTGAATGAGGGAAGAAACACGTTAAAGCTTTGTGACTTTGGTAGTGCAATGTTTGCTGGTACAAACGAAGTTACACCATATCTTGTTAGTCGCTTCTACA

upper sequence: GLYMA10G42220.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv01s0011g03350.t01 (Vitis vinifera), 3'ss of exon 8
gtatgcctaaattactgttgtgtttagattgtttcttttcctagttttgttaatttcaagaagaaatatctattatctaacatttagttcttcaatttcctcttttgataagGTAAATGAGTCTAAAAATGTTTTGAAGCTTTGTGACTTTGGCAATGCCATGTTTGCTGGTAAAAATGAAGTTACACCATATCTTGTGAGTCGTTTTTATC
||| |  | || ||   || | | |  |  ||| | |  | ||||||| |   | | |  |  || | |  |||   |   | |   |  |   ||| |||||||     ||||||||||| | ||||||||  |||| || ||||| ||||| |||||||||||| |||||||||||||| ||||||||||||||||||| || |||||||
gtaggttttaagtatacttttatgtcca--gttgcctgccttagttttttatttgttataataaattttgcattgaattttactatatattc--attgcctctttc----agGTAAATGAGGCCAAAAATGTCCTGAAACTCTGTGATTTTGGTAATGCCATGTTTTCTGGTAAAAATGAAATTACACCATATCTTGTGAGCCGCTTTTATC

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|6913830|gb|AW395360.1|AW395360
EST:     TCCGGAACTGTGGTGTTCTTCATTGTGATATAAAGCCAGATAATATGTTG                         GTAAATGAGTCTAAAAATGTTTTGAAGCTTTGTGACTTTGGCAATGCCATG
genomic: TCCGGAACTGTGGTGTTCTTCATTGTGATATAAAGCCAGATAATATGTTGgtatgcctaa ... ttttgataagGTAAATGAGTCTAAAAATGTTTTGAAGCTTTGTGACTTTGGCAATGCCATG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagaagaaatatctattatctaacatttagttcttcaatttcctcttttgataagGTAAATGAGTCTAAAAATGTTTTGAAGCTTTGTGACTTTGGCAATGCCATGTTTGCTGGTAAAAATGAAGTTACACCATATCTTGTGAGTCGTTTTTATC
                 atctaac  putative branch site (score: 2)
                              ttcttcaatttcctct  putative PPT
      aaatatctattatcta  TA-rich tract