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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatatagcttttggttattctgatggaattatgtgtggtacctgtgttggaagtgtaattgataaaacgtgttgtttatgttggtgtgattggcaatagGTGCCTACAAGTATGTTTCAGAGCTATGGCGCAAGAAGCAGTCTGATGTCATGCGCTTCTTGCAGCGGGTGAGGTGCTGGGAGTATAGGCAGCAACCTTC

Basic information

species Glycine max
transcript GLYMA01G41620.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G41620.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g40180.1 (Oryza sativa), 3'ss of exon 1
---------atatatagcttttggttattctgatggaattatgtgtggta-cctgtgttggaagtgtaattgataaaacgtgttgtttatgttggtgtgattggcaatagGTGCCTACAAGTATGTTTCAGAGCTATGGCGCAAGAAGCAGTCTGATGTCATGCGCTTCTTGCAGCGGGTGAGGTGCTGGGAGTATAGGCAGCAACCTTC
            |    |      |   ||        |  | |   ||  ||         |     ||   |     |    ||      | || |   ||   | |||||| |||||||| || || ||||||||| | | ||||||||| || || ||| | ||| ||||||| ||| ||||||||||||| |||||||| ||  |
gtgagctcctcctccgacgccgcctccctccatcactctcgtctccagtttcccacccctccacctccatctctctcctgatccgtcctccgtcgttttgctgtgcacagGTGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGGTGCTGGGAGTACAGGCAGCAGCCGGC

upper sequence: GLYMA01G41620.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G034794_T02 (Zea mays), 3'ss of exon 1
atatatagcttttggttattctgatggaattatgtgtggtacctgtgttggaagtgtaattgataaaacgtgttgtttatgttggtgtgattggcaatagGTGCCTACAAGTATGTTTCAGAGCTATGGCGCAAGAAGCAGTCTGATGTCATGCGCTTCTTGCAGCGGGTGAGGTGCTGGGAGTATAGGCAGCAACCTTC
   |  |||| | |  | | | | ||      | |  | | |   ||  |   || | |  | |    ||| |  ||| ||| | ||||       | |||||| |||||||| || || ||||||||||| | ||||||||| ||||| ||||| ||| ||||||| ||| | ||||||||||| |||||||| ||  |
--gtg-agctctcgtatttaccgctgatggcctctccgattcgcatgc-gtgggtcttaccg-tgtgtcgtatcattt-tgtcgctgtggc-----acagGTGCGTACAAGTACGTCTCGGAGCTATGGCGGAGGAAGCAGTCCGATGTGATGCGGTTCGTGCAGCGCGTGCGCTGCTGGGAGTACAGGCAGCAGCCGGC

upper sequence: GLYMA01G41620.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G024354_T01 (Zea mays), 3'ss of exon 1
atatatagcttttggttattctgatggaattatgtgtggtacctgtgttggaagtgtaa-ttgataaaacgtgttgtttatgttggtgtgattggca-atagGTGCCTACAAGTATGTTTCAGAGCTATGGCGCAAGAAGCAGTCTGATGTCATGCGCTTCTTGCAGCGGGTGAGGTGCTGGGAGTATAGGCAGCAACCTTC
                     |||   |||  | ||||||  ||  || | | | | |  ||       ||| |  | | || | || || | | |    ||| || |||||||| || || || |||||| | | ||||||||| || || ||||||||| ||||||| ||| | ||||||||||| |||||||| || ||
--------------------gtgagcaaatgttctgtggtctctccgt-gcaggcgaacctttgcgcgtcgtctc-tctctgatagtctgttcgtcgcgcagGGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGATGCGCTTCGTGCAGCGCGTGCGCTGCTGGGAGTACAGGCAGCAGCCGTC

upper sequence: GLYMA01G41620.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G180724_T01 (Zea mays), 3'ss of exon 1
atatatagcttttggttattctgatggaattatgtgtggtacctgtgttggaagtgtaattgataaaacgtgttgtttatgttggtgtgattggcaatagGTGCCTACAAGTATGTTTCAGAGCTATGGCGCAAGAAGCAGTCTGATGTCATGCGCTTCTTGCAGCGGGTGAGGTGCTGGGAGTATAGGCAGCAACCTTC
   |  || | | || ||              | |  | | |   ||   |   | | |  | ||    |  | |||| |   | ||||         ||| || ||||||||||| || ||| ||||| | | |||||| || || || ||||| ||| ||||||| ||| | ||||||||||| |||||||| ||  |
--gtg-agttctcggctac------aaggccgtctccgattcgcatgcatgggtttttac-ggtatgttgcatcgtttct--cgctgtggc-----gcagGGGCGTACAAGTATGTCTCGGAGTTATGGAGGAGGAAGCAATCCGACGTGATGCGGTTCGTGCAGCGCGTGCGCTGCTGGGAGTACAGGCAGCAGCCGGC

upper sequence: GLYMA01G41620.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G16720.1 (Arabidopsis thaliana), 3'ss of exon 1
-------------------------------------------------atatatagcttttggttattc-tgatggaattatgtgtggtacctgtgttggaagtgtaattgataaaacgtgttgtttatgttggtgtgattggcaatagGTGCCTACAAGTATGTTTCAGAGCTATGGCGCAAGAAGCAGTCTGATGTCATGCGCTTCTTGCAGCGGGTGAGGTGCTGGGAGTATAGGCAGCAACCTTC
                                                  || || | ||  | || | | |  |    | |  ||  ||  ||||   | |  ||| ||||  |||     | | |||   || | ||||||  | ||||||| ||||||||||| || ||||||||| | ||||| ||||| ||||| ||| | ||| | ||| |||| |||||||||||||| || |||||||||||
gtaaatccttcttctccatcccttcttctagatcaaatcctctcgtttcttagatcgattcagcttctccattgtttgttcaaatgatgtttctgttacgtatctgttattg-caaactacttagctta--atgatttgattgata-tagGTGCGTACAAGTATGTATCTGAGCTATGGAGGAAGAAACAGTCCGATGTGATGAGATTCCTCCAGAGGGTTAGGTGCTGGGAGTACAGACAGCAACCTTC

upper sequence: GLYMA01G41620.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0013g02020.t01 (Vitis vinifera), 3'ss of exon 1
----atatatagcttttggttattctgatggaattatgtgtggtacctgtgttggaagtgt---aattgataaaacgtgttgtttatgttggtgtgattggcaatagGTGCCTACAAGTATGTTTCAGAGCTATGGCGCAAGAAGCAGTCTGATGTCATGCGCTTCTTGCAGCGGGTGAGGTGCTGGGAGTATAGGCAGCAACCTTC
      |   ||||||   | | |||  |    |    |      |   | || |   | |   | |||      | |||| ||    ||| |     ||||| |||| || |||||||| || || ||||||||| | |||||||| || ||||| ||| | ||||||||| |||||||||||||||||||| | ||||| |||||
gtaagcaccaagctttccttcactctctttttctctacttccaagcggatattagggttttccgatttgtggcttcctgttattggcattgttcgtggtggcattagGGGCTTACAAGTACGTGTCGGAGCTATGGAGGAAGAAGCAATCCGATGTGATGAGGTTCTTGCAGAGGGTGAGGTGCTGGGAGTATCGCCAGCACCCTTC

upper sequence: GLYMA01G41620.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv15s0021g02480.t01 (Vitis vinifera), 3'ss of exon 1
-----atatatagcttttggttattctgatggaattatgtgtggtacctgtgttggaagtgtaattgataaaacgtgttgtttatgttggtgtgattggcaatagGTGCCTACAAGTATGTTTCAGAGCTATGGCGCAAGAAGCAGTCTGATGTCATGCGCTTCTTGCAGCGGGTGAGGTGCTGGGAGTATAGGCAGCAACCTTC
     ||  |  |  |     | || | | |  ||| | | |  |   | | ||  || |    || ||   |  ||  ||||   | ||| |   ||     ||| || |||| ||||||||| ||  ||||| | ||||||||||| ||||| ||| | ||  ||||| |||| ||||||||||||||| | || || |||||
tgtaaattaactgaatgaaagtgttattaagttattttattttatttttatttttaaattt---tttatttgagttgaggtttt--tcggttttggtgatgtcagGGGCTTACATGTATGTTTCTGAATTATGGAGAAAGAAGCAGTCCGATGTTATGAGGTTTCTGCAGAGGGTCAGGTGCTGGGAGTATCGCCAACACCCTTC

upper sequence: GLYMA01G41620.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S152_141V6.1 (Physcomitrella patens), 3'ss of exon 1
----------------------------------------------------------------------atatatagcttttggttattctgatggaattatgtgtggtac--ctgtgttggaagtgtaattgataaaacgtgttgtttatgttggtgtgattggcaatagGTGCCTACAAGTATGTTTCAGAGCTATGGCGCAAGAAGCAGTCTGATGTCATGCGCTTCTTGCAGCGGGTGAGGTGCTGGGAGTATAGGCAGCAACCTTC
                                                                       | | ||  ||||     |||   | ||  | || |  ||      | | |  || || | ||  |      | || ||| | ||  |   |||  |   |||||| ||||||||  |    ||||| ||| | |||||||||||||||||  |||| ||||||| ||| ||| | ||||||||||| |||||||  ||   
gtattcattcccagctccctctctctctagcgctgcgtagctgcgtagctgcgtttttttattttttttattttttatttttttccctttccttttgaggtttgcgcagtgtgatcgagatctaactggagttttttttttttttttttttttttttttaaatttcctccagGTGCGTACAAGTACATCGAGGAGCTGTGGAGGAAGAAGCAGTCTGATGTGCTGCGTTTCTTGCTGCGTGTGCGCTGCTGGGAGTACAGGCAGCTCCCCGG

upper sequence: GLYMA01G41620.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S34_445V6.1 (Physcomitrella patens), 3'ss of exon 1
---atatatagcttttggttattctga--tggaattatgtgtggtacctgtgttggaagtgtaattgataaaacgtgttgtttatgttggtgtgattggcaatagGTGCCTACAAGTATGTTTCAGAGCTATGGCGCAAGAAGCAGTCTGATGTCATGCGCTTCTTGCAGCGGGTGAGGTGCTGGGAGTATAGGCAGCAACCTTC
    |  |  ||| ||   | |||  |  | || ||  ||  | |    || || |  || | ||||    |  || | || | | ||| |    |||     ||| |||||||||||  ||   ||| | ||||| |||||||||||||||||  |||| || |||| ||| ||| | ||||||||||| |||||||  ||   
ttggtgcaatgctgttcaattttcacaattagagttccgtcggttcggagttttaggtgt-tgattgtctgattgt-tggtatttattgatt---ttgctctcagGCGCCTACAAGTACATTGAGGAGTTGTGGCGGAAGAAGCAGTCTGATGTGCTGCGGTTTTTGCTGCGTGTGCGCTGCTGGGAGTACAGGCAGCTCCCCGG

upper sequence: GLYMA01G41620.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S28_15V6.1 (Physcomitrella patens), 3'ss of exon 1
-atatatagcttttggttattctgatggaattatgtgtggtacctgtgttggaagtgtaattga---taaaacgtgttgtttatgttggtgtgattggcaatagGTGCCTACAAGTATGTTTCAGAGCTATGGCGCAAGAAGCAGTCTGATGTCATGCGCTTCTTGCAGCGGGTGAGGTGCTGGGAGTATAGGCAGCAACCTTC
  |  ||||||    |||   | | ||    |   ||| ||   |||    ||| |||   ||    |     || || ||||| ||| | || || |   |||| || ||||| ||  ||   ||||||||||| ||||||||||| |||||  |||| |||||||  || ||| | ||||||||||| |||||||  ||   
cttcgatagctac--gttgcaccggtgttgcttcatgttgttagtgttggcgaattgtgtatggggtttcggggtcttatttat-ttgttttggtttgtt-tagGGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGTTGCGATTCTTGCTTCGTGTGCGCTGCTGGGAGTACAGGCAGCTTCCCGG

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|8827482|gb|BE211212.1|BE211212
EST:     GGTAGAACCCTTCCACTGTGGTGACTCTGCGATGG                         GTGCCTACAAGTATGTTTCAGAGCTATGGCGCAAGAAGCAGTCTGATGTCA
genomic: GGTAGAACCCTTCCACTGTGGTGACTCTGCGATGGgtactgcctc ... ttggcaatagGTGCCTACAAGTATGTTTCAGAGCTATGGCGCAAGAAGCAGTCTGATGTCA
EST: gi|15287650|gb|BI471541.1|BI471541
EST:     GTAGAACCCTTCCACTGTGGTGACTCTGCGATGG                         GTGCCTACAAGTATGTTTCAGAGCTATGGCGCAAGAAGCAGTCTGATGTCA
genomic: GTAGAACCCTTCCACTGTGGTGACTCTGCGATGGgtactgcctc ... ttggcaatagGTGCCTACAAGTATGTTTCAGAGCTATGGCGCAAGAAGCAGTCTGATGTCA
EST: gi|193429363|gb|FK398511.1|FK398511
EST:     GGCGCGGGTGAGGTAGAACCCTTCCACTGTGGTGACTCTGCGATGG                         GTGCCTACAAGTATGTTTCAGAGCTATGGCGCAAGAAGCAGTCTGATGTCA
genomic: GGCGCGGGTGAGGTAGAACCCTTCCACTGTGGTGACTCTGCGATGGgtactgcctc ... ttggcaatagGTGCCTACAAGTATGTTTCAGAGCTATGGCGCAAGAAGCAGTCTGATGTCA
EST: gi|23729345|gb|BU762755.1|BU762755
EST:     AGGTAGAACCCTTCCACTGTGGTGACTCTGCGATGG                         GTGCCTACAAGTATGTTTCAGAGCTATGGCGCAAGAAGCAGTCTGATGTCA
genomic: AGGTAGAACCCTTCCACTGTGGTGACTCTGCGATGGgtactgcctc ... ttggcaatagGTGCCTACAAGTATGTTTCAGAGCTATGGCGCAAGAAGCAGTCTGATGTCA
EST: gi|7796785|gb|AW782179.1|AW782179
EST:     GCGCGGGTGAGGTAGAACCCTTCCACTGTGGTGACTCTGCGATGG                         GTGCCTACAAGTATGTTTCAGAGCTATGGCGCAAGAAGCAGTCTGATGTCA
genomic: GCGCGGGTGAGGTAGAACCCTTCCACTGTGGTGACTCTGCGATGGgtactgcctc ... ttggcaatagGTGCCTACAAGTATGTTTCAGAGCTATGGCGCAAGAAGCAGTCTGATGTCA
EST: gi|193354576|gb|FK319084.1|FK319084
EST:     GCGGGTGAGGTAGAACCCTTCCACTGTGGTGACTCTGCGATGG                         GTGCCTACAAGTATGTTTCAGAGCTATGGCGCAAGAAGCAGTCTGATGTCA
genomic: GCGGGTGAGGTAGAACCCTTCCACTGTGGTGACTCTGCGATGGgtactgcctc ... ttggcaatagGTGCCTACAAGTATGTTTCAGAGCTATGGCGCAAGAAGCAGTCTGATGTCA
EST: gi|207810578|gb|GD781687.1|GD781687
EST:     GCGGGTGAGGTAGAACCCTTCCACTGTTTGGTTGTACTCTGCGATGG                         GTGCCTACAAGTATGTTTCAGAGCTATGGCGCAAGAAGCAGTCTGATGTCA
genomic: GCGGGTGAGGTAGAACCCTTCCACTG--TGG-TG-ACTCTGCGATGGgtactgcctc ... ttggcaatagGTGCCTACAAGTATGTTTCAGAGCTATGGCGCAAGAAGCAGTCTGATGTCA
EST: gi|14258879|gb|BG881787.1|BG881787
EST:     GGTGAGGTAGAACCCTTCCACTGTGGTGACTCTGCGATGG                         GTGCCTACAAGTATGTTTCAGAGCTATGGCGCAAGAAGCAGTCTGATGTCA
genomic: GGTGAGGTAGAACCCTTCCACTGTGGTGACTCTGCGATGGgtactgcctc ... ttggcaatagGTGCCTACAAGTATGTTTCAGAGCTATGGCGCAAGAAGCAGTCTGATGTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttggaagtgtaattgataaaacgtgttgtttatgttggtgtgattggcaatagGTGCCTACAAGTATGTTTCAGAGCTATGGCGCAAGAAGCAGTCTGATGTCATGCGCTTCTTGCAGCGGGTGAGGTGCTGGGAGTATAGGCAGCAACCTTC
            aattgat  putative branch site (score: 4)
         tgtaattgataaaa  TA-rich tract