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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatttctcgtgttatttttttggtgaccatctttttgattaattttgtttgcttgatgttttaattgagaaaaagttcatatgtacatttgatttcagttcacctaactgtttttttttttttactatttcttgtttggccagTGGAAGTTTGCATTTCTATCACTAGGGCGTCCTGAGTACCTTCAAGATTCTGACGTTGTTTCCAGTCGTTTTCAG

Basic information

species Glycine max
transcript GLYMA20G11330.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 21
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 29
------------------------------------------------gtgatttc-tcgtgttatttttttggt-gaccatctttttg-attaattttgtttg---cttgatgttttaattgag--aaaaagttcatatgtacatttgatttcagttcacctaactgtttttttttttttactatttcttgtttggccagTGGAAGTTTGCATTTCTATCACTAGGGCGTCCTGAGTACCTTCAAGATTCTGACGTTGTTTCCAGTCGTTTTCAG
                                                 | ||| | | |    ||    |  || ||  || |   |  |  |   | || |    |||  | |||| |||     || ||| |  | || |  | |||  ||| ||     ||      ||| ||| ||    || ||| ||   |||||||| |||||| ||||| |||||||| || || |||||||||||||| |||||| |||| |||||||||||||||
gtatattttccttatgcatccactgtcatattcttctaatgaacactacttattacatggcaccataaaatcagtagatgatatgactacaccatggtggtataaacctttttcttttcattttttcaagaagcttct-tgcaattctgacgtcattttgagcaatctacctttgtttgttgtctttactttttc--ccagTGGAGGTTTGCCTTTCTTTCACTAGGTCGCCCAGAGTACCTTCAAGACTCTGACATTGTCTCCAGTCGTTTTCAG

upper sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 21
lower sequence: PP1S42_181V6.1 (Physcomitrella patens), 3'ss of exon 29
gtgatttctcgtgttatttttttggtgaccatctttttgattaattttgtttgcttgatgt--tttaattgagaaaaagttcatatgtacatttgatttcagttcacctaactgtttttttttttttactatttcttgtttggccagTGGAAGTTTGCATTTCTATCACTAGGGCGTCCTGAGTACCTTCAAGATTCTGACGTTGTTTCCAGTCGTTTTCAG
            || | |   |  | |    |  ||    ||  | |  |||  ||  |||  ||||| ||    ||  ||     ||  |   | || |  || | || |         |||         ||| | ||||  |||||||||||||| ||||| ||||| || || |||||||| ||||||||    || || ||| |   ||||||||||
------------gtaaatagatccgcg---tttgttgcacttggtgtcattttttttgtgtcctttaactgg---aatctttgaccgtgta---ggttcctatttagcttatgaaccaagtttcaacg----ttcctatttgtgcagTGGAAGTTTGCCTTTCTTTCACTGGGTCGACCTGAGTATCTTCAAGACGGCGATGTAGTTGCGGCTCGTTTTCAG

upper sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 21
lower sequence: PP1S123_138V6.1 (Physcomitrella patens), 3'ss of exon 29
gtgatttctcgtgttatttttttggtgaccatctttttga-ttaattttgtttgcttgatgttttaattgagaaaaagttcatatgtacatttgatttcagttcacctaactgtttttttttttttactatttcttgtttggccagTGGAAGTTTGCATTTCTATCACTAGGGCGTCCTGAGTACCTTCAAGATTCTGACGTTGTTTCCAGTCGTTTTCAG
           |||||  |  |   ||  ||||  || || ||| || ||| ||| |   |||  | ||  || ||    |||      |||| ||| ||  ||  |                        || |  ||||  |||||||||||||| ||||| ||||| || || |||||||| |||||||||   || |||||| |    |||||||||
--------gtatgttaactaatgtctg--catcacttggacttacttctgtgtgcgttccgttcaacttttgagaa----catggcggtatttaattacaactcgacg-----------------------ttgtcatttgttcagTGGAAGTTTGCGTTTCTTTCACTGGGCCGACCTGAGTATCTTCAAGATGGAGATGTTGTTGCTGCCCGTTTTCAG

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|18690763|gb|BM519611.1|BM519611
EST:     AAGTGCGAATACAAAAGAAACTTCAAGTTCCTGATGATGAATTCTGCAAG                         TGGAAGTTTGCATTTCTATCACTAGGGCGTCCTGAGTACCTTCAAGATTCT
genomic: AAGTGCGAATACAAAAGAAACTTCAAGTTCCTGATGATGAATTCTGCAAGgtgatttctc ... gtttggccagTGGAAGTTTGCATTTCTATCACTAGGGCGTCCTGAGTACCTTCAAGATTCT
EST: gi|17153585|gb|BM143518.1|BM143518
EST:     AAGTGCGAATACAAAAGAAACTTCAAGTTCCTGATGATGAATTCTGCAAG                         TGGAAGTTTGCATTTCTATCACTAGGGCGTCCTGAGTAC
genomic: AAGTGCGAATACAAAAGAAACTTCAAGTTCCTGATGATGAATTCTGCAAGgtgatttctc ... gtttggccagTGGAAGTTTGCATTTCTATCACTAGGGCGTCCTGAGTAC
EST: gi|193546964|gb|FK502343.1|FK502343
EST:     TGATGAATTCTGCAAG                         TGGAAGTTTGCATTTCTATCACTAGGGCGTCCTGAGTACCTTCAAGATTCT
genomic: TGATGAATTCTGCAAGgtgatttctc ... gtttggccagTGGAAGTTTGCATTTCTATCACTAGGGCGTCCTGAGTACCTTCAAGATTCT
EST: gi|308098749|gb|HO760490.1|HO760490
EST:     AAGTGCGAATACAAAAGAAACTTCAAGTTCCTGATGATGAATTCTGCAAG                         TGGAAGTTTGCATTTCTATCACTAGGGCGTCCTGAGT
genomic: AAGTGCGAATACAAAAGAAACTTCAAGTTCCTGATGATGAATTCTGCAAGgtgatttctc ... gtttggccagTGGAAGTTTGCATTTCTATCACTAGGGCGTCCTGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatttcagttcacctaactgtttttttttttttactatttcttgtttggccagTGGAAGTTTGCATTTCTATCACTAGGGCGTCCTGAGTACCTTCAAGATTCTGACGTTGTTTCCAGTCGTTTTCAG
             acctaac  putative branch site (score: 2)
                   ctgttttttttttttt  CT-rich tract
                taactgtttttttttt  TA-rich tract