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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagatatttcattagtttatgttattgttatcatagtgagcctttttgctgtgtcctgttgcttatcctcgtgttttgtttagGTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGGTTAGCACTAGCTGAGAAACACTTGGCTGCACGATTTAACAAGCCTGACAATGAGATTGTTGACCA

Basic information

species Glycine max
transcript GLYMA20G38720.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38720.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g04270.1 (Oryza sativa), 3'ss of exon 2
--------------------gttagatatttcattagtttatgttattgttatcatagtgagcctttttgctgtgtcctgttgcttatcctcgtgttttgtttagGTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGGTTAGCACTAGCTGAGAAACACTTGGCTGCACGATTTAACAAGCCTGACAATGAGATTGTTGACCA
                     | | |       | ||||| | |  |||    ||||  || | |   || |  |   | ||| ||    ||||    | | |||| |||||||||||||| ||||| ||||| |||||| | || || |||||||| ||| ||||||| || || |||||||| ||||  ||||||||||| ||
gtctgtcatctcaactgaagctcatagcacctttaagtttctatgcttgaatacatacagaac-tgaatgtttcggtttcttgtttggtttcgt----tctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGAAGCACCTGGCTGCTCGTTTCAACAAGCCCGACAGCGAGATTGTTGATCA

upper sequence: GLYMA20G38720.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G033208_T01 (Zea mays), 3'ss of exon 2
----gttagatatttcattagtttatgttattgttat----catagtgagcctttttg--ctgtgtcctgttgcttatcct-cgtgttt--tgtttagGTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGGTTAGCACTAGCTGAGAAACACTTGGCTGCACGATTTAACAAGCCTGACAATGAGATTGTTGACCA
    |||   |  |  ||| |  | ||   | |   |    | |  || ||  | |    ||| |     |||  | ||||   || ||  |||  ||| |||||||||||||| || |||||||| |||||||| ||||| |||||||| ||| ||||||| || || ||||||||||||| |||||| || |||||
gtctgttttcttctctattgggctgtgaattagccgtgccccttgctgtgctgtataaaactgagaaagtttgggtttcctatatggttgctgtgcagGGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGAAGCACCTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCA

upper sequence: GLYMA20G38720.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G010494_T01 (Zea mays), 3'ss of exon 2
gttagatatttcattagtttatgttattgttatcatagtgagcctttttgctgtgtcctgttgcttatcctcgtgttttgtttagGTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGGTTAGCACTAGCTGAGAAACACTTGGCTGCACGATTTAACAAGCCTGACAATGAGATTGTTGACCA
|||      |  |  | ||||  || |  ||  | |  |     |  ||    ||   | |    | | ||  ||   |||  |||||||||||| |||||  |||| |||||||||||  ||||||| |||||||||||  | ||| |||| || |||||| ||||||   |  | || |||||
gttgccagctgaaacattttaaattttgctttgccttcttctgatacttaaattgatatctaaacttttctgatgccatgt--agGTCCTCTTGGGCAGGGTTTTGCAAATGCTGTTGGACTAGCACTTGCTGAGAAACATCTAGCTTCACGTTTCAACAAGACTGACATGAAAGTCGTGGACCA

upper sequence: GLYMA20G38720.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G45290.1 (Arabidopsis thaliana), 3'ss of exon 2
gttagata--tttcattagtttatgttat-tgttatcatagtga--gcctttttgctgtgtcctgttgcttatcctcgtgttttgtttagGTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGGTTAGCACTAGCTGAGAAACACTTGGCTGCACGATTTAACAAGCCTGACAATGAGATTGTTGACCA
||||| ||  |||  |  | || | || | |||| |  | |     |   |||||   | |    |||||| |  | |       |  |||||||||||| || || ||||| ||||||||||| ||||| || || ||||| || ||||||||  |||||||||| |||||||||||||||||||||||
gttagttagattttctctgcttcttttgtgtgttttagttgatgttgatcttttgtaatatagcattgcttgtatttgc-caacatgcagGTCCTCTTGGACAAGGTATTGCAAATGCTGTTGGTTTAGCTCTTGCGGAGAAGCATTTGGCTGCTAGATTTAACAAACCTGACAATGAGATTGTTGACCA

upper sequence: GLYMA20G38720.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G60750.1 (Arabidopsis thaliana), 3'ss of exon 2
gttagatatttca------ttagtttatg-ttattgtta----tcatagtgagcctttttg-ctgtgtc--ctgttg----cttatcctcgtgttttgtttagGTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGGTTAGCACTAGCTGAGAAACACTTGGCTGCACGATTTAACAAGCCTGACAATGAGATTGTTGACCA
||| || ||||        || | ||||| ||  ||| |    ||| ||  |   | | |  |||| |   |  |||    ||   | | |  |  | |  |||||||||||| || || || || ||||||||||| ||||| || |||||||| || ||||||||  |||| ||||| |||||   |||  | || |||||
gtttgagattttgcttcttttggcttatggttcatgtgaaatttcacagaaactatctataactgtatttacaattgtgctctctgctttggctgctatgcagGTCCTCTTGGACAAGGAATCGCTAATGCTGTTGGTTTAGCTCTTGCTGAGAAGCATTTGGCTGCTAGATTCAACAAACCTGATGCTGAAGTAGTCGACCA

upper sequence: GLYMA20G38720.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0022g01440.t01 (Vitis vinifera), 3'ss of exon 2
gttagatatttcattagtttatgttattgttatcatagtgagcctttttgctgtgtcctgttgcttatcc-tcgtgttttgtttagGTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGGTTAGCACTAGCTGAGAAACACTTGGCTGCACGATTTAACAAGCCTGACAATGAGATTGTTGACCA
||| | |  |   |   |  |  ||| |   ||    ||  |      ||||     | | | |||||   |  |   || | |||| |||||||||||||| ||||||||||||||||| || ||    |  ||||| || ||||||||| |||| ||||| ||||||||||||||||| |||||
gttggctgctgt-tccttgaaacttaattcaatgtctgtatgttagaatgctaataaccggtccttatgtgttattgcttttatagGCCCTCTTGGTCAGGGTATTGCCAATGCTGTTGGTTTGGCCGCTGTGGAGAAGCATTTGGCTGCAAGATTCAACAAACCTGACAATGAGATTGTCGACCA

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|213617212|gb|DB971303.1|DB971303
EST:     TCCTGGACATCCTGAGAACTTTGAGACAGTTGGAATTGAAGTGACTACAG                         GTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGGTTAG
genomic: TCCTGGACATCCTGAGAACTTTGAGACAGTTGGAATTGAAGTGACTACAGgttagatatt ... ttttgtttagGTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGGTTAG
EST: gi|22539779|gb|BU089622.1|BU089622
EST:     CTGAGAACTTTGAGACAGTTGGAATTGAAGTGACTACAG                         GTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGGTTAGCACTAGCTGAGA
genomic: CTGAGAACTTTGAGACAGTTGGAATTGAAGTGACTACAGgttagatatt ... ttttgtttagGTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGGTTAGCACTAGCTGAGA
EST: gi|15287320|gb|BI471211.1|BI471211
EST:     TCCTGGACATCCTGAGAACTTTGAGACAGTTGGAATTGAAGTGACTACAG                         GTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGGTTAGCACTAGCTGAGA
genomic: TCCTGGACATCCTGAGAACTTTGAGACAGTTGGAATTGAAGTGACTACAGgttagatatt ... ttttgtttagGTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGGTTAGCACTAGCTGAGA
EST: gi|8826649|gb|BE210379.1|BE210379
EST:     TCCTGGACATCCTGAGAACTTTGAGACAGTTGGAATTGAAGTGACTACAG                         GTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGGTTAGCACTAGCTGAGA
genomic: TCCTGGACATCCTGAGAACTTTGAGACAGTTGGAATTGAAGTGACTACAGgttagatatt ... ttttgtttagGTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGGTTAGCACTAGCTGAGA
EST: gi|18848458|gb|BM567678.1|BM567678
EST:     TCCTGGACATCCTGAGAACTTTGAGACAGTTGGAATTGAAGTGACTACAG                         GTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGGTTAGCACTAGCTGAGA
genomic: TCCTGGACATCCTGAGAACTTTGAGACAGTTGGAATTGAAGTGACTACAGgttagatatt ... ttttgtttagGTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGGTTAGCACTAGCTGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcatagtgagcctttttgctgtgtcctgttgcttatcctcgtgttttgtttagGTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGGTTAGCACTAGCTGAGAAACACTTGGCTGCACGATTTAACAAGCCTGACAATGAGATTGTTGACCA
                                             ttttgttt  CT-rich tract
                                             ttttgttta  TA-rich tract