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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagatgtttcattggtttatgttactgttatcatggtgagcctttttgctgtgttctgttgcttatcctcacgttttgtttagGTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGATTAGCACTAGCTGAGAAGCACTTGGCTGCACGATTTAACAAGCCTGACAATGAGATTGTTGACCA

Basic information

species Glycine max
transcript GLYMA10G43990.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G43990.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g04270.1 (Oryza sativa), 3'ss of exon 2
gttagatgtttcatt---ggtttatgttactgttatcatggtgagcctttttg---------ctgtgttctgttgcttatcctcacgttttgtt---tagGTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGATTAGCACTAGCTGAGAAGCACTTGGCTGCACGATTTAACAAGCCTGACAATGAGATTGTTGACCA
||  |   | |||      | | ||   ||  |||   |  |  || |   |          |||  |  |   | || |  |   |||| |||   |||| |||||||||||||| ||||| ||||| |||||  | || || |||||||||||| ||||||| || || |||||||| ||||  ||||||||||| ||
gtctgtcatctcaactgaagctcatagcacctttaagtttctatgcttgaatacatacagaactgaatgtttcggtttcttgtttggtttcgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGAAGCACCTGGCTGCTCGTTTCAACAAGCCCGACAGCGAGATTGTTGATCA

upper sequence: GLYMA10G43990.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G033208_T01 (Zea mays), 3'ss of exon 2
----gttagatgtttcattggtttatg---ttactgt-tatcatggtgagcctttttg--ctgtgttctgttgcttatcct-cacgttt--tgtttagGTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGATTAGCACTAGCTGAGAAGCACTTGGCTGCACGATTTAACAAGCCTGACAATGAGATTGTTGACCA
    |||   |  |  |||||  | ||   |  | ||    | || || ||  | |    ||| |     |||  | ||||  | | ||  |||  ||| |||||||||||||| || |||||||| ||||| || ||||| |||||||||||| ||||||| || || ||||||||||||| |||||| || |||||
gtctgttttcttctctattgggctgtgaattagccgtgccccttgctgtgctgtataaaactgagaaagtttgggtttcctatatggttgctgtgcagGGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGAAGCACCTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCA

upper sequence: GLYMA10G43990.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G010494_T01 (Zea mays), 3'ss of exon 2
gttagatgtttcattggtttatgttactgttatcatggtgagcctttttgctgtgttctgttgcttatcctcacgttttgtttagGTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGATTAGCACTAGCTGAGAAGCACTTGGCTGCACGATTTAACAAGCCTGACAATGAGATTGTTGACCA
|||    | |  |    ||||  ||    ||  | |  |     |  ||    || | | |    | | || | |   |||  |||||||||||| |||||  |||| |||||||||||| ||||||| |||||||| ||  | ||| |||| || |||||| ||||||   |  | || |||||
gttgccagctgaaacattttaaattttgctttgccttcttctgatacttaaattgatatctaaacttttctgatgccatgt--agGTCCTCTTGGGCAGGGTTTTGCAAATGCTGTTGGACTAGCACTTGCTGAGAAACATCTAGCTTCACGTTTCAACAAGACTGACATGAAAGTCGTGGACCA

upper sequence: GLYMA10G43990.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G45290.1 (Arabidopsis thaliana), 3'ss of exon 2
----gttagatgtttcattggtttatgttactgttatcat-ggtga-gcctttttgctgtgttctgttgcttatcctcacgttttgtttagGTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGATTAGCACTAGCTGAGAAGCACTTGGCTGCACGATTTAACAAGCCTGACAATGAGATTGTTGACCA
    ||||||| ||||  || ||  | |   |||| |  | | ||  |   |||||   | |    |||||| |  |  |      |  |||||||||||| || || ||||| ||||||||||| ||||| || || |||||||| ||||||||  |||||||||| |||||||||||||||||||||||
gttagttagat-tttctctgcttcttttgtgtgttttagttgatgttgatcttttgtaatatagcattgcttgtatttgc-caacatgcagGTCCTCTTGGACAAGGTATTGCAAATGCTGTTGGTTTAGCTCTTGCGGAGAAGCATTTGGCTGCTAGATTTAACAAACCTGACAATGAGATTGTTGACCA

upper sequence: GLYMA10G43990.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G60750.1 (Arabidopsis thaliana), 3'ss of exon 2
gttagatgtttca------ttggtttatgttac-tgtta----tcatggtgagcctttttg-ctgtgttc-----tgttgcttatcctcacgtt-ttgtttagGTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGATTAGCACTAGCTGAGAAGCACTTGGCTGCACGATTTAACAAGCCTGACAATGAGATTGTTGACCA
||| ||  |||        |||| ||||| | | ||| |    |||  |  |   | | |  |||| ||      |||    | | ||   | |  | |  |||||||||||| || || || || ||||||||||| ||||| || ||||||||||| ||||||||  |||| ||||| |||||   |||  | || |||||
gtttgagattttgcttcttttggcttatggttcatgtgaaatttcacagaaactatctataactgtatttacaattgtgctctctgctttggctgctatgcagGTCCTCTTGGACAAGGAATCGCTAATGCTGTTGGTTTAGCTCTTGCTGAGAAGCATTTGGCTGCTAGATTCAACAAACCTGATGCTGAAGTAGTCGACCA

upper sequence: GLYMA10G43990.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0022g01440.t01 (Vitis vinifera), 3'ss of exon 2
gttagatgtttcattggtttatgttactgttatcatggtgagcctttttgctgtgttctgttgcttatcc-tcacgttttgtttagGTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGATTAGCACTAGCTGAGAAGCACTTGGCTGCACGATTTAACAAGCCTGACAATGAGATTGTTGACCA
||| | || |   |   |  |  ||| |   ||    ||  |      ||||     | | | |||||   | |    || | |||| |||||||||||||| ||||||||||||||||| || ||    |  |||||||| ||||||||| |||| ||||| ||||||||||||||||| |||||
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|213618089|gb|DB963722.1|DB963722
EST:     TCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAG                         GTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGA
genomic: TCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAGgttagatgtt ... ttttgtttagGTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGA
EST: gi|8825831|gb|BE209561.1|BE209561
EST:     TCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAG                         GTCCTCTTGGTCAGGGCATTGCCAATGCTCGT-GGATTAGCACTAGCTGAG
genomic: TCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAGgttagatgtt ... ttttgtttagGTCCTCTTGGTCAGGGCATTGCCAATGCT-GTTGGATTAGCACTAGCTGAG
EST: gi|209703817|gb|BW656895.1|BW656895
EST:     TCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAG                         GTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGATTAGCACTAGCTGAGA
genomic: TCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAGgttagatgtt ... ttttgtttagGTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGATTAGCACTAGCTGAGA
EST: gi|209701314|gb|BW655909.1|BW655909
EST:     TCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAG                         GTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGATTAGCACTAGCTGAGA
genomic: TCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAGgttagatgtt ... ttttgtttagGTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGATTAGCACTAGCTGAGA
EST: gi|209704746|gb|BW656700.1|BW656700
EST:     TCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAG                         GTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGATTAGCACTAGCTGAGA
genomic: TCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAGgttagatgtt ... ttttgtttagGTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGATTAGCACTAGCTGAGA
EST: gi|209700040|gb|BW652940.1|BW652940
EST:     TCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAG                         GTCCTCTTGGTCAGGGCATTGCCAATGCTGT
genomic: TCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAGgttagatgtt ... ttttgtttagGTCCTCTTGGTCAGGGCATTGCCAATGCTGT
EST: gi|18692759|gb|BM521607.1|BM521607
EST:     TCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAG                         GTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGATTAGCACTAGCTGAGA
genomic: TCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAGgttagatgtt ... ttttgtttagGTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGATTAGCACTAGCTGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcatggtgagcctttttgctgtgttctgttgcttatcctcacgttttgtttagGTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGATTAGCACTAGCTGAGAAGCACTTGGCTGCACGATTTAACAAGCCTGACAATGAGATTGTTGACCA
                                     tcctcac  putative branch site (score: 2)
                                             ttttgttt  CT-rich tract
                                             ttttgttta  TA-rich tract