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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAGgttagatgtttcattggtttatgttactgttatcatggtgagcctttttgctgtgttctgttgcttatcctcacgttttgtttag

Basic information

species Glycine max
transcript GLYMA10G43990.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G43990.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os06g04270.1 (Oryza sativa), 5'ss of exon 2
GAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAGgttagatgtttcatt---ggtttatgttactgttatcatggtgagcctttttgctgtgttctgttgcttatcctcacgttttgtttag-------------
||  | ||| | ||| ||||| | |||||||||||||  ||||| || ||||| |||||||| ||||| |  ||||||||||| ||||| |||  |   | |||      | | ||   ||  |||   |  |  || |   | |  |       ||  | |       | |||||| |             
GAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTGgtctgtcatctcaactgaagctcatagcacctttaagtttctatgcttgaatac-atacagaactgaatgtttcggtttcttgtttggtttcgttctgtag

upper sequence: GLYMA10G43990.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G033208_T01 (Zea mays), 5'ss of exon 2
GAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAGgttagatgtttcattggtttatgttactgttatcatggtgagcctttttgctgtgttctgttgcttatcctcacgttttgtttag-------------
||  | ||| | ||| | ||| | ||||||||||||||||| || || || ||||||||||||||||| |  ||||||||||| ||||| |||  | | | |  |   ||    |     ||| |   |        | |||||| |     ||   |   |   ||||  | ||              
GAGGAGGACTTGAAGCAGTTCAGGCAATGGGGAAGCAGAACACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCGgtctgttttcttctctattgggctgtgaattagccgtgccccttgctgtgctgtataaaactgagaaagtttgggtttcctatatggttgctgtgcag

upper sequence: GLYMA10G43990.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G010494_T01 (Zea mays), 5'ss of exon 2
GAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAGgttagatgtttcattggtttatgttactgttatcatggtgagcctttttgctgtgttctgttgcttatcctcacgttttgtttag
    | || || ||    |||||||||||| |||||||||||||||| || || || || ||||| || | ||| |||||||| ||||||||||    | |  |    ||||  ||    ||  | |  |     |  ||    || | | |    | | || | |   |||    
ATGGACGATCTGAAAACTTTCCGACAATGGAGAAGCAGAACTCCTGGTCACCCAGAAAATTTTGAAACACCTGGCGTTGAAGTCACCACAGgttgccagctgaaacattttaaattttgctttgccttcttctgatacttaaattgatatctaaacttttctgatgccatgtag--

upper sequence: GLYMA10G43990.1 (Glycine max), 5'ss of exon 2
lower sequence: AT3G60750.2 (Arabidopsis thaliana), 5'ss of exon 2
GAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAGgttagatgtttcattggtttatgttactgttatcatggtgagcctttttgctgtgttctgttgct-tatcctca------cgttttgtttag------------
    ||||  | ||| | ||||| |||||||||||||  || || |||||||||||||| || ||||| | |||| ||||||| || || |||| ||  |||   |  |||  | |  || | |||||   |   |    |      ||| |  || |||   ||      |  | || || |            
---GAAGATTTGAAGCAGTTCCGTCAATGGGGAAGCAAGACACCAGGACATCCTGAGAATTTCGAGACTCCTGGAATTGAAGTCACTACTGgtttgagattttgcttcttttggcttatggt-tcatgtgaaatttcacagaaactatctataactgtatttacaattgtgctctctgctttggctgctatgcag

upper sequence: GLYMA10G43990.1 (Glycine max), 5'ss of exon 2
lower sequence: AT3G60750.1 (Arabidopsis thaliana), 5'ss of exon 2
GAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAGgttagatgtttcattggtttatgttactgttatcatggtgagcctttttgctgtgttctgttgct-tatcctca------cgttttgtttag------------
||  ||||  | ||| | ||||| |||||||||||||  || || |||||||||||||| || ||||| | |||| ||||||| || || |||| ||  |||   |  |||  | |  || | |||||   |   |    |      ||| |  || |||   ||      |  | || || |            
GAGGAAGATTTGAAGCAGTTCCGTCAATGGGGAAGCAAGACACCAGGACATCCTGAGAATTTCGAGACTCCTGGAATTGAAGTCACTACTGgtttgagattttgcttcttttggcttatggt-tcatgtgaaatttcacagaaactatctataactgtatttacaattgtgctctctgctttggctgctatgcag

upper sequence: GLYMA10G43990.1 (Glycine max), 5'ss of exon 2
lower sequence: AT2G45290.1 (Arabidopsis thaliana), 5'ss of exon 2
GAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAGgttagatg---tttcattggtttatgttactgttatcat-ggtga-gcctttttgctgtgttctgttgcttatcctcacgttttgtttag
||  ||||  | |||   ||||| ||||||||||| |  ||||| |||||||||||||| |||||||| | ||| |||||||  || || |||||| |    ||||  || ||  | |   |||| |  | | ||  |   |||||   | |    |||||| |  |  |      |  ||
GAGGAAGATTTGAAGAGCTTCCGTCAATGGGGAAGTAAGACTCCAGGACATCCTGAGAATTTTGAGACTCCTGGTGTTGAAGCCACTACTGgttagttagattttctctgcttcttttgtgtgttttagttgatgttgatcttttgtaatatagcattgcttgtatttgc-caacatgcag

upper sequence: GLYMA10G43990.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv16s0022g01440.t01 (Vitis vinifera), 5'ss of exon 2
GAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAGgttagatgtttcattggtttatgttactgttatcatggtgagcctttttgctgtgttctgttgcttatcc-tcacgttttgtttag
||| | ||  | |||   ||||||||||||||||| ||||||||||| || || |||||||| ||||| | ||| ||||||||||| || |||| | || |   |   |  |  ||| |   ||    ||  |      ||||     | | | |||||   | |    || | |||
GAAGAGGATTTGAAGTCTTTCCGACAATGGGGAAGTAGAACTCCTGGTCACCCAGAGAACTTCGAGACACCTGGGGTTGAAGTGACAACTGgttggctgctgt-tccttgaaacttaattcaatgtctgtatgttagaatgctaataaccggtccttatgtgttattgcttttatag

upper sequence: GLYMA10G43990.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ07729 (Selaginella moellendorffii), 5'ss of exon 2
GAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAGgtta--gatgtttcattggt-ttatgttactgtt-atcatggtgagcctttttgctgtgttctgttgcttatcctcacgttttgtttag
||| | ||  | ||| ||||||| |||||| | |||||||||||||| ||||| |||||||| ||||| |  || || ||||| || || ||| |  | ||  ||| | || ||   |   |||| ||  |||   || |||                                      
GAAGAGGATTTGAAGCAATTCCGTCAATGGAGCAGCAGAACTCCTGGTCATCCAGAGAACTTCGAGACTCCCGGCGTGGAAGTCACGACTGgtaattgttgactcactcgtgttgaatggttgttgattgtggcttgcttttcaaacag-------------------------------

upper sequence: GLYMA10G43990.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ07676 (Selaginella moellendorffii), 5'ss of exon 2
GAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAGgtta--gatgtttcattggt-ttatgttactgtt-atcatggtgagcctttttgctgtgttctgttgcttatcctcacgttttgtttag
||| | ||  | ||| ||||||| |||||||| |||||||||||||| ||||| |||||||| ||||| |  || || ||||| || || ||| |  | ||  ||| | || ||   |   |||| ||  |||   || |||                                      
GAAGAGGATTTGAAGCAATTCCGTCAATGGGGCAGCAGAACTCCTGGCCATCCAGAGAACTTCGAGACTCCCGGCGTGGAAGTCACGACTGgtaattgttgactcactcgtgttgaatggttgttgattgtggcttgcttttcaaacag-------------------------------

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

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAGgttagatgtttcattggtttatgttactgttatcatggtgagcctttttgctgtgttctgttgcttatcctcacgttttgtttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG