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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCATTCAATTCGCGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctatttgcttaatttattattaacgaaatgacacaccaacatatgtcaacattaattcgtctgtgtaggtttttgtgcatgtctagtggaaattgaaatatatgcttgttatatgctattacttcttctattctcctaagtgcaacttcagaagtatctatatggaatgctggaacag

Basic information

species Glycine max
transcript GLYMA20G24790.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G24790.1 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 5'ss of exon 10
GTTCATTCAATTCGCGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctatttgcttaatttattattaacgaaatgacacaccaacatatgtcaacattaattcgtctgtgtaggtttttgtgcatgtctagtggaaat-tgaaatatatgcttgttatatgctattacttcttctattctcctaagtgcaacttcagaagtatctatatggaatgctggaacag
||    |||||  | || || ||||| ||||||||||| ||||| ||||| || ||||| || || ||||| |||||||| ||||| |||||||||     ||||    ||| | | |    | |      |     |  | ||  | | ||||     |||  |   || |  || |  |||| ||||| | || ||                                                                                
GTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAGgtt-----atttataaaatatttgaacc-ctagtcagtatttgcatttgtgaaatccttaagcaagctgacttttttgtaatgtagctctactggaagtctggaac-------------------------------------------------------------------------------

upper sequence: GLYMA20G24790.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G164352_T03 (Zea mays), 5'ss of exon 10
GTTCATTCAATTCGCGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctatttgcttaatttattattaacgaaatgacacaccaacatatgtcaacattaattcgtctgtgtaggtttttgtgcatgtctagtggaaattgaaatatatgcttgttatatgctattacttcttctattctcctaagtgcaacttcagaagtatctatatggaatgctggaacag
||   ||||||  | || || || |||||||||||||| |||||||| ||||| ||||| || |||||||| |||||||| ||||| ||||||||| || ||| | || |  | | ||      | ||  |  || |   |   |   ||| |  |  ||  || | | |  | |   | || |   | |  |  || ||                                                                             
GTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAAGAGTTTGGTCCAGAGTGGGCAATGCAGCATATAATCCCTCAGgtt-atttatatact-atctcaatacc--ttatatttcctacaactgtgc-tgtgcataatataatccttg-atgctaatttatttatc-aacagtagctacaacat-----------------------------------------------------------------------------

upper sequence: GLYMA20G24790.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G122135_T02 (Zea mays), 5'ss of exon 10
GTTCATTCAATTCGCGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctatttgcttaatttattattaacgaaatgacacaccaacatatgtcaacattaattcgtctg-tgtaggtttttgtgcatgtctagtggaaattgaaatatatgcttgttatatgctattacttcttctattctcctaagtgcaacttcagaagtatctatatggaatgctggaacag
||    |||||  | || || || || ||||||||||| |||||||| ||||| || || || |||||||| |||||||| ||||||||||||||| || ||| | ||   |  ||   |    |  |   ||| |     ||   |  ||   |   | |  || |   | || ||  |  | ||                                                                                            
GTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAAGAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAGgtt-atttatctactatgtcaataccttgt-atttcctacaactgtgcataatataatccttctatttcctgcaacctgttctgttttcccag--------------------------------------------------------------------------------------------

upper sequence: GLYMA20G24790.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G102858_T01 (Zea mays), 5'ss of exon 10
GTTCATTCAATTCGCGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctatttgcttaatttattattaacgaaatgacacaccaacatatgtcaacattaattcgtctgtgtaggtttttgtgcatgtctagtggaaattgaaatatatgcttgttatatgctattacttcttctattctcctaagtgcaacttcagaagtatctatatggaatgctggaacag
|||   || ||  | || || | ||| || || || || ||  |  | || |||||||| ||||||||||| ||||| || |||||||||||||||    |   | ||      | | | |  | | |   |   | | | || ||    ||| || ||   |  | | |||    | || || | | ||||    | ||  |                                                                          
GTTTTCTCGATCAGAGATGCTGGTGCCAATAATTTAAAGCGTTTGACAGAGGAATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCTCAGgttagctttagtactgtgaaaaatgtaatagcatt--tattgcgataaatttc----ttattttgttctt--aagctttaaaccttgacttgagcaaat----acatgagtc------------------------------------------------------------------------

upper sequence: GLYMA20G24790.1 (Glycine max), 5'ss of exon 10
lower sequence: AT1G13320.1 (Arabidopsis thaliana), 5'ss of exon 10
GTTCATTCAATTCGCGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctatttgcttaatttattattaacgaaatgacacaccaacatatgtcaacattaattcgtctgtgtaggtttttgtgcatgtctagtggaaattgaaatatatgcttgttatatgctattacttcttctattctcctaagtgcaacttcagaagtatctatatggaatgctggaacag
||||| ||||| || ||||| ||||| |||||  |||| || ||||||||||| ||||| ||||| ||||| |||||||| ||| |||||||||||  | ||        |  | |||   |   | |       |||   |  || |    | ||   || | | | | || | | || | || | |   || |                                                                                  
GTTCACTCAATCCGTGAAGCTGCTGCAAACAATCTGAAGCGTCTTGCTGAAGAGTTTGGTCCTGAATGGGCAATGCAGCATATAGTTCCTCAGgtttgtgta-------gaaatcttaagcatatagtatgttttcaattcaaatcga--gcattttagctat-tggttattggagtatatttacttg---ttcag---------------------------------------------------------------------------------

upper sequence: GLYMA20G24790.1 (Glycine max), 5'ss of exon 10
lower sequence: AT3G25800.1 (Arabidopsis thaliana), 5'ss of exon 9
GTTCATTCAATTCGCGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctatttgcttaatttattattaacgaaatgacacaccaacatatgtcaacattaattcgtctgtgtaggtttttgtgcatgtctagtggaaattgaaatatatgcttgttatatgctattacttcttctattctcctaagtgcaacttcagaagtatctatatggaatgctggaacag
||||| ||||| ||||| || |||||||||||  | || || |||||||| |||||||| ||||| ||||| ||||| || ||| |||||||||||  ||||     || |   |   |||   || | |     | |  | ||| |   |||||| |||  | |   ||  |  |||                                                                                                   
GTTCACTCAATCCGCGATGCTGCTGCTAACAATCTCAAGCGGCTTGCTGAGGAATTTGGTCCTGAATGGGCAATGCAACATATAGTTCCTCAGgtttgtctagaattttta--caactttagaaaagtca-gtgtctatct-tgttagtgttaattagtcgctattcattaatccgcag--------------------------------------------------------------------------------------------------

upper sequence: GLYMA20G24790.1 (Glycine max), 5'ss of exon 10
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 5'ss of exon 9
GTTCATTCAATTCGCGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctatttgcttaatttattattaacga--aatgacacaccaacatatgtcaacattaattcgtctgtgtaggtttttgtgcatgtctagtggaaattgaaatatatgcttgttatatgctattacttcttctattctcctaagtgcaacttcagaagtatctatatggaatgctggaacag
||| | || ||||| || || |||||||||||||| || |||||||| ||||||||||| ||||| ||||| ||||||||| ||||||| ||||||  |||| | | |      |||| |  | |  | || |     ||     ||  | || | ||      |     | ||  | ||| | | ||     |                                                                                     
GTTTACTCCATTCGTGATGCTGCTGCTAACAACTTAAAGCGCCTTGCAGAAGAATTTGGTCCTGACTGGGCAATGCAGCACTTAATTCCACAGgtttgtctagtggttgtgacaattaattgctattagtggcttgtaaaggatagtggatatgagttt-caaattctcatcttatttcat-tttggtttgtctc------------------------------------------------------------------------------------

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|22930981|gb|BU548120.1|BU548120
EST:     TTGCTGAAGAATTTGGACCTGAGTGGNNNATGCAGCACATAATTCCTCAG                         GTTNTGGAGATGAACAACAATCCACACTATTTGTATCGGATGACCATTCTT
genomic: TTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctat ... gctggaacagGTTTTGGAGATGAACAACAATCCACACTATTTGTATCGGATGACCATTCTT
EST: gi|192298924|gb|FG987669.1|FG987669
EST:     TTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAG                         GTTTTGGAGATGAACAACAATCCACACTATTTGTATCGGATGACCATTCTT
genomic: TTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctat ... gctggaacagGTTTTGGAGATGAACAACAATCCACACTATTTGTATCGGATGACCATTCTT
EST: gi|9205515|gb|BE331739.1|BE331739
EST:     TTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAT                         GTTTTGGAGATGAACAACAATCCACACTATTTGTATCGGATGACCATTCTT
genomic: TTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctat ... gctggaacagGTTTTGGAGATGAACAACAATCCACACTATTTGTATCGGATGACCATTCTT
EST: gi|151394585|gb|EV264456.1|EV264456
EST:     GGGCTATGCAGCACATAATTCCTCAG                         GTTTTGGAGATGAACAACAATCCACACTATTTGTATCGGATGACCATTCTT
genomic: GGGCTATGCAGCACATAATTCCTCAGgttcatctat ... gctggaacagGTTTTGGAGATGAACAACAATCCACACTATTTGTATCGGATGACCATTCTT
EST: gi|6914739|gb|AW396269.1|AW396269
EST:     TTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAG                         GTTTTGGAGATGAACAACAATCCACACTATTTGTATCGGATGACCATTCTT
genomic: TTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctat ... gctggaacagGTTTTGGAGATGAACAACAATCCACACTATTTGTATCGGATGACCATTCTT
EST: gi|254327333|gb|GR836942.1|GR836942
EST:     TTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAG                         GTTTTGGAGATGAACAACAATCCACACTATTTGTATCGGATGACCATTCTT
genomic: TTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctat ... gctggaacagGTTTTGGAGATGAACAACAATCCACACTATTTGTATCGGATGACCATTCTT
EST: gi|308098474|gb|HO760215.1|HO760215
EST:     TTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAG                         GTTTTGGAGATGAACAACAATCCACACTATTTGTATCGGATGACCATTCTT
genomic: TTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctat ... gctggaacagGTTTTGGAGATGAACAACAATCCACACTATTTGTATCGGATGACCATTCTT
EST: gi|308098470|gb|HO760211.1|HO760211
EST:     TTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAG                         GTTTTGGAGATGAACAACAATCCACACTATTTGTATCGGATGACCATTCTT
genomic: TTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctat ... gctggaacagGTTTTGGAGATGAACAACAATCCACACTATTTGTATCGGATGACCATTCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCATTCAATTCGCGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctatttgcttaatttattattaacgaaatgacacaccaacatatgtcaacattaattcgtctgtgtaggtttttgtgcatgtctagtggaaattgaaatatatgcttgttatatgctattacttcttctattctcctaagtgcaacttcagaagtatctatatggaatgctggaacag

- - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - -  TGAAGA