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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctatttacttaatttattattaacgaaatgatacaccaacatatgtcaacattaattcgtctgtgtgggtttttgtgcatgtcttgaaatatatgtttgctatatgctattaccttttctattctcccaagtgtaacttcagaagtatctatatggaatgtgtggaacag

Basic information

species Glycine max
transcript GLYMA10G42250.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 5'ss of exon 10
GTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctatttacttaatttattattaacgaaatgatacaccaacatatgtcaacattaattcgtctgtgtgggtttttgtgcatgtcttgaaatatatgtttgctatatgctattaccttttctattctcccaagtgtaacttcagaagtatctatatggaatgtgtggaacag
||    |||||  | || || ||||| ||||||||||| ||||| ||||| || |||||||| || ||||| |||||||| ||||| |||||||||     |||||   ||| | | |    | |     ||     |  | ||  | | ||||     |||  |   || |  || |  |||   | |  | || ||  |                                                                    
GTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAGgtt-----atttataaaatatttgaacc-ctagtcagtatttgcatttgtgaaatccttaagcaagctgacttttttgtaatgtagctct---actggaagtctggaac-------------------------------------------------------------------

upper sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G164352_T03 (Zea mays), 5'ss of exon 10
GTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctatttacttaatttattattaacgaaatgatacaccaacatatgtcaacattaattcgtctgtgtgggtttttgtgcatgtcttgaaatatatgtttgctatatgctattaccttttctattctcccaagtgtaacttcagaagtatctatatggaatgtgtggaacag
||   ||||||  | || || || |||||||||||||| |||||||| ||||| |||||||| |||||||| |||||||| ||||| ||||||||| || ||| |||| |  | | ||      |  |  |||| |         ||  ||  | || |   ||    |||      || | |  | |    |   | | | ||                                                                 
GTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAAGAGTTTGGTCCAGAGTGGGCAATGCAGCATATAATCCCTCAGgtt-atttatatact-atctcaataccttatatttcctacaactgtgctgtgcataatataatccttgatgctaattt------atttatcaaca---gtagctacaacat-----------------------------------------------------------------

upper sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G122135_T02 (Zea mays), 5'ss of exon 10
GTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctatttacttaatttattattaacgaaatgatacaccaacatatgtcaacattaattcgtctg-tgtgggtttttgtgcatgtcttgaaatatatgtttgctatatgctattaccttttctattctcccaagtgtaacttcagaagtatctatatggaatgtgtggaacag
||    |||||  | || || || || ||||||||||| |||||||| ||||| || ||||| |||||||| |||||||| ||||||||||||||| || ||| ||||   |  ||   |    |  |  |||| |     ||   |  ||   |   | |  ||     | || ||  |  |  |                                                                                    
GTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAAGAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAGgtt-atttatctactatgtcaataccttgt-atttcctacaactgtgcataatataatccttctatttcctgcaacctgttctgttttcccag------------------------------------------------------------------------------------

upper sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G102858_T01 (Zea mays), 5'ss of exon 10
GTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctatttacttaatttattattaacgaaatgatacaccaacatatgtcaacattaattcgtctgtgtgggtttttgtgcatgtcttgaa-atatatgtttgctatatgctattaccttttctattctcccaagtgtaacttcagaagtatctatatggaatgtgtggaacag
|||   || ||  | || || | ||| || || || || ||  |  | || |||||||| ||||||||||| ||||| || |||||||||||||||    |   ||||      | | | |  | | |  ||   | | | || ||    ||| || ||   |    | |||    | || |||||  | |||  |  |                                                                       
GTTTTCTCGATCAGAGATGCTGGTGCCAATAATTTAAAGCGTTTGACAGAGGAATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCTCAGgttagctttagtactgtgaaaaatgtaatagcatt--tattgcgataaatttc----ttattttgttctta--agctttaaaccttgacttgagcaaatacatgagtc---------------------------------------------------------------------

upper sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 10
lower sequence: AT1G13320.1 (Arabidopsis thaliana), 5'ss of exon 10
GTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctatttacttaatttattattaacgaaatgatacaccaacatatgtcaacattaattcgtctgtgtgggtttttgtgcatgtcttgaaatatatgtttgctatatgctattaccttttctattctcccaagtgtaacttcagaagtatctatatggaatgtgtggaacag
||||| ||||| |||||||| ||||| |||||  |||| || ||||||||||| ||||||||||| ||||| |||||||| ||| |||||||||||  | ||   |  | |   ||     |    ||| |    |||   |  || |    | ||   || | ||| | || | | || | |     |  |                                                                             
GTTCACTCAATCCGTGAAGCTGCTGCAAACAATCTGAAGCGTCTTGCTGAAGAGTTTGGTCCTGAATGGGCAATGCAGCATATAGTTCCTCAGgtttgtgtagaaatcttaagcat-----atagtatgttt--tcaattcaaatcga--gcattttagctat-tggttattggagtatatttacttgttcag----------------------------------------------------------------------------

upper sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 10
lower sequence: AT3G25800.1 (Arabidopsis thaliana), 5'ss of exon 9
GTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctatttacttaatttattattaacgaaatgatacaccaacatatgtcaacattaattcgtctgtgtgggtttttgtgcatgtcttgaaatatatgtttgctatatgctattaccttttctattctcccaagtgtaacttcagaagtatctatatggaatgtgtggaacag
||||| ||||| || || || |||||||||||  | || || |||||||| |||||||||||||| ||||| ||||| || ||| |||||||||||  ||||   | ||  |  |   |||   || | |     | |  | ||| |   |||||| |||  | |   ||  |  |||                                                                                           
GTTCACTCAATCCGCGATGCTGCTGCTAACAATCTCAAGCGGCTTGCTGAGGAATTTGGTCCTGAATGGGCAATGCAACATATAGTTCCTCAGgtttgtcta--gaatttttacaactttagaaaagtca-gtgtctatct-tgttagtgttaattagtcgctattcattaatccgcag------------------------------------------------------------------------------------------

upper sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 10
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 5'ss of exon 9
GTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctatttacttaatttattattaacga--aatgatacaccaacatatgtcaacattaattcgtctgtgtgggtttttgtgcatgtcttgaaatatatgtttgctatatgctattaccttttctattctcccaagtgtaacttcagaagtatctatatggaatgtgtggaacag
||| | || |||||||| || |||||||||||||| || |||||||| ||||||||||||||||| ||||| ||||||||| ||||||| ||||||  |||| |   |      |||| |  | |  | ||       ||     ||  | || | ||            || |  | | | | |    || |  |||||                                                                       
GTTTACTCCATTCGTGATGCTGCTGCTAACAACTTAAAGCGCCTTGCAGAAGAATTTGGTCCTGACTGGGCAATGCAGCACTTAATTCCACAGgtttgtctagtggttgtgacaattaattgctattagtggcttgtaaaggatagtggatatgagttt-------caaattctcat-cttatttc---attttggtttgtctc-------------------------------------------------------------------

upper sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 10
lower sequence: PP1S214_34V6.1 (Physcomitrella patens), 5'ss of exon 9
GTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctatttacttaatt-tattattaacgaaatgatacaccaacata----tgtcaacattaattcgtctgtgtgggtttttgtgcatgtcttgaaatatatgtttgctatatgctattaccttttctattctcccaagtgtaacttcagaagtatctatatggaatgtgtggaacag
||  | || || || || |||||||| |||||  | || || ||||| ||||| |||||||||||||||||  |||||||||| ||||| ||||| | ||  ||||    ||| || |    || |  |     || |   ||     ||   | || |     | |    || || | |   ||||     | ||  |||    ||  | ||       ||| ||||   |     |   ||| || | ||     ||| |  ||  |     
GTGTACTCTATCCGAGAGGCAGCTGCCAACAATCTCAAGCGTCTTGCCGAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAGgtac-tcgctttataagattgtagtgaggactatcttggtaacgagtgtagaatcgtgggcttttacata-cagcacaggcttgtctatctgtc-----agatccgttaaacatgagataactttcattcaattcctacgttattgttttctgatgaattgg--tgggacttgcag-----

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|151403929|gb|EV273739.1|EV273739
EST:     TTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAG                         GTTTTGGAGATGAACAACAACCCACACTATTTGTATCGGATGACTATTCTT
genomic: TTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctat ... tgtggaacagGTTTTGGAGATGAACAACAACCCACACTATTTGTATCGGATGACTATTCTT
EST: gi|151407658|gb|EV277473.1|EV277473
EST:     TTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAG                         GTTTTGAAGATGAACAACAACCCACACTATTTGTATCGGATGACTATTCTT
genomic: TTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctat ... tgtggaacagGTTTTGGAGATGAACAACAACCCACACTATTTGTATCGGATGACTATTCTT
EST: gi|17153685|gb|BM143618.1|BM143618
EST:     TTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAG                         GTTTTGGAGATGAACAACAACCCACACTATTTGTATCGGATGACTATTCTT
genomic: TTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctat ... tgtggaacagGTTTTGGAGATGAACAACAACCCACACTATTTGTATCGGATGACTATTCTT
EST: gi|14012021|gb|BG726943.1|BG726943
EST:     TTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAG                         GTTTTGGAGATGAACAACAACCCACACTATTTGTATCGGATGACTATTCTT
genomic: TTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctat ... tgtggaacagGTTTTGGAGATGAACAACAACCCACACTATTTGTATCGGATGACTATTCTT
EST: gi|254336135|gb|GR841460.1|GR841460
EST:     TTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAG                         GTTTTGGAGATGAACAACAACCCACACTATTTGTATCGGATGACTATTCTT
genomic: TTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctat ... tgtggaacagGTTTTGGAGATGAACAACAACCCACACTATTTGTATCGGATGACTATTCTT
EST: gi|254343718|gb|GR857474.1|GR857474
EST:     TTGCTGAAGAATTTGGT-CTGAGTGGGCTATGCAGCACATAATTCCTCAG                         GTTTTGGAGATGAACAACAACCCACACTATTTGTATCGGATGACTATTCTT
genomic: TTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctat ... tgtggaacagGTTTTGGAGATGAACAACAACCCACACTATTTGTATCGGATGACTATTCTT
EST: gi|254331030|gb|GR842295.1|GR842295
EST:     TTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAG                         GTTTTGGAGATGAACAACAACCCACACTATTTGTATCGGATGACTATTC
genomic: TTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctat ... tgtggaacagGTTTTGGAGATGAACAACAACCCACACTATTTGTATCGGATGACTATTC
EST: gi|19270079|gb|BM886335.1|BM886335
EST:     TTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAG                         GTTTTGGAGATGAACAACAACCCACACTATTTGTATCGGATGACTATTCTT
genomic: TTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctat ... tgtggaacagGTTTTGGAGATGAACAACAACCCACACTATTTGTATCGGATGACTATTCTT
EST: gi|254331031|gb|GR842296.1|GR842296
EST:     TGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAG                         GTTTTGGAGATGAACAACAACCCACACTATTTGTATCGGATGACTATTCTT
genomic: TGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctat ... tgtggaacagGTTTTGGAGATGAACAACAACCCACACTATTTGTATCGGATGACTATTCTT
EST: gi|16105352|gb|BI893092.1|BI893092
EST:     TTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAG                         GTTTTGGAGATGAACAACAACCCACACTATTTGTATCGGATGACTATTCTT
genomic: TTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctat ... tgtggaacagGTTTTGGAGATGAACAACAACCCACACTATTTGTATCGGATGACTATTCTT
EST: gi|7926502|gb|AW832528.1|AW832528
EST:     TTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAT                         GTTTTGGAGATGAACAACAACCCACACTATCTGTATCGGATGACTATTCTG
genomic: TTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctat ... tgtggaacagGTTTTGGAGATGAACAACAACCCACACTATTTGTATCGGATGACTATTCTT
EST: gi|254343474|gb|GR857230.1|GR857230
EST:     TTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAG                         GTTTTGGAGATGAACAACAACCCACACTATTTGTATCGGATGACTATTCTT
genomic: TTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctat ... tgtggaacagGTTTTGGAGATGAACAACAACCCACACTATTTGTATCGGATGACTATTCTT
EST: gi|254343473|gb|GR857229.1|GR857229
EST:     TTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAG                         GTTTTGGAGATGAACAACAACCCACACTATTTGTATCGGATGACTATTCTT
genomic: TTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctat ... tgtggaacagGTTTTGGAGATGAACAACAACCCACACTATTTGTATCGGATGACTATTCTT
EST: gi|17400839|gb|BM177621.1|BM177621
EST:     TTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAG                         GTTTTGGAGATGAACAACAACCCACACTATTTGTATCGGATGACTATTCTT
genomic: TTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctat ... tgtggaacagGTTTTGGAGATGAACAACAACCCACACTATTTGTATCGGATGACTATTCTT
EST: gi|26059184|gb|CA802098.1|CA802098
EST:     TTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATACTTCCTCAG                         GTTTTGGAGATGAACAACAACCCACACTATTTGTATCGGATGACTATTCTT
genomic: TTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctat ... tgtggaacagGTTTTGGAGATGAACAACAACCCACACTATTTGTATCGGATGACTATTCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctatttacttaatttattattaacgaaatgatacaccaacatatgtcaacattaattcgtctgtgtgggtttttgtgcatgtcttgaaatatatgtttgctatatgctattaccttttctattctcccaagtgtaacttcagaagtatctatatggaatgtgtggaacag

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