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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCACTTGGCAACCATTCCAATCACAGGAACTGGCATTAACCCAGCTAGGAGTCTTGGTGCTGCTATAATATACAACAGAGACCATGCTTGGGATGACCATgtatatacatgtcctttcacttatgtgcctctttgttttgcatgaaagtgactttatttaactgtttaattttaattgtggcttacag

Basic information

species Glycine max
transcript GLYMA11G02530.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G02530.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os04g47220.1 (Oryza sativa), 5'ss of exon 2
CCACTTGGCAACCATTCCAATCACAGGAACTGGCATTAACCCAGCTAGGAGTCTTGGTGCTGCTATAATATACAACAGAGACCATGCTTGGGATGACCATgtatatacatgtccttt-----cacttatgtgcctctttgttttgcatgaaagtgactttatttaactgtttaattttaattgtg-gcttacag------
 ||| |||| ||||| || ||||| || || ||||| |||||||| ||||| ||||| ||||| || || |||||||| | |||||| ||||||||||||||   |  |  | |  |     ||      | |  | |  ||     |  || |   | ||| ||  | | ||  | ||  | |     || |       
TCACCTGGCCACCATCCCCATCACCGGCACCGGCATCAACCCAGCGAGGAGCCTTGGCGCTGCCATCATCTACAACAGGGGCCATGCCTGGGATGACCATgtgagtttaaattcactgaaaccaacccctttctccctccttacatgtagaaatatatatatatatatatatatatatatatatatatatatatatatat

upper sequence: GLYMA11G02530.1 (Glycine max), 5'ss of exon 3
lower sequence: AC209208.3_FGT002 (Zea mays), 5'ss of exon 3
CCACTTGGCAACCATTCCAATCACAGGAACTGGCATTAACCCAGCTAGGAGTCTTGGTGCTGCTATAATATACAACAGAGACCATGCTTGGGATGACCATgtatatacatgtcctttca-----cttatgtgcctctttgttttgcatgaaagtgactttatttaactgtttaat-tttaattgtggcttacag------
|||| | || ||||| || || || || |||||||| |||||||||||||| ||||| ||||| || || |||||||| || || || ||| | ||||||||   |  |  | || ||      | | |   |  ||||   || | |  |  |   |     |  | || |||| | |   |     |  |||      
CCACCTTGCCACCATCCCCATTACTGGCACTGGCATCAACCCAGCTAGGAGCCTTGGCGCTGCCATCATCTACAACAGGGATCACGCCTGGAACGACCATgtgagtggaactactctcgattcccctctaaccaactttccatttcctacagtttggtaccactcgcagtgtaatgtctccatccaaatatcagacatcc

upper sequence: GLYMA11G02530.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv15s0046g02410.t01 (Vitis vinifera), 5'ss of exon 3
CCACTTGGCAACCATTCCAATCACAGGAACTGGCATTAACCCAGCTAGGAGTCTTGGTGCTGCTATAATATACAACAGAGACCATGCTTGGGATGAC----CATgtatatacatgtcctttca------cttatgtgcctctttgttttgcatgaaa--gtgacttta---tttaactgtttaattttaattgtggcttacag
 ||  |||||||||| || ||||| ||||| ||||| ||||| ||||||||||| || || || || || |||||||| |   |||| |||||||||     | ||  | ||||  |  |  |      |  |   || |||    |   |||  |   |||| | |    | ||    ||| ||| |  ||||  |   |||
TCATCTGGCAACCATCCCCATCACCGGAACCGGCATCAACCCTGCTAGGAGTCTCGGGGCCGCCATCATCTACAACAGGGGGAATGCCTGGGATGACATGgtaagtgaaaacattgctctataagaagacccaatagcttctcatctcgtcatctatctgtgaatctgacttgtattgatttcattcttgttgttcccatcag

upper sequence: GLYMA11G02530.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv15s0046g02420.t01 (Vitis vinifera), 5'ss of exon 3
CCACTTGGCAACCATTCCAATCACAGGAACTGGCATTAACCCAGCTAGGAGTCTTGGTGCTGCTATAATATACAACAGAGACCATGCTTGGGATGACCATgta-------tatacatgtcctttcacttatgtgcctctttgttt-tgcatgaaagtgactttatttaactgtttaattttaattgtggcttacag
 ||  |||||||||| || ||||| ||||| ||||| ||||| ||||||||||| || || || || || ||||||||||| ||||| |||||||||   |||       |   ||   ||  |||||| |    ||| |  ||| |   ||||  || |||   || | |   |  ||||  ||||  | | |||
TCATCTGGCAACCATCCCCATCACCGGAACCGGCATCAACCCTGCTAGGAGTCTGGGGGCCGCCATCATCTACAACAGAGAGCATGCCTGGGATGACATGgtaagctccatgatcagacccaatcacttct-catctcatcatttatctgtgaatctgccttgtattgatttcattcttttg-ttgttcccttcag

upper sequence: GLYMA11G02530.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv02s0025g03390.t01 (Vitis vinifera), 5'ss of exon 3
CCACTTGGCAACCATTCCAATCACAGGAACTGGCATTAACCCAGCTAGGAGTCTTGGTGCTGCTATAATATACAACAGAGACCATGCTTGGGATGAC----CATgtatatacatgtcctttcacttatgtgcctc-------tttgttttgcatgaaagtgactttatttaactgtttaa-ttttaattgtggcttacag--------------
 |||||||| ||||| || |||||||||||||||||||||||||| ||||||||||| |||||||| || | ||||||||| ||||| |||||||||     | || | |  |||       |   |     |         ||||  |    |||  || |  ||   |  | ||| || || | |||||| |||                  
TCACTTGGCCACCATCCCCATCACAGGAACTGGCATTAACCCAGCCAGGAGTCTTGGAGCTGCTATCATCTTCAACAGAGAGCATGCATGGGATGACATGgtaggtgttttgatgagaaaaaaaaaaaaaaacctaaggaattttgcatcctttgatggttaaattgagtttcagttcaagttcttattgtgactttttttctcttgctttcag

upper sequence: GLYMA11G02530.1 (Glycine max), 5'ss of exon 3
lower sequence: PP1S102_107V6.1 (Physcomitrella patens), 5'ss of exon 3
CCACTTGGCAACCATTCCAATCACAGGAACTGGCATTAACCCAGCTAGGAGTCTTGGTGCTGCTATAATATACAACA---GAGACCATGCTTGGGATGACCATgtatat-acatgtcctttcacttatgtgcctctttgttttgcatgaaagt---gactt--tatttaactgtttaattttaattg---tggcttacag--------------------------------------------------------------------
    ||||| |||||||| ||||| ||||||||||||||||| ||  | ||||| || || || |  || |||||||      || |||| ||||  || || ||   |  |||   ||| |||   |    ||     ||     | || ||   |||||    | |     |||| |||  || |    ||  || |                                                                     
---TTTGGCCACCATTCCCATCACCGGAACTGGCATTAACCCTGCACGTAGTCTGGGCGCGGCCACCATCTACAACACGCAGCACAATGCCTGGGCCGATCACgtgagttgcattctcttccaccactcctgctgaaaattcaaggttaaggttaggacttatcgtctggagatttattttctatgggttcggtctagaaacgaatggttatcaggcacaatatgaaggagctgtaacctctctgaaatgttgattgtgctgctgcag

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|208295980|gb|GE092230.1|GE092230
EST:     GTCTTGGTGCTGCTATAATATACAACAGAGACCATGCTTGGGATGACCAT                         TGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCAGCTTTATAT
genomic: GTCTTGGTGCTGCTATAATATACAACAGAGACCATGCTTGGGATGACCATgtatatacat ... tggcttacagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCAGCTTTATAT
EST: gi|6848062|gb|AW350352.1|AW350352
EST:     GTCTTGGTGCTGCTATAATATACAACAGAGACCATGCTTGGGATGACCAT                         TGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCAGCTTTATAT
genomic: GTCTTGGTGCTGCTATAATATACAACAGAGACCATGCTTGGGATGACCATgtatatacat ... tggcttacagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCAGCTTTATAT
EST: gi|19270654|gb|BM886910.1|BM886910
EST:     GTCTTGGTGCTGCTATAATATACAACAGAGACCATGCTTGGGATGACCAT                         TGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCAGCTTTATAT
genomic: GTCTTGGTGCTGCTATAATATACAACAGAGACCATGCTTGGGATGACCATgtatatacat ... tggcttacagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCAGCTTTATAT
EST: gi|192325960|gb|FK016637.1|FK016637
EST:     GTCTTGGTGCTGCTATAATATACA-CAGAGACCATGCTTGGGATGACCAT                         TGGATTTTCTGGGT-GGAC-TTTCATTGGAGCTGCCCTTGCAGCTTTATAT
genomic: GTCTTGGTGCTGCTATAATATACAACAGAGACCATGCTTGGGATGACCATgtatatacat ... tggcttacagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCAGCTTTATAT
EST: gi|21601397|gb|BQ611728.1|BQ611728
EST:     GTCTTGGTGCTGCTATAATATACAACAGAGACCATGCTTGGGATGACCAT                         TGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCAGCTTTATAT
genomic: GTCTTGGTGCTGCTATAATATACAACAGAGACCATGCTTGGGATGACCATgtatatacat ... tggcttacagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCAGCTTTATAT
EST: gi|10842879|gb|BF066240.1|BF066240
EST:     GTCTTGGTGCTGCTATAATATACAACAGAGACCATGCTTGGGATGACCAT                         AGGATTTTCTGGGTTGGACCTCTCATTGGAGCTGCCCTTGCAGCTTTATAT
genomic: GTCTTGGTGCTGCTATAATATACAACAGAGACCATGCTTGGGATGACCATgtatatacat ... tggcttacagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCAGCTTTATAT
EST: gi|4285014|gb|AI440853.1|AI440853
EST:     GTCTTGGTGCTGCTATAATATACAACAGAGACCATGCTTGGGATGACCAT                         TGGATTNTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCAGCTTTATAT
genomic: GTCTTGGTGCTGCTATAATATACAACAGAGACCATGCTTGGGATGACCATgtatatacat ... tggcttacagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCAGCTTTATAT
EST: gi|192317537|gb|FK011299.1|FK011299
EST:     GTCTTGGTGCTGCTATAATATACAACAGAGACCATGCTTGGGATGACCAT                         TGGATTTTTTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCAGCTTTATAT
genomic: GTCTTGGTGCTGCTATAATATACAACAGAGACCATGCTTGGGATGACCATgtatatacat ... tggcttacagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCAGCTTTATAT
EST: gi|15663877|gb|BI701248.1|BI701248
EST:     GTCTTGGTGCTGCTATAATATACAACAGAGACCATGCTTGGGATGACCAT                         TGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCAGCTTTATAT
genomic: GTCTTGGTGCTGCTATAATATACAACAGAGACCATGCTTGGGATGACCATgtatatacat ... tggcttacagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCAGCTTTATAT
EST: gi|193433096|gb|FK398730.1|FK398730
EST:     GGGATGACCAT                         TGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCAGCTTTATAT
genomic: GGGATGACCATgtatatacat ... tggcttacagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCAGCTTTATAT
EST: gi|14125700|gb|BG790138.1|BG790138
EST:     GTCTTGGTGCTGCTATAATATACAACAGAGACCATGCTTGGGATGACCAT                         TGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTCGCAGCTTTATAT
genomic: GTCTTGGTGCTGCTATAATATACAACAGAGACCATGCTTGGGATGACCATgtatatacat ... tggcttacagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCAGCTTTATAT
EST: gi|18848973|gb|BM568083.1|BM568083
EST:     GTCTTGGTGCTGCTATAATATACAACAGAGACCATGCTTGGGATGACCAT                         TGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCAGCTTTATAT
genomic: GTCTTGGTGCTGCTATAATATACAACAGAGACCATGCTTGGGATGACCATgtatatacat ... tggcttacagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCAGCTTTATAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCACTTGGCAACCATTCCAATCACAGGAACTGGCATTAACCCAGCTAGGAGTCTTGGTGCTGCTATAATATACAACAGAGACCATGCTTGGGATGACCATgtatatacatgtcctttcacttatgtgcctctttgttttgcatgaaagtgactttatttaactgtttaattttaattgtggcttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT