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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGAAACAATATCTCTGTTGGTGCTTCTGGTGCTCTATTTGGACTTCTTGGTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAGgtgagtataaagtcattggttcccatcctatttttgttttctgtgtgtttgttagttcttttgaaaaggaaaatgattaatgttatgaaaagattgacaa...

Basic information

species Glycine max
transcript GLYMA09G26610.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G26610.2 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os09g35730.1 (Oryza sativa), 5'ss of exon 3
TAGAAACAATATCTCTGTTGGTGCTTCTGGTGCTCTATTTGGACTTCTTGGTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAGgtgagtataaagtcattggttcccatcctatttttgttttctgtgtgtttgttagttcttttgaaaaggaaaatgattaatgttatgaaaagattgacaa
||  ||| | ||||||||||| || ||||| ||| |||||||||| |||||  |||||||||| || ||||| |  ||||||| ||||||| |||| ||||| |||| || |  || | | | ||| | |||||   | |     || ||| |  || ||||||  | |  |||    | | ||                
TAATAACTACATCTCTGTTGGAGCCTCTGGAGCTTTATTTGGACTGCTTGGATCAATGCTTTCTGAGCTTATTATGAACTGGACTATTTATTCCAACAAGgttagta-aatgagatagatgcacatac-attttcactattcagttgcttgatgtttgttttgatcaagctaat--ccactcttgcag------------

upper sequence: GLYMA09G26610.2 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G033937_T01 (Zea mays), 5'ss of exon 3
TAGAAACAATATCTCTGTTGGTGCTTCTGGTGCTCTATTTGGACTTCTTGGTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAGgtgagtataaagtcattggttcccatcctatttttgttttctgtgtgtttgttagttcttttgaaaaggaaaatgattaatgttatgaaaagattgacaa
 |  ||| | |||||||||||||||||||| ||| ||||||| || |||||  | |||||||| || ||  |||  ||||||| ||| ||  |||| ||||  |||| ||  | |  | |    ||    ||| | || ||    || ||| ||||  ||| |       |  | |||  || | |   |          
GAATAACTACATCTCTGTTGGTGCTTCTGGAGCTTTATTTGGCCTGCTTGGATCCATGCTTTCTGAGCTACTCATGAACTGGACTATATACTCCAACAAGgccagtacaat-taacagataaatatatactttattttatccagctgcttgatagtcatttagctcgtatacttaatt--tgctcttgcag---------

upper sequence: GLYMA09G26610.2 (Glycine max), 5'ss of exon 3
lower sequence: AT5G07250.2 (Arabidopsis thaliana), 5'ss of exon 3
TAGAAACAATATCTCTGTTGGTGCTTCTGGTGCTCTATTTGGACTTCTTGGTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAGgtgagtataaa---gtcattggttcccatcctatttttgttttctgtgtgtttgttagttcttttgaaaaggaaa-atgattaatgttatgaaaagattgacaa
 ||||||| |||||||||||| |||||||||||||| ||||| || |||||  ||||||| || |||||| |||| |||||||  || ||  | || ||||| | ||  ||   |   ||  || | | | ||    |   | |    |||| | |  |  || |||   |   | |||    |  ||     |    ||    
CAGAAACAGTATCTCTGTTGGAGCTTCTGGTGCTCTTTTTGGCCTCCTTGGCTCAATGCTCTCTGAACTTTTCACCAACTGGACAATCTACTCTAACAAGgttaataccaatctgcttttcatttcaaacatacaaatcactccatcatgttggctcatgtttctgatctgagcatatgtaccagattgctgcactcctg----

upper sequence: GLYMA09G26610.2 (Glycine max), 5'ss of exon 3
lower sequence: AT5G07250.1 (Arabidopsis thaliana), 5'ss of exon 3
TAGAAACAATATCTCTGTTGGTGCTTCTGGTGCTCTATTTGGACTTCTTGGTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAGgtgagtataaa---gtcattggttcccatcctatttttgttttctgtgtgtttgttagttcttttgaaaaggaaaatgattaatgttatgaaaagattgacaa
 ||||||| |||||||||||| |||||||||||||| ||||| || |||||  ||||||| || |||||| |||| |||||||  || ||  | || ||||| | ||  ||   |   ||  || | | | ||    |   | |    |||| | |  |  || |||   | |  ||   ||                     
CAGAAACAGTATCTCTGTTGGAGCTTCTGGTGCTCTTTTTGGCCTCCTTGGCTCAATGCTCTCTGAACTTTTCACCAACTGGACAATCTACTCTAACAAGgttaataccaatctgcttttcatttcaaacatacaaatcactccatcatgttggctcatgtttctgatctg-agcatatgtaccag-----------------

upper sequence: GLYMA09G26610.2 (Glycine max), 5'ss of exon 3
lower sequence: Vv16s0100g00640.t01 (Vitis vinifera), 5'ss of exon 3
TAGAAACAATATCTCTGTTGGTGCTTCTGGTGCTCTATTTGGACTTCTTGGTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAGgtgagtataaagtcattggttcccatcctatttttgttttctgtgtgtttgttagttcttttgaaaaggaaaatgattaatgttatgaaaagattgacaa
|  ||| |  ||||||||||| |||||||||||||| ||||| ||| | || |||||||||||||| ||||| |||||||||   || ||||| || | |||||| |  |  |       |    || || |  | |   || || | |  ||||   | ||           |                          
TCAAAATAGCATCTCTGTTGGGGCTTCTGGTGCTCTTTTTGGGCTTTTGGGAGCAATGCTTTCAGAGCTTATTACAAACTGGTCCATGTATACAAACAGGgtgagca--atctagcccactgttgtcttactcct-taccctttgagataattagccttgtttgttgcttttgtag------------------------

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|208205195|gb|GE004038.1|GE004038
EST:     GTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAG                         GCAGCTGCTTTGTTCACACTTCTGTT-AT-ATTGTCATCAATCTTGCCATT
genomic: GTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAGgtgagtataa ... cattttgcagGCAGCTGCTTTGTTCACACTTCTGTTTATTATTGTCATCAATCTTGCCATT
EST: gi|193477386|gb|FK441857.1|FK441857
EST:     GTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAG                         GCAGCTGCTTTGTTCACACTTCTGTTTATTATTGTCATCAATCTTGCCATT
genomic: GTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAGgtgagtataa ... cattttgcagGCAGCTGCTTTGTTCACACTTCTGTTTATTATTGTCATCAATCTTGCCATT
EST: gi|208195977|gb|GD988140.1|GD988140
EST:     GTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAG                         GCAGCTGCTTTGTTCACACTTCTGTTTATTATTGTCATCAATCTTGCCATT
genomic: GTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAGgtgagtataa ... cattttgcagGCAGCTGCTTTGTTCACACTTCTGTTTATTATTGTCATCAATCTTGCCATT
EST: gi|207729643|gb|GD707749.1|GD707749
EST:     CAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAG                         GCAGCTGCTTTGTTCACACTTCTGTTTATTATTGTCATCAATCTTGCCATT
genomic: CAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAGgtgagtataa ... cattttgcagGCAGCTGCTTTGTTCACACTTCTGTTTATTATTGTCATCAATCTTGCCATT
EST: gi|6454385|gb|AW185068.1|AW185068
EST:     GTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAG                         GCAGCTGCTTTGTTCACACTTCTGTTTATTATTGTCATCAATCTTGCCATT
genomic: GTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAGgtgagtataa ... cattttgcagGCAGCTGCTTTGTTCACACTTCTGTTTATTATTGTCATCAATCTTGCCATT
EST: gi|193679314|gb|FK619300.1|FK619300
EST:     GTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAG                         GCAGCTGCTTTGTTCACACTTCTGTTTATTATTGTCATCAATCTTGCCATT
genomic: GTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAGgtgagtataa ... cattttgcagGCAGCTGCTTTGTTCACACTTCTGTTTATTATTGTCATCAATCTTGCCATT
EST: gi|208249423|gb|GE050450.1|GE050450
EST:     GTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAG                         GCAGCTGCTTTGTTCACACTTCTGCTTATTATTGTCATCAATCTTGCCATT
genomic: GTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAGgtgagtataa ... cattttgcagGCAGCTGCTTTGTTCACACTTCTGTTTATTATTGTCATCAATCTTGCCATT
EST: gi|207766706|gb|GD738334.1|GD738334
EST:     GTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAG                         GCAGCTGCTTTGTTCACACTTCTGTTTATTATTGTCATCAATCTTGCCATT
genomic: GTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAGgtgagtataa ... cattttgcagGCAGCTGCTTTGTTCACACTTCTGTTTATTATTGTCATCAATCTTGCCATT
EST: gi|207732792|gb|GD713537.1|GD713537
EST:     AGTATTTATACCAATAAG                         GCAGCTGCTTTGTTCACACTTCTGTTTATTATTGTCATCAATCTTGCCATT
genomic: AGTATTTATACCAATAAGgtgagtataa ... cattttgcagGCAGCTGCTTTGTTCACACTTCTGTTTATTATTGTCATCAATCTTGCCATT
EST: gi|208282257|gb|GE076855.1|GE076855
EST:     GTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAG                         GCAGCTGCTTTGTTCACACTTCTGTTTATTATTGTCATCAATCTTGCCATT
genomic: GTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAGgtgagtataa ... cattttgcagGCAGCTGCTTTGTTCACACTTCTGTTTATTATTGTCATCAATCTTGCCATT
EST: gi|208227406|gb|GE025053.1|GE025053
EST:     GTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAG                         GCAGCTGCTTTGTTCACACTTCTGTTTATTATTGTCATCAATCTTGCCATT
genomic: GTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAGgtgagtataa ... cattttgcagGCAGCTGCTTTGTTCACACTTCTGTTTATTATTGTCATCAATCTTGCCATT
EST: gi|207805140|gb|GD778677.1|GD778677
EST:     GTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAG                         GCAGCTGCTTTGTTCACACTTCTGTTTATTATTGTCATCAATCTTGCCATT
genomic: GTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAGgtgagtataa ... cattttgcagGCAGCTGCTTTGTTCACACTTCTGTTTATTATTGTCATCAATCTTGCCATT
EST: gi|208297763|gb|GE094518.1|GE094518
EST:     GTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAG                         GCAGCTGCTTTGTTCACACTTCTGTTTATTATTGTCATCAATCTTGCCATT
genomic: GTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAGgtgagtataa ... cattttgcagGCAGCTGCTTTGTTCACACTTCTGTTTATTATTGTCATCAATCTTGCCATT
EST: gi|208248377|gb|GE048074.1|GE048074
EST:     ATCACAAACTGGAGTATTTATACCAATAAG                         GCAGCTGCTTTGTTCACACTTCTGTTTATTATTGTCATCAATCTTGCCATT
genomic: ATCACAAACTGGAGTATTTATACCAATAAGgtgagtataa ... cattttgcagGCAGCTGCTTTGTTCACACTTCTGTTTATTATTGTCATCAATCTTGCCATT
EST: gi|208112685|gb|GD909708.1|GD909708
EST:     GTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAG                         GCAGCTGCTTTGTTCACACTTCTGTTTATTATTGTCATCAATCTTGCCATT
genomic: GTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAGgtgagtataa ... cattttgcagGCAGCTGCTTTGTTCACACTTCTGTTTATTATTGTCATCAATCTTGCCATT
EST: gi|193548681|gb|FK505800.1|FK505800
EST:     GTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAG                         GCAGCTGCTTTGTTCACACTTCTGTTTATTATTGTCATCAATCTTGCCATT
genomic: GTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAGgtgagtataa ... cattttgcagGCAGCTGCTTTGTTCACACTTCTGTTTATTATTGTCATCAATCTTGCCATT
EST: gi|208288768|gb|GE086573.1|GE086573
EST:     GTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAG                         GCAGCTGCTTTGTTCACACTTCTGTTTATTATTGTCATCAATCTTGCCATT
genomic: GTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAGgtgagtataa ... cattttgcagGCAGCTGCTTTGTTCACACTTCTGTTTATTATTGTCATCAATCTTGCCATT
EST: gi|208261221|gb|GE058675.1|GE058675
EST:     GTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAG                         GCAGCTGCTTTGTTCACACTTCTGTTTATTATTGTCATCAATCTTGCCATT
genomic: GTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAGgtgagtataa ... cattttgcagGCAGCTGCTTTGTTCACACTTCTGTTTATTATTGTCATCAATCTTGCCATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAGAAACAATATCTCTGTTGGTGCTTCTGGTGCTCTATTTGGACTTCTTGGTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAGgtgagtataaagtcattggttcccatcctatttttgttttctgtgtgtttgttagttcttttgaaaaggaaaatgattaatgttatgaaaagattgacaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccatcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaatga