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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATGAAGAAGGCACTTCCTGCCAACGGTAAAATCGCAAAGGACGCCAAAGAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGAgttagtgtgttttttttttcttctgattcttttctcctccgtttttcttatttatcatcgcctgcttttaatttaaaattccttgaattctgtag

Basic information

species Glycine max
transcript GLYMA03G33490.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G33490.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os05g38820.5 (Oryza sativa), 5'ss of exon 1
TCATGAAGAAGGCACTTCCTGCCAACGGTAAAATCGCAAAGGACGCCAAAGAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGAgttagtgtgttttttttttcttctgattcttttctcctccgtttttcttatttatcatcgcct--gcttttaatttaaaattccttgaat--tctgtag-----------------------------------------------------
|||||||||||||  | || |||||||| || ||||| ||||||||||| |||||||| ||||| ||||||||||||||||||  ||||||||||||||||| |||        |  | || |    |||| |   || |  |  |||  | | || ||   |  | ||| |  ||  |  || |||  |    ||| |                                                     
TCATGAAGAAGGCCATCCCGGCCAACGGGAAGATCGCCAAGGACGCCAAGGAGACCGTGCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACCAGCGAgtgagtcgtcgccctcgtcctcccccctcttgtgctctgctctgctctgctctgtcttcttttgagttttgagctttgagctcgttgtttgacttgtcgttggcggcgatgagatgtgactgggtttttgttgtggtggggcaacattacag

upper sequence: GLYMA03G33490.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os01g61810.3 (Oryza sativa), 5'ss of exon 2
TCATGAAGAAGGCACTTCCTGCCAACGGTAAAATCGCAAAGGACGCCAAAGAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGAgttagt--gtgttttttttttcttctgattcttttctcctccgtttttcttatttatcatcgcctgcttttaatttaaaattccttgaattctgtag---------------------------
|||||||||||||  | || || ||||| || ||||| ||||||||||| |||||| | ||||| |||||||| |||||||||  |||| |||||||||||| |||  | |     |   |    |||| ||   |||| |     |||||  || | || |   | ||    | | |  || |||   || ||| |                           
TCATGAAGAAGGCCGTCCCGGCGAACGGCAAGATCGCCAAGGACGCCAAGGAGACCCTGCAGGAGTGCGTCTCGGAGTTCATCTCCTTCGTCACCAGCGAgtgagtctgcgcgggctcggtaccgtgatcctgccctccccacaccttctt--ttgtgatggttggtttagggtgtgattttgctttgctt-tgtggtttgggcggtggtgcgggatgggacag

upper sequence: GLYMA03G33490.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM5G804893_T01 (Zea mays), 5'ss of exon 2
TCATGAAGAAGGCACTTCCTGCCAACGGTAAAATCGCAAAGGACGCCAAAGAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGAgttagtgtgttttttttttcttctgattcttttctcctccgtttttcttatttatcatcgcctgcttttaa---tttaaaattccttgaattctgtag-----------------------------------------
|||||||||||||  | || || ||||| || ||||| |||||||| || |||||||| ||||| ||||||||||||||||||  ||||||||| ||||||| ||||     |    | |  |||| ||||   |   |     || ||    ||        || || |    ||||   |  || |  || |||                                           
TCATGAAGAAGGCCATCCCGGCTAACGGGAAGATCGCCAAGGACGCTAAGGAGACCGTGCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACTAGCGAgtaagtgc---ctcagctgcggctgactcttacttttgcttggcttgttgggaatttggagtggcgttcagggctttagcttggctggggttttgtgttgacttgtccatgtccacgtttttttgtccgctctttgcag

upper sequence: GLYMA03G33490.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G064426_T02 (Zea mays), 5'ss of exon 2
TCATGAAGAAGGCACTTCCTGCCAACGGTAAAATCGCAAAGGACGCCAAAGAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGAgttagtgtgttttttttttct---tctgattcttttctcctccgtttttcttatttatcatcgcctgcttttaatttaaaattccttgaattctgtag--------------------------------------------------
|||||||||||||  | || || ||||| || ||||| |||||||| || |||||||| ||||| |||||||| |||||||||  ||||||||| ||||||| |||   |         ||   ||||| |||| | |   |      | ||    ||        || |||     |     | ||   ||  || |                                                  
TCATGAAGAAGGCCATCCCGGCTAACGGGAAGATCGCCAAGGACGCTAAGGAGACCGTGCAGGAGTGCGTCTCGGAGTTCATCTCCTTCATCACTAGCGAgtaagtccctcggccgcggctgactctgactcttctgtttgcttggcatgttgggaattcagagtggcgtttcgcaaaccgcactttagcttaggtggggttttgtgttgacttgtctacgtccacgttccttgtctgctgtttgcag

upper sequence: GLYMA03G33490.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G303465_T04 (Zea mays), 5'ss of exon 1
TCATGAAGAAGGCACTTCCTGCCAACGGTAAAATCGCAAAGGACGCCAAAGAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGAgttagtgtgttttttttttcttctgatt--------cttttctcctccgtttttcttatttatcatcgcctgcttttaatttaaaattccttgaattctgtag------------------------
|||||||||||||  | || |||||||| || ||||| |||||||| || |||||| | ||||| |||||||||||||||||    ||| | |||||||||| |||      ||     |  ||| |         | |  |    || |  |  |   |     | |  |   |||  |||||  |    |   |||||  |                        
TCATGAAGAAGGCCGTCCCGGCCAACGGCAAGATCGCCAAGGACGCTAAGGAGACCCTGCAGGAGTGCGTCTCCGAGTTCATATCATTCGTGACCAGCGAgtaagttgacagttggcaccgcctggtagacggtagcgtagcgtagccttggtcttggatcgggttggtttttctttgttttaatgtaggataggttctgatgtaagttcacgggtgctggttgcag

upper sequence: GLYMA03G33490.1 (Glycine max), 5'ss of exon 2
lower sequence: AT3G53340.1 (Arabidopsis thaliana), 5'ss of exon 2
TCATGAAGAAGGCACTTCCTGCCAACGGTAAAATCGCAAAGGACGCCAAAGAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGAgttagtgtgttttttttttcttctgattcttttctcctccgtttttcttatttatcatcgcctg------cttttaattta--aaattccttgaattctgtag-----------------------------------------------------------
|||||||||  |   | |||   || || |||||||| || || || ||||||||  | |||||||| ||||| || |||||||||||| |||||||||||| | |   || | |  ||  ||  |    || |   |  |||  | ||  |  | || || ||      | | |  |||   || ||   |  ||  | ||                                                            
TCATGAAGAGAGGTTTACCTCTAAATGGCAAAATCGCTAAAGATGCTAAAGAGACTATGCAGGAATGTGTCTCTGAATTCATCAGCTTCGTCACCAGCGAgtaatttctttctctactttctcaaaaatgttacctttttgttgct-ttggtggttatagcgtgtaaagccctcttctttgttaagttagattgatgttatattcattgggttgttaagcaaagtcactatgtcgattttggaatattgttttgccttttag

upper sequence: GLYMA03G33490.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv08s0040g03260.t01 (Vitis vinifera), 5'ss of exon 1
TCATGAAGAAGGCACTTCCTGCCAACGGTAAAATCGCAAAGGACGCCAAAGAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGAgt-tagtgtgttttttttttcttctgattcttttctcctccgtttttcttatttatcatcgcctgcttttaatttaaaattccttgaattctgtag
||||||||||||| ||||| || || || || ||||| ||||| || ||||||| | | || ||||||||||| ||||||||||| |||||||| ||||||| | |    |   ||||||||| | | | ||      | |||  ||  |  |  |  | |  |  ||||    |   || ||| |          
TCATGAAGAAGGCGCTTCCCGCGAATGGAAAGATCGCTAAGGATGCGAAAGAGATCATGCAAGAATGCGTCTCGGAGTTCATCAGTTTCATCACTAGCGAgtatggctgatgcattttttctttttaattttaggcggtgcgtgattgatggtgttgttggttttgtttttcaattggatgcctag----------

upper sequence: GLYMA03G33490.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ15374 (Selaginella moellendorffii), 5'ss of exon 1
TCATGAAGAAGGCACTTCCTGCCAACGGTAAAATCGCAAAGGACGCCAAAGAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGAgttagtgtgttttttttttcttctgattcttttctcctccgtttttcttatttatcatcgcctgcttttaatttaaaattccttgaattctgtag
| ||||||||||| || || || || |  || ||||| ||||| ||||| ||||| || || ||||||||||| |||||||||||||||||||| ||||||| ||| |   ||   |   || || |  | ||  |   | || ||||  ||| |                                        
TAATGAAGAAGGCGCTGCCGGCGAATGCAAAGATCGCCAAGGATGCCAAGGAGACGGTGCAAGAATGCGTCTCGGAGTTCATCAGCTTCATCACTAGCGAgtaagtattgcttcgatcctttgtggtgatgttaactatc-ttcttctactttgtag--------------------------------------

upper sequence: GLYMA03G33490.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ24973 (Selaginella moellendorffii), 5'ss of exon 1
TCATGAAGAAGGCACTTCCTGCCAACGGTAAAATCGCAAAGGACGCCAAAGAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGAgttagtgtgttttttttttcttctgattcttttctcctccgtttttcttatttatcatcgcctgcttttaatttaaaattccttgaattctgtag
| ||||||||||| || || || || |  || ||||| ||||| ||||| ||||| || || ||||||||||| |||||||||||||||||||| ||||||| ||| |   |     |||||  ||| ||||          | |  |  | || | | ||                                  
TAATGAAGAAGGCGCTGCCGGCGAATGCAAAGATCGCCAAGGATGCCAAGGAGACGGTGCAAGAATGCGTCTCAGAGTTCATCAGCTTCATCACTAGCGAgtaagtattgctggaagttctttcgatcctttgtggtgatactatcttcttcta-ctttgcag--------------------------------

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|8826311|gb|BE210041.1|BE210041
EST:     GAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGA                         GGCCTCTGATAAGTGTCAGAGAGAAAAGAGAAAGACTATTAACGGCGATGA
genomic: GAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGAgttagtgtgt ... aattctgtagGGCCTCTGATAAGTGTCAGAGAGAAAAGAGAAAGACTATTAACGGCGATGA
EST: gi|21677121|gb|BQ629472.1|BQ629472
EST:     GAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGA                         GGCCTCTGATAAGTGTCAGAGAGAAAAGAGAAAGACTATTAACGGCGATGA
genomic: GAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGAgttagtgtgt ... aattctgtagGGCCTCTGATAAGTGTCAGAGAGAAAAGAGAAAGACTATTAACGGCGATGA
EST: gi|6133966|gb|AW132359.1|AW132359
EST:     GAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGA                         GGCCTCTGATAAGTGTCAGAGAGAAAAGAGAAAGACTATTAACGGCGATGA
genomic: GAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGAgttagtgtgt ... aattctgtagGGCCTCTGATAAGTGTCAGAGAGAAAAGAGAAAGACTATTAACGGCGATGA
EST: gi|5605926|gb|AI900024.1|AI900024
EST:     GAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGA                         GGCCTCTGATAAGTGTCAGAGAGAAAAGAGAAAGACTATTAACGGCGATGA
genomic: GAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGAgttagtgtgt ... aattctgtagGGCCTCTGATAAGTGTCAGAGAGAAAAGAGAAAGACTATTAACGGCGATGA
EST: gi|298195680|gb|HO044071.1|HO044071
EST:     GAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGA                         GGCCTCTGATAAGTGTCAGAGAGAAAAGAGAAAGACTATTAACGGCGATGA
genomic: GAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGAgttagtgtgt ... aattctgtagGGCCTCTGATAAGTGTCAGAGAGAAAAGAGAAAGACTATTAACGGCGATGA
EST: gi|298176576|gb|HO023163.1|HO023163
EST:     GAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGA                         GGCCTCTGATAAGTGTCAGAGAGAAAAGAGAAAGACTATTAACGGCGATGA
genomic: GAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGAgttagtgtgt ... aattctgtagGGCCTCTGATAAGTGTCAGAGAGAAAAGAGAAAGACTATTAACGGCGATGA
EST: gi|298176152|gb|HO015557.1|HO015557
EST:     GAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGA                         GGCCTCTGATAAGTGTCAGAGAGAAAAGAGAAAGACTATTAACGGCGATGA
genomic: GAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGAgttagtgtgt ... aattctgtagGGCCTCTGATAAGTGTCAGAGAGAAAAGAGAAAGACTATTAACGGCGATGA
EST: gi|16346723|gb|BI972318.1|BI972318
EST:     GAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGA                         GGCCTCTGATAAGTGTCAGAGAGAAAAGAGAAAGACTATTAACGGCGATGA
genomic: GAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGAgttagtgtgt ... aattctgtagGGCCTCTGATAAGTGTCAGAGAGAAAAGAGAAAGACTATTAACGGCGATGA
EST: gi|7285143|gb|AW597630.1|AW597630
EST:     GAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGA                         GGCCTCTGATAAGTGTCAGAGAGAAAAGAGAAAGACTATTAACGGCGATGA
genomic: GAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGAgttagtgtgt ... aattctgtagGGCCTCTGATAAGTGTCAGAGAGAAAAGAGAAAGACTATTAACGGCGATGA
EST: gi|5761187|gb|AI966550.1|AI966550
EST:     GTCTCCCAGTTCATCAGCTTCATCACCAGCGA                         GGCCTCTGATTAGTGTCAGAGAGAAAAGAGAAAGACTATTAACGGCGATGA
genomic: GTCTCCGAGTTCATCAGCTTCATCACCAGCGAgttagtgtgt ... aattctgtagGGCCTCTGATAAGTGTCAGAGAGAAAAGAGAAAGACTATTAACGGCGATGA
EST: gi|298168250|gb|HO013513.1|HO013513
EST:     GAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGA                         GGCCTCTGATAAGTGTCAGAGAGAAAAGAGAAAGACTATTAACGGCGATGA
genomic: GAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGAgttagtgtgt ... aattctgtagGGCCTCTGATAAGTGTCAGAGAGAAAAGAGAAAGACTATTAACGGCGATGA
EST: gi|18730588|gb|BM525962.1|BM525962
EST:     GAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGA                         GGCCTCTGATAAGTGTCAGAGAGAAAAGAGAAAGACTATTAACGGCGATGA
genomic: GAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGAgttagtgtgt ... aattctgtagGGCCTCTGATAAGTGTCAGAGAGAAAAGAGAAAGACTATTAACGGCGATGA
EST: gi|7029546|gb|AW459387.1|AW459387
EST:     GAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGA                         GGCCTCTGATAAGTGTCAGAGAGAAAAGAGAAAGACTATTAACGGCGATGA
genomic: GAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGAgttagtgtgt ... aattctgtagGGCCTCTGATAAGTGTCAGAGAGAAAAGAGAAAGACTATTAACGGCGATGA
EST: gi|8284382|gb|BE021941.1|BE021941
EST:     GAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGA                         GGCCTCTGATAAGTGTCAGAGAGAAAAGAGAAAGACTATTAACGGCGATGA
genomic: GAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGAgttagtgtgt ... aattctgtagGGCCTCTGATAAGTGTCAGAGAGAAAAGAGAAAGACTATTAACGGCGATGA
EST: gi|14991093|gb|BI316766.1|BI316766
EST:     GAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGA                         GGCCTCTGATAAGTGTCAGAGAGAAAAGAGAAAGACTATTAACGGCGATGA
genomic: GAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGAgttagtgtgt ... aattctgtagGGCCTCTGATAAGTGTCAGAGAGAAAAGAGAAAGACTATTAACGGCGATGA
EST: gi|298179158|gb|HO027629.1|HO027629
EST:     GAGACCGTTCGGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGA                         GGCCTCTGATAAGTGTCAGAGAGAAAAGAGAAAGACTATTAACGGCGATGA
genomic: GAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGAgttagtgtgt ... aattctgtagGGCCTCTGATAAGTGTCAGAGAGAAAAGAGAAAGACTATTAACGGCGATGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCATGAAGAAGGCACTTCCTGCCAACGGTAAAATCGCAAAGGACGCCAAAGAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGAgttagtgtgttttttttttcttctgattcttttctcctccgtttttcttatttatcatcgcctgcttttaatttaaaattccttgaattctgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT