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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgccaccccccccccccccccccccccaccagaagttttaaattttttctgatgtcttaatagacttatatatgttacgtgtgatcaactgatgatcatgcagaaaacagaaattaactttttgtgtatgtgaattttaatttttttgaggttttgttttttctattcaacagGCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAA

Basic information

species Glycine max
transcript GLYMA05G03730.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G03730.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os08g41460.4 (Oryza sativa), 3'ss of exon 1
gtatgccaccccccccccccccccccccccaccagaagttttaaattttttctgatgtcttaatagacttatatatgttacgtgtgatcaactgatgatcatgcagaaaacagaaattaactttttgtgtatgtgaattttaatttttttgaggttttgttttttctattcaacagGCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAA
                                                                           ||||   |  |   | ||  | | | | || | |  | |  |  |  |    ||  |   ||||| ||||   ||    |  | ||||| ||  ||   |||| || ||||| ||    |||||  | ||||| ||||| ||||| ||||| |||||||| || || ||||||||||||||||||||||| |||||||
--------------------------------------------------------------------------ttgttgaatccggctacctcct-accttacatacactatacttacaagtcaattgagtcacaattt-aattcgattagattcctctttttccttctctttagGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAA

upper sequence: GLYMA05G03730.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os08g41460.2 (Oryza sativa), 3'ss of exon 1
gtatgccaccccccccccccccccccccccaccagaagttttaaattttttctgatgtcttaatagacttatatatgttacgtgtgatcaactgatgatcatgcagaaaacag-aaattaactttttgtgtatgtga-attttaatttttttgaggttttgttttttctattcaacagGCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAA
                                                   |   || | |      |   |   | ||   ||    |  ||       |      | |||  | | | ||   |    |  || | | |||||||   ||    |  | ||||| ||  ||   |||| || ||||| ||    |||||  | ||||| ||||| ||||| ||||| |||||||| || || ||||||||||||||||||||||| |||||||
--------------------------------------------------gcccgtgccctgccctgcccttccctcttgt-tgaatccggctacctcctaccttacatacactatacttacaagtcaattgagtcacaatttaattcgattagattcctctttttccttctctttagGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAA

upper sequence: GLYMA05G03730.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os08g21900.1 (Oryza sativa), 3'ss of exon 1
gtatgccaccccccccccccccccccccccaccagaagttttaaattttttctgatgtcttaatagacttatatatgttacgtgtgatcaactgatgatcatgcagaaaacagaaattaactttttgtgtatgtga-attttaatttttttgaggttttgttttttctattcaacagGCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAA
                                                       || |||       |      ||||   |  |   | ||  | | ||| || |  | | |   | ||   |    |  || | | |||||     ||    |  | ||||   | |||   |||| || ||||| ||    ||||| || || || || || | ||| ||||| |||||||| || || ||||||||||||||||||||||| |||||||
------------------------------------------------------gtgccttgccc--ttccctcttgttgaatccggctacctcct-accatacatactatata--ctcacaagtcaattgagtcacaatttaacccgattagattcctcttttccttcttctttagGCCTTTTATTACGACAAGAAGGCCATAATATCGAACGAGGTGTTCGATAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAA

upper sequence: GLYMA05G03730.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G885392_T01 (Zea mays), 3'ss of exon 1
gtatgccaccccccccccccccccccccccaccagaagttttaaattttttctgatgtcttaatagacttatatatgttacgtgtgatcaactgatgatcatgcagaaaacagaaattaactttttgtgtatgtgaattttaatttttttgaggttttgttttttctattcaacagGCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAA
                                                                  ||  |   | |  ||| ||  |  | ||||        |||   | |       | ||| |       |  |||| ||   |    |  ||||| || | | |     |||| ||||| || || || ||||| |||||||| || || ||||| || || |||||||| || |||||||||||||| |||||||| || |||||||
----------------------------------------------------------------gcacgcacgcacgc-acgcgtcgttgaatgat--------agagtcccgccgcatgcgtttcgctcgctggcgttttcatgcgt---ggtgtttgtgttgtgtgt-----agGCCTTCTACTACGAAGGCAAGGCGATCATGTCGAACGAGGAGTTCGACAACCTCAAGGAGGAGCTCATGTGGGAAGGGAGCAGCGTCGTGATGCTAA

upper sequence: GLYMA05G03730.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G896082_T03 (Zea mays), 3'ss of exon 2
gtatgccaccccccccccccccccccccccaccagaagttttaaattttttctgatgtcttaatagacttatatatgttacgtgtgatcaactgatgatcatgcagaaaacagaaattaactttttgtgtatgtgaattttaatttttttgaggttttgttttttctattcaacagGCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAA
                                                                            ||  | |   |  |    |||||  |          || || |  |   |     | | |   || ||         |         | | ||  | ||||| ||||| |||||    ||||| |||||||| || || ||||| || || |||||||| || ||||||||||| || |||||||| ||||||||||
----------------------------------------------------------------------------gtaccctacaacaaggacatgattttcagcttctttgatatgatttcgcttcacgtctcatcattgatc--------gccccccccctccaatggaccagGCCTTCTACTATGACCAGAAGGCCATCATGTCCAACGAGGAGTTCGACAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAA

upper sequence: GLYMA05G03730.1 (Glycine max), 3'ss of exon 2
lower sequence: AC203966.5_FGT002 (Zea mays), 3'ss of exon 2
gtatgccaccccccccccccccccccccccaccagaagttttaaattttttctgatgtcttaatagacttatatatgttacgtgtgatcaactgatgatcatgcagaaaacagaaattaactttttgtgtatgtgaattttaatttttttgaggttttgttttttctattcaacagGCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCAT-GCTAA
                                                                                 ||  | |  |   | ||     ||| |     |  ||  ||||   |  || |   ||    | |  |    | |       | | |   | ||||| ||||| |||||    ||||| |||||||| || || |||||||| || |||||||| || ||||||||||| || |||||||| ||||| |||||
---------------------------------------------------------------------------------gtacgctacaacaagga-----cagtattttcagctt--ctttgaattgatttcgcttcacgtctcatcactgatcgtcccctccaacggaccagGCCTTCTACTATGACCAGAAGGCCATCATGTCCAACGAGGAGTTTGACAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATTGCTAA

upper sequence: GLYMA05G03730.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G22890.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatgccaccccccccccccccccccccccaccagaagttttaaattttttctgatgtcttaatagacttatatatgttacgtgtgatcaactgatgatcatgcagaaaacagaaattaactttttgtgtatgtgaattttaatttttttgaggttttgttttttctattca--acagGCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAA
                                                                       || | | |||     || |||   |  |  |  ||    || ||  | |     | | ||| | ||| || |      ||||  ||  |||| ||| || |  |||| | ||||||||||| || || || |||||||| ||||||||||||||||| || || |||||  | ||||||||||||||||| ||||| |||||||
----------------------------------------------------------------------gtaaacgctac----aataaaccattttttttatagttgccaaaacatga-----tatatatct-aatcttcaagagcctgagaattgcttttgtcttttgattacagTCTTTCTATTATGATGGCAAAGCGATCATGTCTAATGAAGAGTTTGATAACCTTAAAGAAGAGTTAATGTGGGAAGGAAGCAGTGTTGTGATGCTAA

upper sequence: GLYMA05G03730.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G11960.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatgccaccccccccccccccccccccccaccagaagttttaaattttttctgatgtcttaatagacttatatatgttacgtgtgatcaactgatgatcatgcagaaaacagaaattaactttttgtgtatgtgaattttaatttttttgagg-----ttttgttttttctattcaacagGCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAA
                                                                                               | |     || | ||      || |   || || |  ||  || |  || |  | ||||     || ||||| || | ||   ||| | || ||||| || || || || || ||||| ||||||||||||||||| || || |||||  | ||||||||||||||||| |||||||||||||
----------------------------------------------------------------------------------------------gtaacacatcaaataaagtgtttttatcattagtatgggtttatctctatataatcgaggattgtttctgtttcttttcttttgcagTCGTTTTATTACGAAGGCAAAGCGATTATGTCTAATGAAGAGTTTGATAACCTTAAAGAAGAGTTGATGTGGGAAGGAAGCAGTGTTGTCATGCTAA

upper sequence: GLYMA05G03730.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0025g04710.t01 (Vitis vinifera), 3'ss of exon 2
gtatgccaccccccccccccccccccccccaccagaagttttaaattttttctgatgtcttaatagacttatatatgttacgtgtga-tcaactgatgatcatgcagaaaacagaaattaactttttgtgtatgtgaattttaatttttttgaggttttgttttttctattcaacagGCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAA
                                                                     | || |    |  ||    || |||  |     ||  |          || | | |   |  || |   || |||| || ||      |   ||||||| ||    || | || |||||||||||||||||||| ||||||||||| || ||||| || |||||||||||||||||||||||||||||||||||||| |||||||
--------------------------------------------------------------------ctttagagcaaatttgcagctccactattttgtgtggggtgtgtttgtgtttattctcattacattttg-ttgtaatattctt------tccatttttctgtt--gtagTCTTTTTATTATGAGGGAAAGGCTATTATGTCAAATGAGGAATTTGACAACCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTTATGCTAA

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|209698686|gb|BW656511.1|BW656511
EST:     AGAAGAAATCAATTGGTGAACTTGAGCAGGAATTCCTCCAAGCACTGCAA                         GCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAAT
genomic: AGAAGAAATCAATTGGTGAACTTGAGCAGGAATTCCTCCAAGCACTGCAAgtatgccacc ... tattcaacagGCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAAT
EST: gi|23056602|gb|BU577755.1|BU577755
EST:     AGAAGAAATCAATTGGTGAACTTGAGCAGGAATTCCTCCAAGCACTGCAA                         GCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAAT
genomic: AGAAGAAATCAATTGGTGAACTTGAGCAGGAATTCCTCCAAGCACTGCAAgtatgccacc ... tattcaacagGCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAAT
EST: gi|10844643|gb|BF067842.1|BF067842
EST:     AGAAGAAATCAATTGGTGAACTTGAGCAGGAATTCCTCCAAGCACTGCAA                         GCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAG
genomic: AGAAGAAATCAATTGGTGAACTTGAGCAGGAATTCCTCCAAGCACTGCAAgtatgccacc ... tattcaacagGCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAG
EST: gi|18733004|gb|BM527371.1|BM527371
EST:     AGAAGAAATCAATTGGTGAACTTGAGCAGGAATTCCTCCAAGCACTGCAA                         GCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAAT
genomic: AGAAGAAATCAATTGGTGAACTTGAGCAGGAATTCCTCCAAGCACTGCAAgtatgccacc ... tattcaacagGCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAAT
EST: gi|209729083|gb|BW655073.1|BW655073
EST:     AGAAGAAATCAATTGGTGAACTTGAGCAGGAATTCCTCCAAGCACTGCAA                         GCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAAT
genomic: AGAAGAAATCAATTGGTGAACTTGAGCAGGAATTCCTCCAAGCACTGCAAgtatgccacc ... tattcaacagGCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAAT
EST: gi|192306405|gb|FG997159.1|FG997159
EST:     AGAAGAAATCAATTGGTGAACTTGAGCAGGAATTCCTCCAAGCACTGCAA                         GCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAAT
genomic: AGAAGAAATCAATTGGTGAACTTGAGCAGGAATTCCTCCAAGCACTGCAAgtatgccacc ... tattcaacagGCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAAT
EST: gi|8669781|gb|BE190888.1|BE190888
EST:     AGAAGAAATCAATTGGTGAACTTGAGCAGGAATTCCTCCAAGCACTGCAA                         GCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAAT
genomic: AGAAGAAATCAATTGGTGAACTTGAGCAGGAATTCCTCCAAGCACTGCAAgtatgccacc ... tattcaacagGCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAAT
EST: gi|192303161|gb|FG997737.1|FG997737
EST:     AGAAGAAATCAATTGGTGAACTTGAGCAGGAATTCCTCCAAGCACTGCAA                         GCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAAT
genomic: AGAAGAAATCAATTGGTGAACTTGAGCAGGAATTCCTCCAAGCACTGCAAgtatgccacc ... tattcaacagGCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgtgtatgtgaattttaatttttttgaggttttgttttttctattcaacagGCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAA
                ttttaat  putative branch site (score: 3)
                                 ttttgttttttctatt  putative PPT
              aattttaatttttttg  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgccaccccccccccccccccccccccaccagaagttttaaattttttctgatgtcttaatagacttatatatgttacgtgtgatcaactgatgatcatgcagaaaacagaaattaactttttgtgtatgtgaattttaatttttttgaggttttgttttttctattcaacagGCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA