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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctttatcacattctcagtttggtgatgctatttgatatttagatgccttattttattcaattctaaaattatatagcattgtggcatgcaatgaaatgattaaatttcgtatcatctgagacttgttagaaactcaaatatgagaacatgacgtttgccatttaccggtatttttgttggtgtttttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTGGACAGCCAAGGAGAAATTGTAAATCACGTGAGCGAAGAAAGAGCGTAAA

Basic information

species Glycine max
transcript GLYMA10G40340.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G40340.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os10g20630.1 (Oryza sativa), 3'ss of exon 11
gtaagctttatcacattctcagtttggtgatgctatttgatatttagatgccttattttattcaattctaaaattatatagcattgtggcatgcaatgaaatgattaaatttcgtatcatctgagacttgttagaaac-tcaaatatgagaacatgacgtttg-ccatttaccggtatttttgt-tggtgttt-ttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTGGACAGCCAAGGAGAAATTGTAAATCACGTGAGCGAAGAAAGAGCGTAAA-
                                                                                                    ||||| | |  |  |    |  ||||   |  |    |  || || |     |||  | | || ||   ||    || |   || || ||||| || |||||||| ||||| ||||| |||||||| |||||||||||||| |||||  ||||||| ||||| ||  |   ||||||    |  || ||| || |   |  
----------------------------------------------------------------------------------------------------atgatcagacctttttcatttcgagatcagaaatgtccaccacatctttatccatagcttatgacctgctaatattaatcccgtgtgctgtttctttcagTCATACATGGACTCTGAGATCAGAGCAATCATGGCACAGTACATGCCACTGGACAGTCAAGGGGAGGTGCCAAATCATACAAATGATGAA-GAACACCATT

upper sequence: GLYMA10G40340.1 (Glycine max), 3'ss of exon 11
lower sequence: AT2G14740.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaagctttatcacattctcagtttggtgatgctatttgatatttagatgccttattttattcaattctaaaattatatagcattgtggcatgcaatgaaatgattaaatttcgtatcatctgagacttgttagaaactcaaatatgagaacatgacgtttgccatttaccggtatttttgttggtgtttttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTGGACAGCCAAGGAGAAATTGTAAATCACGTGAGCGAAGAAAGAGCGTAAA
                                           | || |   ||| | | |||   |||    || | |    |||||  |   |  |||  |||||| | | ||||          |||  | |  |   | |  | ||| ||    |||  ||||          | ||    || |||| |||  ||| ||||| || || ||||||||||| ||||||||||| ||||| ||||||||||||   || ||    || |||||||  || ||| | || | | 
------------------------------------------gtaagcttttttaatctcttctgctctt---ttgttttctgttgtgtta-atagcgaa--gattaa-tcttgtat----------ttgccatatccgttacttggggaaaattgt-tttaacatt--------cctatgcccctggttttacagCAATACATGGACTCAGAGATCAGAGCCATAATGGCACAGTACATGCCATTGGACAGCCAACCCGAGATCCCGAACCACGTGAATGATGAACGCGCCTGAG

upper sequence: GLYMA10G40340.1 (Glycine max), 3'ss of exon 11
lower sequence: AT2G14720.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaagctttatcacattctcagtttggtgatgctatttgatatttagatgccttattttattcaattctaaaattatatagcattgtggcatgcaatgaaatgattaaatttcgtatcatctgagacttgttagaaactcaaatatgagaacatgacgtttgccatttaccggtatttttgttggtgtttttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTGGACAGCCAAGGAGAAATTGTAAATCACGTGAGCGAAGAAAGAGCGTAAA
||||||||| |   ||||    ||      ||||||||     ||||| ||   |  ||| |   || ||   ||   | ||  || |   |    | |||   |    |||  | | | | || |     | | || |  |            ||   |||  ||  ||  |    | ||||  ||  ||| |||  ||| ||||| || || ||||||||||| ||||||||||| |||||  |||||||||||   ||  |    || |||  ||  || ||| | || ||| 
gtaagcttttt---attcatccttc-----tgctattt--ctgttagaagcaaaagattaat--gttttatgttttggttgc-ctgagatgtctcttaaaacatt---gttttatgtaacccgatatcgtcttggaattgtatcgattacttgggaaaattgttatgaacttgc---tatgttcatggatttacagCAATACATGGACTCAGAGATCAGAGCCATAATGGCACAGTACATGCCACTGGACAGCCAACCTGAGGTCCCGAACCACACGAATGATGAACGTGCCTAAG

upper sequence: GLYMA10G40340.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv03s0091g00740.t01 (Vitis vinifera), 3'ss of exon 11
gtaagctttatcacattctcagtttggtgatgctatttgatatttagatgccttattttattcaattctaaaattatatagcattgtggcatgcaatgaaatgattaaatttcgtatcatctgagacttgttagaaactcaaatatgagaacatgacgtttgccatttaccggtatttttgttggtgtttttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTGGACAGCCAAGGAGAAATTGTAAATCACGTGAGCGAAGAAAGAGCGTAAA
                                                                                          |||   | |   | | | |  | | |  || | ||  |    | |        | |   |   |    ||    ||| |  | | |||   | | || |||| |||||||| ||||| || || |||||||| || |||||||| || |||||| |||||||||||   ||| |   |||||| ||    || ||    || | ||
-----------------------------------------------------------------------------------------aatgttttaatgagttgagaaattgca--atgtaaggttgacaatatttgttggttttgcacttttggatt----attgattgatgtttc-atggttgctttttcagTCATACATGGACTCGGAGATCAGAGCTATAATGGCACAATACATGCCCCTGGACAGCCAAACGGAAGTCCCAAATCATGTCTCTGAGGATCATGCATGAA

upper sequence: GLYMA10G40340.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ31111 (Selaginella moellendorffii), 3'ss of exon 10
gtaagctttatcacattctcagtttggtgatgctatttgatatttagatgccttattttattcaattctaaaattatatagcattgtggcatgcaatgaaatgattaaatttcgtatcatctgagacttgttagaaactcaaatatgagaacatgacgtttgccatttaccggtatttttgttggtgtttttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTGGACAGCCAAGGAGAAATTGTAAATCACGTGAGCGAAGAAAGAGCGTAAA
                                                                                                                                 ||  |  |      |  |    |||  || |||  ||| | | || |   || |||    || |||||| ||||||||||| || || ||||| |||||||| ||||| |||||  ||||||||||    ||| |       ||| |    || |||     || | 
---------------------------------------------------------------------------------------------------------------------------------gtacgtgatctctctg-gcattcattccggttggtattgagctgtgtggctgctgg----ttggcagTCTTATATGGATTCGGAGATTAGAGCGATCATGGCGCAGTACATGCCTCTGGACAGCCAGAACGAAGTCCACCGCCACCTCGAGGAGGAAGCGTAGTGAT

upper sequence: GLYMA10G40340.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ06539 (Selaginella moellendorffii), 3'ss of exon 10
gtaagctttatcacattctcagtttggtgatgctatttgatatttagatgccttattttattcaattctaaaattatatagcattgtggcatgcaatgaaatgattaaatttcgtatcatctgagacttgttagaaactcaaatatgagaacatgacgtttgccatttaccggtatttttgttggtgtttttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTGGACAGCCAAGGAGAAATTGTAAATCACGTGAGCGAAGAAAGAGCGTAAA
                                                                                                                                 ||  |  |      |  |    |||  || |||  ||| | | || |   || |||    || |||||| ||||||||||| || || ||||| |||||||| ||||| |||||  ||||||||||    ||| |       ||  |    || |||     || | 
---------------------------------------------------------------------------------------------------------------------------------gtacgtgatctctctg-gcattcattccggttggtattgagctgtgtggctgctgg----ttggcagTCTTATATGGATTCGGAGATTAGAGCGATCATGGCGCAGTACATGCCTCTGGACAGCCAGAACGAAGTCCACCGCCATCTCGAGGAGGAAGCGTAGTGAT

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|208310294|gb|GE107656.1|GE107656
EST:     TAGTTGTGGCTGCTGCAGGGGTATACCTTGTGTACAAATATAGAATAAGG                         TCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
genomic: TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATATAGAATAAGGgtaagcttta ... gtttttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
EST: gi|6746932|gb|AW317388.1|AW317388
EST:     TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATATAGAATAAGG                         TCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
genomic: TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATATAGAATAAGGgtaagcttta ... gtttttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
EST: gi|208087431|gb|GD888515.1|GD888515
EST:     TAGTTGTGGCTGCTGCAGGGGCACACCTTGTGTACAAATATAGAATAAGG                         TCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
genomic: TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATATAGAATAAGGgtaagcttta ... gtttttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
EST: gi|207771835|gb|GD745606.1|GD745606
EST:     TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATATAGAATAAGG                         TCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
genomic: TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATATAGAATAAGGgtaagcttta ... gtttttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
EST: gi|9901269|gb|BE610237.1|BE610237
EST:     GCTGCTGCAGGGGCATACCTTGTGTACAAATATAGAATAAGG                         TCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
genomic: GCTGCTGCAGGGGCATACCTTGTGTACAAATATAGAATAAGGgtaagcttta ... gtttttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
EST: gi|254320314|gb|GR831122.1|GR831122
EST:     TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATATAGAATAAGG                         TCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
genomic: TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATATAGAATAAGGgtaagcttta ... gtttttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
EST: gi|208257201|gb|GE052346.1|GE052346
EST:     TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATATAGAATAAGG                         TCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
genomic: TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATATAGAATAAGGgtaagcttta ... gtttttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
EST: gi|31469332|gb|CD411360.1|CD411360
EST:     TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATATAGAATAAGG                         TCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
genomic: TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATATAGAATAAGGgtaagcttta ... gtttttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
EST: gi|208227123|gb|GE027304.1|GE027304
EST:     TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATATAGAATAAGG                         TCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
genomic: TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATATAGAATAAGGgtaagcttta ... gtttttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
EST: gi|208120192|gb|GD919301.1|GD919301
EST:     TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATATAGAATAAGG                         TCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
genomic: TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATATAGAATAAGGgtaagcttta ... gtttttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
EST: gi|193352941|gb|FK315167.1|FK315167
EST:     TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATATAGAATAAGG                         TCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
genomic: TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATATAGAATAAGGgtaagcttta ... gtttttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
EST: gi|193565442|gb|FK527235.1|FK527235
EST:     TGCTGCAGGGGCATACCTTGTGTACAAATATAGAATAAGG                         TCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
genomic: TGCTGCAGGGGCATACCTTGTGTACAAATATAGAATAAGGgtaagcttta ... gtttttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
EST: gi|10845475|gb|BF068594.1|BF068594
EST:     TAGTTGTGGCTGCTGCATGGGCATACCTTGTGTACAAATATACAATAAGG                         GCATATATGGATTCTGAAATCAGAGCCATCATGGGACAGTATATGCCCTTT
genomic: TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATATAGAATAAGGgtaagcttta ... gtttttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatatgagaacatgacgtttgccatttaccggtatttttgttggtgtttttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTGGACAGCCAAGGAGAAATTGTAAATCACGTGAGCGAAGAAAGAGCGTAAA
                                            tgttttt  CT-rich tract
                                tatttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctttatcacattctcagtttggtgatgctatttgatatttagatgccttattttattcaattctaaaattatatagcattgtggcatgcaatgaaatgattaaatttcgtatcatctgagacttgttagaaactcaaatatgagaacatgacgtttgccatttaccggtatttttgttggtgtttttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTGGACAGCCAAGGAGAAATTGTAAATCACGTGAGCGAAGAAAGAGCGTAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA