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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctagaaacttgcctatcctgaatttttatcccctgcccccaactcccttcattttaataatatttttatagcattatggttttactctgtacatactatttcttgaatatgacctgatttcatgtatcctattctgatgaacatggacagGTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCATCCAAGCAAACTTCATCTCCTGATA

Basic information

species Glycine max
transcript GLYMA16G24290.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G24290.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G082502_T02 (Zea mays), 3'ss of exon 9
gtctagaaacttgcctatcctgaatttttatcccctgcccccaactcccttcattttaataatatttttatagcattatggttttactctgtacatactatttcttgaatatgacctgatttcatgtatcctattctgatgaacatggacagGTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCATCCAAGCAAACTTCATCTCCTGATA
          | | || ||   |  |      |  ||    |   |    | |  | || | |        ||||   |  ||  |||    |      | | ||    |   |  |  | | |||  || |    | ||  |     |||| ||| |||||  | |||||||||||||| ||||| || ||||||||||| |||||||| |  |||||    || |
--------gttcgtctctctctagctagctagctttggttgcctgttgtgtgacatcaaaagtgacaacg-agcagc-tctttcgacttcccaatcgggactcctcttttcccatttc-tctgatgcttcatcaaat-atatatgcacacagCTTCTAAAATCGTGTTTACAAATGGCTCCCAAGACCCATGGCGCCATGCCTCCAAGCAGAAATCATCGAAAGACA

upper sequence: GLYMA16G24290.1 (Glycine max), 3'ss of exon 9
lower sequence: AT4G36195.2 (Arabidopsis thaliana), 3'ss of exon 9
gtctagaaacttgcctatcctgaatttttatcccctgcccccaactcccttcattttaataatatttttatagcattatggttttactctgtacatactatttcttgaatatgacctgatttcatgtatcctattctgatgaacatggacagGTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCATCCAAGCAAACTTCATCTCCTGATA
                                                                    |||   || | ||    |   | |  || ||| | | |  || |   |  ||| ||    |    |  |  |    ||   |||   | || || || || |||||||| ||||| ||||| ||||| ||||||||||| || || |||||||||||  
-------------------------------------------------------------------gtatgtaataacgga--aaacatctcgatgctact-catatattttcgcacattccaacagtttcttcttattcgtaatttgcagCGACCAAGATTATCTTCACAAATGGGTCACAGGATCCATGGCGTCATGCATCCAAACAGACCTCATCTCCTGAAC

upper sequence: GLYMA16G24290.1 (Glycine max), 3'ss of exon 9
lower sequence: AT4G36190.1 (Arabidopsis thaliana), 3'ss of exon 9
gtctagaaacttgcctatcctgaatttttatcccctgcccccaactcccttcattttaataatatttt-tatagcattatggttttactctgtacatactatttcttgaatatgacctgatttcatgtatcctattctgatgaacatggacagGTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCATCCAAGCAAACTTCATCTCCTGATA
                                                              ||| |  ||| | |  |    |  ||  |     ||   ||      ||   | | | ||    | ||| | || |  | ||  | |  ||   | || || || || |||||||| ||||| ||||| ||||| ||||||||||| ||||| |||||||||||  
-------------------------------------------------------------gtatgtaatatcggaaaacttctcgacgatccttttagacttgtgcacattccaacagtttcttcgcatcttcttattctcaattttg-tagCGACCAAGATTATCTTCACAAATGGGTCACAGGATCCATGGCGTCATGCATCCAAACAAACCTCATCTCCTGACC

upper sequence: GLYMA16G24290.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv04s0023g03020.t01 (Vitis vinifera), 3'ss of exon 9
gtctagaaacttgcctatcctgaatttttatcccctgcccccaactcccttcattttaataatatttttatagcattatggttttactctgtacatactatttcttgaatat----gacctgatttcatgtatcctattctga-tgaacatggacagGTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCATCCAAGCAAACTTCATCTCCTGATA
                                                        |||||||  | ||  ||    |   | ||| | |    |||  ||| |  | ||||    | |   || |||||||| || ||   | || | || | |||||||||||||||| ||||| |||||||| || || || ||||| ||||||||||| |  || ||| | || || |
--------------------------------------------------------taataatgctgttg-aggtccactttattattattataatataattgccaggatatatttggctacatctcatgtattcttttggaaatgtaaattgccagGTTCAAAAATAATTTTTACGAATGGCTCCCAGGACCCCTGGCGACATGCATCCAAACTGACCTCAACCCCGGACA

upper sequence: GLYMA16G24290.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ13517 (Selaginella moellendorffii), 3'ss of exon 10
gtctagaaacttgcctatcctgaatttttatcccctgcccccaactcccttcattttaataatatttttatagcattatggttttactctgtacatactatt--tcttgaatatgacctgatttcatgtatcctattctgatgaacatggacagGTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCATCCAAGCAAACTTCATCTCCTGATA
                                                                                          |||  | |  ||  | |||    |   | |   ||||  ||||| |  |  |     || |   | |  || ||  | || |  || || || |||||||||||||| ||||| |||||||||||||| || | | || 
------------------------------------------------------------------------------------------gtatttccagttgatgttgtccgttggcagtcatcattcatcctttgtttgt-----tgtagGAGAT--AAGATTTTGTTCATGAACGGTTCCCAAGATCCTTGGCGTCATGCCTCCAAGCAAACTTCTTCGCGTAATG

upper sequence: GLYMA16G24290.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ19221 (Selaginella moellendorffii), 3'ss of exon 10
gtctagaaacttgcctatcctgaatttttatcccctgcccccaactcccttcattttaataatatttttatagcattatggttttactctgtacatactatttcttgaatatgacctgatttcatgtatcctattctgatgaacatggacagGTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCATCCAAGCAAACTTCATCTCCTGATA
                                                                                || || | | ||  ||  | |   |||    | |       ||||  ||||| |  |  |     || |   | |  || ||  | || |  || || || |||||||||||||| ||||| |||||||||||||| || |   || 
--------------------------------------------------------------------------------gtatttcccagttgatggtgtccgttggcagtca-------tcattcatcctttgtttgt-----tgtagGAGAT--AAGATTTTGTTCATGAACGGTTCCCAAGATCCTTGGCGTCATGCCTCCAAGCAAACTTCTTCCCGCAATG

upper sequence: GLYMA16G24290.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ13597 (Selaginella moellendorffii), 3'ss of exon 10
gtctagaaacttgcctatcctgaatttttatcccctgcccccaactcccttcattttaataatatttttatagcattatggttttactctgtacatactatttcttgaatatgacctgatttcatgtatcctattctgatgaacatggacagGTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCATCCAAGCAAACTTCATCTCCTGATA
                                                                                || || | | ||  ||  | |   |||        | |   ||||  ||||| |  |  |     || |   | |  || ||  | || |  || || || |||||||||||||| ||||| |||||||||||||| || |   || 
--------------------------------------------------------------------------------gtatttcccagttgatgttgtccgttgg-------cagccatcattcatcctttgtttgt-----tgtagGAGAT--AAGATTTTGTTCATGAACGGTTCCCAAGATCCTTGGCGTCATGCCTCCAAGCAAACTTCTTCCCGCAATG

upper sequence: GLYMA16G24290.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ19082 (Selaginella moellendorffii), 3'ss of exon 10
gtctagaaacttgcctatcctgaatttttatcccctgcccccaactcccttcattttaataatatttttatagcattatggttttactctgtacatactatt--tcttgaatatgacctgatttcatgtatcctattctgatgaacatggacagGTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCATCCAAGCAAACTTCATCTCCTGATA
                                                                                          |||  | |  ||  | |||    |   | |   ||||  ||||   | || |   | | |  || |   || ||  | || |  || || || |||||||||||||| ||||| |||||||||||||| || | | || 
------------------------------------------------------------------------------------------gtatttccagttgatgttgtccgttggcagtcatcattcatcc---tttgtttgtcgtagG-AGAT---AAGATCTTGTTCATGAACGGTTCCCAAGATCCTTGGCGTCATGCCTCCAAGCAAACTTCTTCGCGTAATG

upper sequence: GLYMA16G24290.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ13595 (Selaginella moellendorffii), 3'ss of exon 10
gtctagaaacttgcctatcctgaatttttatcccctgcccccaactcccttcattttaataatatttttatagcattatggttttactctgtacatactatttcttgaatatgacctgatttcatgtatcctattctgatgaacatggacagGTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCATCCAAGCAAACTTCATCTCCTGATA
                                                                                                             |||  |||  ||     | |||     | || |       ||||    || ||  | ||||  || ||||| |||||||||||||| ||||| |||||||||||||| || |   || 
------------------------------------------------------------------------------------------------------------gtatttcctagttgatgctgtccatcattcataatttgttgcagGAGATAAGATTTTGTTTATGAACGGCTCCCAAGATCCTTGGCGTCATGCCTCCAAGCAAACTTCTTCCCGCAATG

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|254323221|gb|GR840026.1|GR840026
EST:     TCCTGATGTTGATGCAACTAATTTATACTACGGAGGCACTAAAATTGCTG                         GTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCAT
genomic: TCCTGATGTTGATGCAACTAATTTATACTACGGAGGCACTAAAATTGCTGgtctagaaac ... acatggacagGTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCAT
EST: gi|193547219|gb|FK499588.1|FK499588
EST:     TCCTGATGTTGATGCAACTAATTTATACTACGGAGGCACTAAAATTGCTG                         GTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCA
genomic: TCCTGATGTTGATGCAACTAATTTATACTACGGAGGCACTAAAATTGCTGgtctagaaac ... acatggacagGTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCA
EST: gi|193469219|gb|FK435467.1|FK435467
EST:     TCCTGATGTTGATGCAACTAATTTATACTACGGAGGCACTAAAATTGCTG                         GTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCA
genomic: TCCTGATGTTGATGCAACTAATTTATACTACGGAGGCACTAAAATTGCTGgtctagaaac ... acatggacagGTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCA
EST: gi|193547333|gb|FK499646.1|FK499646
EST:     TCCTGATGTTGATGCAACTAATTTATACTACGGAGGCACTAAAATTGCTG                         GTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCA
genomic: TCCTGATGTTGATGCAACTAATTTATACTACGGAGGCACTAAAATTGCTGgtctagaaac ... acatggacagGTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCA
EST: gi|163918185|gb|EH039901.1|EH039901
EST:     TCCTGATGTTGATGCAACTAATTTATACTACGGAGGCACTAAAATTGCTG                         GTTCAAAAATAATATTTACAAATGGCTCGCAAGATCCTTGGCGCCATGCAT
genomic: TCCTGATGTTGATGCAACTAATTTATACTACGGAGGCACTAAAATTGCTGgtctagaaac ... acatggacagGTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCAT
EST: gi|193393943|gb|FK358074.1|FK358074
EST:     TCCTGATGTTGATGCAACTAATTTATACTACGGAGGCACTAAAATTGCTG                         GTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCAT
genomic: TCCTGATGTTGATGCAACTAATTTATACTACGGAGGCACTAAAATTGCTGgtctagaaac ... acatggacagGTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCAT
EST: gi|193657700|gb|FK606347.1|FK606347
EST:     TCCTGATGTTGATGCAACTAATTTATACTACGGAGGCACTAAAATTGCTG                         GTTCAAAAATA-TATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCA
genomic: TCCTGATGTTGATGCAACTAATTTATACTACGGAGGCACTAAAATTGCTGgtctagaaac ... acatggacagGTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCA
EST: gi|208098374|gb|GD894767.1|GD894767
EST:     TCCTGATGTTGATGCAACTAATTTATACTACGGAGGCACTAAAATTGCTG                         GTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCAT
genomic: TCCTGATGTTGATGCAACTAATTTATACTACGGAGGCACTAAAATTGCTGgtctagaaac ... acatggacagGTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCAT
EST: gi|254333270|gb|GR850520.1|GR850520
EST:     TCCTGATGTTGATGCAACTAATTTATACTACGGAGGCACTAAAATTGCTG                         GTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCAT
genomic: TCCTGATGTTGATGCAACTAATTTATACTACGGAGGCACTAAAATTGCTGgtctagaaac ... acatggacagGTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCAT
EST: gi|192325369|gb|FK018355.1|FK018355
EST:     TCCTGATGTTGATGCAACTAATTTATACTACGGAGGCACTAAAATTGCTG                         GTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCAT
genomic: TCCTGATGTTGATGCAACTAATTTATACTACGGAGGCACTAAAATTGCTGgtctagaaac ... acatggacagGTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCAT
EST: gi|193704130|gb|FK647450.1|FK647450
EST:     TCCTGATGTTGATGCAACTAATTTATACTACGGAGGCACTAAAATTGCTG                         GTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCA
genomic: TCCTGATGTTGATGCAACTAATTTATACTACGGAGGCACTAAAATTGCTGgtctagaaac ... acatggacagGTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCA
EST: gi|254333269|gb|GR850519.1|GR850519
EST:     TCCTGATGTTGATGCAACTAATTTATACTACGGAGGCACTAAAATTGCTG                         GTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCAT
genomic: TCCTGATGTTGATGCAACTAATTTATACTACGGAGGCACTAAAATTGCTGgtctagaaac ... acatggacagGTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCAT
EST: gi|192318972|gb|FK010592.1|FK010592
EST:     TCCTGATGTTGATGCAACTAATTTATACTACGGAGGCACTAAAATTGCTG                         GTTCAAAGATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCAT
genomic: TCCTGATGTTGATGCAACTAATTTATACTACGGAGGCACTAAAATTGCTGgtctagaaac ... acatggacagGTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCAT
EST: gi|192318971|gb|FK010591.1|FK010591
EST:     TCCTGATGTTGATGCAACTAATTTATACTACGGAGGCACTAAAATTGCTG                         GTTCAAAGATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCAT
genomic: TCCTGATGTTGATGCAACTAATTTATACTACGGAGGCACTAAAATTGCTGgtctagaaac ... acatggacagGTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCAT
EST: gi|7283900|gb|AW596501.1|AW596501
EST:     TCCTGATGTTGATGCAACTAATTTATACTACGGAGGCACTAAAATTGCTG                         GTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCAT
genomic: TCCTGATGTTGATGCAACTAATTTATACTACGGAGGCACTAAAATTGCTGgtctagaaac ... acatggacagGTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatttcttgaatatgacctgatttcatgtatcctattctgatgaacatggacagGTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCATCCAAGCAAACTTCATCTCCTGATA
                                    ttctgat  putative branch site (score: 3)
       ttgaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctagaaacttgcctatcctgaatttttatcccctgcccccaactcccttcattttaataatatttttatagcattatggttttactctgtacatactatttcttgaatatgacctgatttcatgtatcctattctgatgaacatggacagGTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCATCCAAGCAAACTTCATCTCCTGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA