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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactgatctctttctcccacattatctgatataaatttaacctacgctagaatgtagtataggcaatgtgtcaatcttttgagtcttatgcatcataatatgtctcctcatgaagGAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACGTTGTTGGATGGAAGCCCGGCGCTTCATTTGAAGATATGTGATTTTGGATACTCCAAG

Basic information

species Glycine max
transcript GLYMA01G39020.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G39020.2 (Glycine max), 3'ss of exon 4
lower sequence: AT3G50500.2 (Arabidopsis thaliana), 3'ss of exon 4
gtaactgatctctttctcccacattatctgatataaatttaacctacgctagaatgtagtataggcaatgtgtcaatcttttgagtcttatgcatcataatatgtctcctcatgaagGAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACGTTGTTGGATGGAAGCCCGGCGCTTCATTTGAAGATATGTGATTTTGGATACTCCAAG-------
                    ||         | |   |  ||| ||  || |||  |  | | |     ||||  | |  |   || |||       |  |   | | |   ||||| || | || || ||||| |||||| ||||||| || ||||| |||||||| ||||| | || |||||| |||||||||||||| || ||||||       
------------------gtacgcagagcagtgttcttgcaactta--cttgaacttt-tctcgttctcgtgtataccactctggtttta-attctgtgtttgattttcctgtgaagCAAATATGCCATCGGGATCTGAAGCTGGAAAATACATTGTTAGATGGAAGTCCGGCACCTCGTTTGAAAATATGTGATTTTGGTTATTCCAAGGTACTAT

upper sequence: GLYMA01G39020.2 (Glycine max), 3'ss of exon 4
lower sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaactgatctctttctcccacattatctgatataaatttaacctacgctagaatgtagtataggcaatgtgtcaatcttttgagtcttatgcatcataatatgtctcctcatgaagGAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACGTTGTTGGATGGAAGCCCGGCGCTTCATTTGAAGATATGTGATTTTGGATACTCCAAG
                    ||         | |   |  ||| ||  || |||  |  | | |     ||||  | |  |   || |||       |  |   | | |   ||||| || | || || ||||| |||||| ||||||| || ||||| |||||||| ||||| | || |||||| |||||||||||||| || ||||||
------------------gtacgcagagcagtgttcttgcaactta--cttgaacttt-tctcgttctcgtgtataccactctggtttta-attctgtgtttgattttcctgtgaagCAAATATGCCATCGGGATCTGAAGCTGGAAAATACATTGTTAGATGGAAGTCCGGCACCTCGTTTGAAAATATGTGATTTTGGTTATTCCAAG

upper sequence: GLYMA01G39020.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 4
gtaactgatctctttctcccacattatctgatataaatttaacctacgctagaatgtagtataggcaatgtgtcaatcttttgagtcttatg-catcataatatgtctcctcatgaagGAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACGTTGTTGGATGGAAGCCCGGCGCTTCATTTGAAGATATGTGATTTTGGATACTCCAAG
|||  ||| || |||||      | |    | | |  || ||  |  |      | || | ||   |   |  ||||  | | | |  | || | |    |||| |||  | |||||| || | |||||||||||| ||||||||||||| || ||||||||||||||||| || |  | ||||||||||||||||||||| |||||||||
gtatttgagct-tttcttttttctgaaaaaaaaaatcttgaaaatttgtattcctttattctactaa---ttccaattatataatttatctgacttttctatat-tcttttgatgaagCAAATATGTCACCGGGACTTGAAGTTGGAAAATACTTTGTTGGATGGAAGCCCAGCTCCACGTTTGAAGATATGTGATTTTGGGTACTCCAAG

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|6071033|gb|AW100420.1|AW100420
EST:     GCTTCTTCTTTCAACAACTCATATCTGAGGTCAGCTATTGTCATGCAATG                         GAAGTGTGTCACCGG
genomic: GTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTATTGTCATGCAATGgtaactgatc ... cctcatgaagGAAGTGTGTCACCGG
EST: gi|19453479|gb|BM954889.1|BM954889
EST:     GTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTATTGTCATGCAATG                         GAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACGTTGTTGGATGGAAGC
genomic: GTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTATTGTCATGCAATGgtaactgatc ... cctcatgaagGAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACGTTGTTGGATGGAAGC
EST: gi|11412769|gb|BF424780.1|BF424780
EST:     GTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTATTGTCATGCAATG                         GAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACGTTGTTGGATGGAAGC
genomic: GTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTATTGTCATGCAATGgtaactgatc ... cctcatgaagGAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACGTTGTTGGATGGAAGC
EST: gi|14259499|gb|BG882407.1|BG882407
EST:     GTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTATTGTCATGCAATG                         GAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACGTTGTTGGATGGAAGC
genomic: GTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTATTGTCATGCAATGgtaactgatc ... cctcatgaagGAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACGTTGTTGGATGGAAGC
EST: gi|58015703|gb|CX702445.1|CX702445
EST:     TCTGGGGTCAGCTA-TGTTCATGCAATG                         GAAGTGTGTCACCGGGACCTGAAGTTGAAAAACACGTTGTNGGATGGAAGC
genomic: TCTGGGGTCAGCTATTG-TCATGCAATGgtaactgatc ... cctcatgaagGAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACGTTGTTGGATGGAAG-
EST: gi|21888347|gb|BQ741560.1|BQ741560
EST:     GTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCAATG                         GAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACTTTGTTGGATGGAAGC
genomic: GTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTATTGTCATGCAATGgtaactgatc ... cctcatgaagGAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACGTTGTTGGATGGAAGC
EST: gi|27424851|gb|CA936371.1|CA936371
EST:     GTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCAATG                         GAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACTTTGTTGGATGGAAGC
genomic: GTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTATTGTCATGCAATGgtaactgatc ... cctcatgaagGAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACGTTGTTGGATGGAAGC
EST: gi|11413312|gb|BF425323.1|BF425323
EST:     AACAACTCATATCTGGGGTCAGCTACTGTCATGCAATG                         GAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACTTTGTTGGATGGAAGC
genomic: AACAACTCATATCTGGGGTCAGCTATTGTCATGCAATGgtaactgatc ... cctcatgaagGAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACGTTGTTGGATGGAAGC
EST: gi|58015395|gb|CX702137.1|CX702137
EST:     GTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTATTGTCATGCAATG                         GAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACGTTGTTGGATGGAAGC
genomic: GTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTATTGTCATGCAATGgtaactgatc ... cctcatgaagGAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACGTTGTTGGATGGAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggcaatgtgtcaatcttttgagtcttatgcatcataatatgtctcctcatgaagGAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACGTTGTTGGATGGAAGCCCGGCGCTTCATTTGAAGATATGTGATTTTGGATACTCCAAG
                                        tgtctcctc  CT-rich tract
                               atcataatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactgatctctttctcccacattatctgatataaatttaacctacgctagaatgtagtataggcaatgtgtcaatcttttgagtcttatgcatcataatatgtctcctcatgaagGAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACGTTGTTGGATGGAAGCCCGGCGCTTCATTTGAAGATATGTGATTTTGGATACTCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA