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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactgatctctttctccctcactatctaatataaattgtatttaacctatgccagaatgtagtataggcaatgtgtcaatcttgagtattatgtctgatgtgatgtatgagtcttatgtatcataatatgtctcctcatgaagGAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACTTTGTTGGATGGAAGCCCGGCACTTCATTTGAAGATATGTGATTTTGGATACTCCAAG

Basic information

species Glycine max
transcript GLYMA11G06250.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G06250.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G50500.2 (Arabidopsis thaliana), 3'ss of exon 4
gtaactgatctctttctccctcactatctaatataaattgtatttaacctatgccagaatgtagtataggcaatgtg-tcaatcttgagtattatgtctgatgtgatgtatgagtcttatgtatcataatatgtctcctcatgaagGAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACTTTGTTGGATGGAAGCCCGGCACTTCATTTGAAGATATGTGATTTTGGATACTCCAAG-------
                                                 || || |||     ||    ||||  |  |  | |||   |  | | ||   | |         || |||  |    |  |   | | |   ||||| || | || || ||||| |||||| ||||||| || ||||| |||||||| ||||||| || |||||| |||||||||||||| || ||||||       
------------------------------------------------gtacgc-agagcagtgttcttgcaacttacttgaacttttctcgt-tctcgtgtataccactctggtttta-attctgtgtttgattttcctgtgaagCAAATATGCCATCGGGATCTGAAGCTGGAAAATACATTGTTAGATGGAAGTCCGGCACCTCGTTTGAAAATATGTGATTTTGGTTATTCCAAGGTACTAT

upper sequence: GLYMA11G06250.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaactgatctctttctccctcactatctaatataaattgtatttaacctatgccagaatgtagtataggcaatgtg-tcaatcttgagtattatgtctgatgtgatgtatgagtcttatgtatcataatatgtctcctcatgaagGAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACTTTGTTGGATGGAAGCCCGGCACTTCATTTGAAGATATGTGATTTTGGATACTCCAAG
                                                 || || |||     ||    ||||  |  |  | |||   |  | | ||   | |         || |||  |    |  |   | | |   ||||| || | || || ||||| |||||| ||||||| || ||||| |||||||| ||||||| || |||||| |||||||||||||| || ||||||
------------------------------------------------gtacgc-agagcagtgttcttgcaacttacttgaacttttctcgt-tctcgtgtataccactctggtttta-attctgtgtttgattttcctgtgaagCAAATATGCCATCGGGATCTGAAGCTGGAAAATACATTGTTAGATGGAAGTCCGGCACCTCGTTTGAAAATATGTGATTTTGGTTATTCCAAG

upper sequence: GLYMA11G06250.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 4
gtaactgatctctttctccctcactatctaatataaattgtatttaacctatgccagaatgtagtataggcaatgtgtcaatcttgagtattatgtctgatgtgatgtatgagtcttatgt-atcataatatgt-ctcctcatgaagGAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACTTTGTTGGATGGAAGCCCGGCACTTCATTTGAAGATATGTGATTTTGGATACTCCAAG
                            || |  |  || | |||   ||     | ||   | | | |  ||| |||    |||   |||| |  || ||   |  |||     |||| | |   |  ||| | ||  | |||||| || | |||||||||||| ||||||||||||| |||||||||||||||||||| || |  | ||||||||||||||||||||| |||||||||
---------------------------gtatttgagcttttcttttttctgaaaaaaaa---aatcttgaaaatttgtattcctt---tattcta-ctaattccaattatataatttatctgacttttctatattcttttgatgaagCAAATATGTCACCGGGACTTGAAGTTGGAAAATACTTTGTTGGATGGAAGCCCAGCTCCACGTTTGAAGATATGTGATTTTGGGTACTCCAAG

upper sequence: GLYMA11G06250.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S240_91V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaactgatctctttctccctcactatctaatataaattgtatttaacctatgccagaatgtagtataggcaatgtgtcaatcttgagtattatgtctgatgtgatgt-atgagtctta-----tgtatcat----aatatgtctcctca--tgaagGAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACTTTGTTGGATGGAAGCCCGGCACTTCATTTGAAGATATGTGATTTTGGATACTCCAAG
                                     |  | |||  |  |  |  |||| | || |      ||| ||||| ||||| |||   | |  || | ||| || ||| ||      ||  | ||    ||| || |   |||  || || || | || || || ||  |||| |||||||||||||||||||||||||| || || | |    |||| || ||||||||||| || || |||
------------------------------------gtaatgttt--ctgaaccttgaatcttgtgtgt----tgtttcaattttgag-attggattttttgagttgtgattagttttccctcctgcctgatcccgaatgtgccggttcaattgcagCAAATTTGCCATCGTGATTTGAAATTGGAAAACACTTTGTTGGATGGAAGTCCTGCGCCTAGGCTGAAAATCTGTGATTTTGGGTATTCAAAG

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|22931738|gb|BU548877.1|BU548877
EST:     GTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCAATG                         GAAGTGTGTCACCGGGANNTGAAGTTGGAAAACACTTTGTTGGATGGAAGC
genomic: GTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCAATGgtaactgatc ... cctcatgaagGAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACTTTGTTGGATGGAAGC
EST: gi|213618240|gb|DB973010.1|DB973010
EST:     GTTTCTTCTTTCA-CAACTCATATCTGGNGTCAGCTACTGTCATGCAATG                         GAAGTGTGTCACCCGGGACCTGAAGTTGGAAAACACTTTGTTGGATGGAAG
genomic: GTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCAATGgtaactgatc ... cctcatgaagGAAGTGTGTCACC-GGGACCTGAAGTTGGAAAACACTTTGTTGGATGGAAG
EST: gi|9258485|gb|BE346632.1|BE346632
EST:     GTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCAATG                         GAAGTGTGTCACCGGGACCTGAAGTTTGAANACACTTTGTTGGATGGAAGC
genomic: GTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCAATGgtaactgatc ... cctcatgaagGAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACTTTGTTGGATGGAAGC
EST: gi|254317661|gb|GR826645.1|GR826645
EST:     GTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCAATG                         GAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACTTTGTTGGATGGAAGC
genomic: GTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCAATGgtaactgatc ... cctcatgaagGAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACTTTGTTGGATGGAAGC
EST: gi|19348943|gb|BM893475.1|BM893475
EST:     GTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCAATG                         GAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACTTTGTTGGATGGAAGC
genomic: GTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCAATGgtaactgatc ... cctcatgaagGAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACTTTGTTGGATGGAAGC
EST: gi|7684855|gb|AW755503.1|AW755503
EST:     GTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCAATG                         GAAGTGTGTCACCGGGACCTGAAG
genomic: GTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCAATGgtaactgatc ... cctcatgaagGAAGTGTGTCACCGGGACCTGAAG
EST: gi|209697502|gb|BW670003.1|BW670003
EST:     GTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCAATG                         GAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACTTTGTTGGATGGAAGC
genomic: GTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCAATGgtaactgatc ... cctcatgaagGAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACTTTGTTGGATGGAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgtctgatgtgatgtatgagtcttatgtatcataatatgtctcctcatgaagGAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACTTTGTTGGATGGAAGCCCGGCACTTCATTTGAAGATATGTGATTTTGGATACTCCAAG
    gtctgat  putative branch site (score: 4)
                                        tgtctcctc  putative PPT
                         ttatgtatcataatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactgatctctttctccctcactatctaatataaattgtatttaacctatgccagaatgtagtataggcaatgtgtcaatcttgagtattatgtctgatgtgatgtatgagtcttatgtatcataatatgtctcctcatgaagGAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACTTTGTTGGATGGAAGCCCGGCACTTCATTTGAAGATATGTGATTTTGGATACTCCAAG

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