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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttaatatcatattatcattgtgccctttctttagaatttgttgcattagtggtttttttctttaggcttttacttatatgacatgatgctttgttgcagGGTTGGAGCATTTGGTATTTCGTGGCTGTTGGGAACCTTCTTGATGGTGTCAGTAATTCCTCCTATTACCATACTTAAGGGACCAAGGGCATTTGAAGTG

Basic information

species Glycine max
transcript GLYMA02G05670.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G05670.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s0199g00120.t01 (Vitis vinifera), 3'ss of exon 3
---gttaatatcatattatcattgtgccctttctttagaatttgttgcattagtggtttttttctttaggcttttacttatatgacatgatgctttgttgcagGGTTGGAGCATTTGGTATTTCGTGGCTGTTGGGAACCTTCTTGATGGTGTCAGTAATTCCTCCTATTACCATACTTAAGGGACCAAGGGCATTTGAAGTG------
     || |   || |    | |     | |||   |   |  ||||   |||||||   | | |     || | |  ||| |||  |  || | |||  |||||  ||||| |||  | | ||||||||  |||||||||||||||||||||| || ||||| |      | |||||||| || || |||   || ||||||      
acccctactgctat-tcccaactcaaagcattcagaactctgagttgttatagtggtagatatttcacatctctcaaatat-tgatttattggtctgt-acagGGCAGGAGCTTTTATTCTCTCGTGGCTACTGGGAACCTTCTTGATGGTGTCTGTGATTCCAC------CAATACTTAAAGGGCCTAGGAGTTTGGAAGTGACAACT
















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|193314417|gb|FK278818.1|FK278818
EST:     TATTTTATCCATGAACGGCTGAAGAGCAACATACGAGCTTCGCTATATGG                         GGTTGGAGCATTTGGTATTTCGTGGCTGTTGGGAACCTTCTTGATGGTGTC
genomic: TATTTTATCCATGAACGGCTGAAGAGCAACATACGAGCTTCGCTATATGGgtacatacaa ... tttgttgcagGGTTGGAGCATTTGGTATTTCGTGGCTGTTGGGAACCTTCTTGATGGTGTC
EST: gi|193413409|gb|FK377378.1|FK377378
EST:     TATTTTATCCATGAACGGCTGAAGAGCAACATACGAGCTTCGCTATATGG                         GGTTGGAGCATTTGGTATTTCGTGGCTGTTGGGAACCTTCTTGATGGTGTC
genomic: TATTTTATCCATGAACGGCTGAAGAGCAACATACGAGCTTCGCTATATGGgtacatacaa ... tttgttgcagGGTTGGAGCATTTGGTATTTCGTGGCTGTTGGGAACCTTCTTGATGGTGTC
EST: gi|7692222|gb|AW760335.1|AW760335
EST:     TATTTTATCCATGAACGGCTGAAGAGCAACATACGAGCTTCGCTATATGG                         GGTTGGAGCATTTGGTATTTCGTGGCTGTTGGGAACCTTCTTGATGGTGTC
genomic: TATTTTATCCATGAACGGCTGAAGAGCAACATACGAGCTTCGCTATATGGgtacatacaa ... tttgttgcagGGTTGGAGCATTTGGTATTTCGTGGCTGTTGGGAACCTTCTTGATGGTGTC
EST: gi|19453380|gb|BM954790.1|BM954790
EST:     TATTTTATCCATGAACGGCTGAAGAGCAACATACGAGCTTCGCTATATGG                         GGTTGGAGCATTTGGTATTTCGTGGCTGTTGGGAACCTTCTTGATGGTGTC
genomic: TATTTTATCCATGAACGGCTGAAGAGCAACATACGAGCTTCGCTATATGGgtacatacaa ... tttgttgcagGGTTGGAGCATTTGGTATTTCGTGGCTGTTGGGAACCTTCTTGATGGTGTC
EST: gi|213616854|gb|DB977053.1|DB977053
EST:     TATTTTATCCATGAACGGCTGAAGAGCAACATACGAGCTTCGCTATATGG                         GGTTGGAGCATTTGGTATTTCGTGGCTGTTGGGAACCTTCTTGATGGTGTC
genomic: TATTTTATCCATGAACGGCTGAAGAGCAACATACGAGCTTCGCTATATGGgtacatacaa ... tttgttgcagGGTTGGAGCATTTGGTATTTCGTGGCTGTTGGGAACCTTCTTGATGGTGTC
EST: gi|193339373|gb|FK303572.1|FK303572
EST:     TGAAGAGCAACATACGAGCTTCGCTATATGG                         GGTTGGAGCATTTGGTATTTCGTGGCTGTTGGGAACCTTCTCGATGGTGTC
genomic: TGAAGAGCAACATACGAGCTTCGCTATATGGgtacatacaa ... tttgttgcagGGTTGGAGCATTTGGTATTTCGTGGCTGTTGGGAACCTTCTTGATGGTGTC
EST: gi|207709918|gb|GD690602.1|GD690602
EST:     TATTTTATCCATGAACGGCTGAAGAGCAACATACGAGCTTCGCTATATGG                         GGTTGGAGCATTTGGTATTTCGTGGCTGTTGGGAACCTTCTTGATGGTGTC
genomic: TATTTTATCCATGAACGGCTGAAGAGCAACATACGAGCTTCGCTATATGGgtacatacaa ... tttgttgcagGGTTGGAGCATTTGGTATTTCGTGGCTGTTGGGAACCTTCTTGATGGTGTC
EST: gi|9900083|gb|BE609051.1|BE609051
EST:     TATTTTATCCATGAACGGCTGAAGAGCAACATACGAGCTTCGCTATATGG                         GGTTGGAGCATTTGGTATTTCGTGGCTGTTGGGAACCTTCTTGATGGTGTC
genomic: TATTTTATCCATGAACGGCTGAAGAGCAACATACGAGCTTCGCTATATGGgtacatacaa ... tttgttgcagGGTTGGAGCATTTGGTATTTCGTGGCTGTTGGGAACCTTCTTGATGGTGTC
EST: gi|22928984|gb|BU546123.1|BU546123
EST:     TATTTTATCCATGAACGGCTGAAGAGCAACATACGAGCTTCGCTATATGG                         GGTTGGAGCATTTGGTATTTCGTGGCTGTTGGGAACCTTCTTGATGGTGTC
genomic: TATTTTATCCATGAACGGCTGAAGAGCAACATACGAGCTTCGCTATATGGgtacatacaa ... tttgttgcagGGTTGGAGCATTTGGTATTTCGTGGCTGTTGGGAACCTTCTTGATGGTGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attagtggtttttttctttaggcttttacttatatgacatgatgctttgttgcagGGTTGGAGCATTTGGTATTTCGTGGCTGTTGGGAACCTTCTTGATGGTGTCAGTAATTCCTCCTATTACCATACTTAAGGGACCAAGGGCATTTGAAGTG
                                            ctttgtt  CT-rich tract
                       ttttacttatatga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaatatcatattatcattgtgccctttctttagaatttgttgcattagtggtttttttctttaggcttttacttatatgacatgatgctttgttgcagGGTTGGAGCATTTGGTATTTCGTGGCTGTTGGGAACCTTCTTGATGGTGTCAGTAATTCCTCCTATTACCATACTTAAGGGACCAAGGGCATTTGAAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG