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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaggaagccttttttatattatctaaagtctgcactgtttaacaaattgcaggaaccttctactttatttaattgactgattttttttcctctttatagGGTCCTTTCATCAACGGTAGTGAGATATCTGCAGCTGACCTATCACTTGGACCAAAGCTATACCATTTAGAGATTGCTTTGGGGCATTATAAGAAATGGA

Basic information

species Glycine max
transcript GLYMA11G33700.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G33700.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0006g00630.t01 (Vitis vinifera), 3'ss of exon 4
-tgaggaagccttttttatat-tatctaaagtctgcactgtttaacaaattgcaggaaccttctactttatttaattgactgattttttttcctctttatagGGTCCTTTCATCAACGGTAGTGAGATATCTGCAGCTGACCTATCACTTGGACCAAAGCTATACCATTTAGAGATTGCTTTGGGGCATTATAAGAAATGGA
 ||||     | ||   || | ||   |||| ||||| |   |      ||  |    |  || |   |  || |     ||||||| | |  |  ||| |||| ||||| ||||| || |  || |||||||| | |||| | || ||||||||||| ||||||||| |||||||||||||||||||||| ||||| ||||
ttgagttgttcgttgacatgtgtacaaaaagactgcatttgct--tgttttataatctctctccaaccttcttgaaaacttgattttctcttgtgcttaaagGGCCCTTTTATCAATGGGAAAGACATATCTGCTGTTGACTTGTCTCTTGGACCAAAACTATACCATCTAGAGATTGCTTTGGGGCATTACAAGAAGTGGA
















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|192296135|gb|FG989495.1|FG989495
EST:     AAGCATTACTTAGTGAACTGAGCTCTTTCAGTGATTACATCAAGGAAAAT                         GGTCCTTTCATCAACGGTAGTGAGATATCTGCAGCTGACCTATCACTTGGA
genomic: AAGCATTACTTAGTGAACTGAGCTCTTTCAGTGATTACATCAAGGAAAATgtatgacatt ... ctctttatagGGTCCTTTCATCAACGGTAGTGAGATATCTGCAGCTGACCTATCACTTGGA
EST: gi|209722386|gb|BW665859.1|BW665859
EST:     AAGCATTACTTAGTGAACTGAGCTCTTTCAGTGATTACATCAAGGAAAAT                         GGTCCTTTCATCAACGGTAGTGAGATATCTGCAGCTGACCTATCACTTGGA
genomic: AAGCATTACTTAGTGAACTGAGCTCTTTCAGTGATTACATCAAGGAAAATgtatgacatt ... ctctttatagGGTCCTTTCATCAACGGTAGTGAGATATCTGCAGCTGACCTATCACTTGGA
EST: gi|193679587|gb|FK622737.1|FK622737
EST:     AAGCATTACTTAGTGAACTGAGCTCTTTCAGTGATTACATCAAGGAAAAT                         GGTCCTTTCATCAACGGTAGTGAGATATCTGCAGCTGACCTATCACTTGGA
genomic: AAGCATTACTTAGTGAACTGAGCTCTTTCAGTGATTACATCAAGGAAAATgtatgacatt ... ctctttatagGGTCCTTTCATCAACGGTAGTGAGATATCTGCAGCTGACCTATCACTTGGA
EST: gi|31470635|gb|CD412663.1|CD412663
EST:     AAGCATTACTTAGTGAACTGAGCTCTTTCAGTGATTACATCAAGGAAAAT                         GGTCCTTTCATCAACGGTAGTGAGAAATCTGCAGCTGACCTATCACTTGGA
genomic: AAGCATTACTTAGTGAACTGAGCTCTTTCAGTGATTACATCAAGGAAAATgtatgacatt ... ctctttatagGGTCCTTTCATCAACGGTAGTGAGATATCTGCAGCTGACCTATCACTTGGA
EST: gi|7147501|gb|AW509423.1|AW509423
EST:     AAGCATTACTTAGTGAACTGAGCTCTTTCAGTGATTACATCAAGGCAAAT                         GGTCCTTTCATCAACCGTAGTGAGATATCTGCAGCTGACCTATCACTTGGA
genomic: AAGCATTACTTAGTGAACTGAGCTCTTTCAGTGATTACATCAAGGAAAATgtatgacatt ... ctctttatagGGTCCTTTCATCAACGGTAGTGAGATATCTGCAGCTGACCTATCACTTGGA
EST: gi|151403447|gb|EV273257.1|EV273257
EST:     AAGCATTACTTAGTGAACTGAGCTCTTTCAGTGATTACATCAAGGAAAAT                         GGTCCTTTCATCAACGGTAGTGAGATATCTGCAGCTGACCTATCACTTGGA
genomic: AAGCATTACTTAGTGAACTGAGCTCTTTCAGTGATTACATCAAGGAAAATgtatgacatt ... ctctttatagGGTCCTTTCATCAACGGTAGTGAGATATCTGCAGCTGACCTATCACTTGGA
EST: gi|192299879|gb|FG990087.1|FG990087
EST:     AAGCATTACTTAGTGAACTGAGCTCTTTCAGTGATTACATCAAGGAAAAT                         GGTCCTTTCATCAACGGTAGTGAGATATCTGCAGCTGACCTATCACTTGGA
genomic: AAGCATTACTTAGTGAACTGAGCTCTTTCAGTGATTACATCAAGGAAAATgtatgacatt ... ctctttatagGGTCCTTTCATCAACGGTAGTGAGATATCTGCAGCTGACCTATCACTTGGA
EST: gi|120534693|gb|EH262826.1|EH262826
EST:     AAGCATTACTTAGTGAACTGAGCTCTTTCAGTGATTACATCAAGGAAAAT                         GGTCCTTTCATCAACGGTAGTGAGATATCTGCAGCTGACCTATCACTTGGA
genomic: AAGCATTACTTAGTGAACTGAGCTCTTTCAGTGATTACATCAAGGAAAATgtatgacatt ... ctctttatagGGTCCTTTCATCAACGGTAGTGAGATATCTGCAGCTGACCTATCACTTGGA
EST: gi|298165886|gb|HO008857.1|HO008857
EST:     AAGCATTACTTAGTGAACTGAGCTCTTTCAGTGATTACATCAAGGAAAAT                         GGTCCTTTCATCAACGGTAGTGAGATATCTGCAGCTGACCTATCAC
genomic: AAGCATTACTTAGTGAACTGAGCTCTTTCAGTGATTACATCAAGGAAAATgtatgacatt ... ctctttatagGGTCCTTTCATCAACGGTAGTGAGATATCTGCAGCTGACCTATCAC
EST: gi|120534677|gb|EH262810.1|EH262810
EST:     AAGCATTACTTAGTGAACTGAGCTCTTTCAGTGATTACATCAAGGAAAAT                         GGTCCTTTCATCAACGGTAGTGAGATATTTGCAGCTGACCTATCACTTGGA
genomic: AAGCATTACTTAGTGAACTGAGCTCTTTCAGTGATTACATCAAGGAAAATgtatgacatt ... ctctttatagGGTCCTTTCATCAACGGTAGTGAGATATCTGCAGCTGACCTATCACTTGGA
EST: gi|209722400|gb|BW665860.1|BW665860
EST:     AAGCATTACTTAGTGAACTGAGCTCTTTCAGTGATTACATCAAGGAAAAT                         GGTCCTTTCATCAACGGTAGTGAGATATCTGCAGCTGACCTATCACTTGGA
genomic: AAGCATTACTTAGTGAACTGAGCTCTTTCAGTGATTACATCAAGGAAAATgtatgacatt ... ctctttatagGGTCCTTTCATCAACGGTAGTGAGATATCTGCAGCTGACCTATCACTTGGA
EST: gi|10233723|gb|BE802611.1|BE802611
EST:     AAGCATTACTTAGTGAACTGAGCTCTTTCAGTGATTACATCAAGGAAAAT                         GGTCCTTTCATCAACGGTAGTGAGATATCTGCAGCTGACCTATCACTTGGA
genomic: AAGCATTACTTAGTGAACTGAGCTCTTTCAGTGATTACATCAAGGAAAATgtatgacatt ... ctctttatagGGTCCTTTCATCAACGGTAGTGAGATATCTGCAGCTGACCTATCACTTGGA
EST: gi|12691145|gb|BG157481.1|BG157481
EST:     AAGCATTACTTAGTGAACTGAGCTCTTTCAGTGATTACATCAAGGAAAAT                         GGTCCTTTCATCAACGGTAGTGAGATATCTGCAGCTGACCTATCACTTGGA
genomic: AAGCATTACTTAGTGAACTGAGCTCTTTCAGTGATTACATCAAGGAAAATgtatgacatt ... ctctttatagGGTCCTTTCATCAACGGTAGTGAGATATCTGCAGCTGACCTATCACTTGGA
EST: gi|209708273|gb|BW678645.1|BW678645
EST:     ATTACATCAAGGAAAAT                         GGTCCTTTCATCAACGGTAGTGAGATATCTGCAGCTGACCTATCACTTGGA
genomic: ATTACATCAAGGAAAATgtatgacatt ... ctctttatagGGTCCTTTCATCAACGGTAGTGAGATATCTGCAGCTGACCTATCACTTGGA
EST: gi|193622016|gb|FK569560.1|FK569560
EST:     GCATTACTTAGTGAACTGAGCTCTTTCAGTGATTACATACAAAGGAAAAT                         GGTCCTTTCAT
genomic: GCATTACTTAGTGAACTGAGCTCTTTCAGTGATTACAT-CAA-GGAAAATgtatgacatt ... ctctttatagGGTCCTTTCAT
EST: gi|20813171|gb|BQ297649.1|BQ297649
EST:     AAGCATTACTTAGTGAACTGAGCTCTTTCAGTGATTACATCAAGGAAAAT                         GGTCCTTTCATCAACGGTAGTGAGATATCTGCAGCTGACCTATCACTTGGA
genomic: AAGCATTACTTAGTGAACTGAGCTCTTTCAGTGATTACATCAAGGAAAATgtatgacatt ... ctctttatagGGTCCTTTCATCAACGGTAGTGAGATATCTGCAGCTGACCTATCACTTGGA
EST: gi|5677088|gb|AI938218.1|AI938218
EST:     AAGCATTACTTAGTGAACTGAGCTCTTTCAGTGATTACATCAAGGAAAAT                         GGTCCTTTCATCAACGGTAGTGAGATATCTGCAGCTGACCTATCACTTGGA
genomic: AAGCATTACTTAGTGAACTGAGCTCTTTCAGTGATTACATCAAGGAAAATgtatgacatt ... ctctttatagGGTCCTTTCATCAACGGTAGTGAGATATCTGCAGCTGACCTATCACTTGGA
EST: gi|209705735|gb|BW661403.1|BW661403
EST:     AAGCATTACTTAGTGAACTGAGCTCTTTCAGTGATTACATCAAGGAAAAT                         GGTCCTTTCATCAACGGTAGTGAGATATCTGCAGCTGACCTATCACTTGGA
genomic: AAGCATTACTTAGTGAACTGAGCTCTTTCAGTGATTACATCAAGGAAAATgtatgacatt ... ctctttatagGGTCCTTTCATCAACGGTAGTGAGATATCTGCAGCTGACCTATCACTTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattgcaggaaccttctactttatttaattgactgattttttttcctctttatagGGTCCTTTCATCAACGGTAGTGAGATATCTGCAGCTGACCTATCACTTGGACCAAAGCTATACCATTTAGAGATTGCTTTGGGGCATTATAAGAAATGGA
                              gactgat  putative branch site (score: 3)
                                ctgattttttttcctc  CT-rich tract
                tactttatttaattga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaggaagccttttttatattatctaaagtctgcactgtttaacaaattgcaggaaccttctactttatttaattgactgattttttttcctctttatagGGTCCTTTCATCAACGGTAGTGAGATATCTGCAGCTGACCTATCACTTGGACCAAAGCTATACCATTTAGAGATTGCTTTGGGGCATTATAAGAAATGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA