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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcctgcatacatagctttcatcctactttggttgaaatcaaaattttgctttagattaagtttttcaaatgaagtctttttatttttccttccttgtgctttattttttatatatataaaattcagGTGGTAGCTGGTGGAGGTGCTGTTGAGGCAGCATTATCAGTTTATTTAGAGTACCTTGCTACAACTTTAGGATCTCGGGAGCAGTTGGCTATAGCAGAAT

Basic information

species Glycine max
transcript GLYMA08G12970.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G12970.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv15s0021g02230.t01 (Vitis vinifera), 3'ss of exon 13
gtatcctgcatacatagctttcatcctactttggttgaaatcaaaattttgctttagattaagtttttcaaatgaagtctttttatttttccttcc--ttgtgctttattttttatatatataaaattcagGTGGTAGCTGGTGGAGGTGCTGTTGAGGCAGCATTATCAGTTTATTTAGAGTACCTTGCTACAACTTTAGGATCTCGGGAGCAGTTGGCTATAGCAGAAT
                       |  |  ||||   ||  ||| || || |     || |||    || | ||||    ||  ||  | |  ||    ||||     |  || |   ||| | |||| ||||||||||| |||||||||||||||||||| || ||||| || ||||| ||||||||||| |||||||||||||| || ||||||||||| || |||||||
----------------------tttatgttttgaaagatgtcagaaattag-----gaataa----ttaatatgagagtttgctaaatattgttaagattgtcaaccaacttgtcagtatttgaaatacagGTGGTAGCAGGTGGAGGTGCTGTTGAGGCTGCTTTATCTGTGTATTTGGAGTACCTTGCAACAACTTTAGGATCCCGAGAGCAGTTGGCAATTGCAGAAT
















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|58021211|gb|CX707953.1|CX707953
EST:     CTCTGCATGATGCATTGTCAATTGTCAAGAGAACTCTTGAATCAAATACG                         GTGGTAGCTGGTGGAGGTGCTGTTGAGGCAGCATTATCAGTTTATTTAGAG
genomic: CTCTGCATGATGCATTGTCAATTGTCAAGAGAACTCTTGAATCAAATACGgtatcctgca ... taaaattcagGTGGTAGCTGGTGGAGGTGCTGTTGAGGCAGCATTATCAGTTTATTTAGAG
EST: gi|298168848|gb|HO009778.1|HO009778
EST:     CTCTGCATGATGCATTGTCAATTGTCAAGAGAACTCTTGAATCAAATACG                         GTGGTAGCTGGTGGAGGTGCTGTTGAGGCAGCATTATCAGTTTATTTGGAG
genomic: CTCTGCATGATGCATTGTCAATTGTCAAGAGAACTCTTGAATCAAATACGgtatcctgca ... taaaattcagGTGGTAGCTGGTGGAGGTGCTGTTGAGGCAGCATTATCAGTTTATTTAGAG
EST: gi|298165014|gb|HO011063.1|HO011063
EST:     CTCTGCATGATGCATTGTCAATTGTCAAGAGAACTCTTGAATCAAATACG                         GTGGTAGCTGGTGGAGGTGCTGTTGAGGCAGCATTATCAGTTTATTTGGAG
genomic: CTCTGCATGATGCATTGTCAATTGTCAAGAGAACTCTTGAATCAAATACGgtatcctgca ... taaaattcagGTGGTAGCTGGTGGAGGTGCTGTTGAGGCAGCATTATCAGTTTATTTAGAG
EST: gi|13562760|gb|BG550980.1|BG550980
EST:     CTCTGCATGATGCATTGTCCATTGTCAAGAGAACTCTTGAATCAAATACG                         GTGGTAGCTGGTGGAGGTGCTGTTGAAGCAGCATTATCAGTTTATTTGGAG
genomic: CTCTGCATGATGCATTGTCAATTGTCAAGAGAACTCTTGAATCAAATACGgtatcctgca ... taaaattcagGTGGTAGCTGGTGGAGGTGCTGTTGAGGCAGCATTATCAGTTTATTTAGAG
EST: gi|14011018|gb|BG725940.1|BG725940
EST:     CTCTGCATGATGCATTGTCAATTGTCAAGAGAACTCTTGAATCAAATACG                         GTGGTAGCTGGTGGAGGTGCTGTTGAGGCAGCATTATCAGTTTATTTAGAG
genomic: CTCTGCATGATGCATTGTCAATTGTCAAGAGAACTCTTGAATCAAATACGgtatcctgca ... taaaattcagGTGGTAGCTGGTGGAGGTGCTGTTGAGGCAGCATTATCAGTTTATTTAGAG
EST: gi|58022777|gb|CX709518.1|CX709518
EST:     TCTGCATGATGCATTGTCAATTGTCAAGAGAACTC-TGNAATCAAATACG                         GTGGTAGCTGGTGGAGGTGCTGTTGAGGCAGCATTATCAGTTTATTTAGAG
genomic: TCTGCATGATGCATTGTCAATTGTCAAGAGAACTCTTG-AATCAAATACGgtatcctgca ... taaaattcagGTGGTAGCTGGTGGAGGTGCTGTTGAGGCAGCATTATCAGTTTATTTAGAG
EST: gi|14125209|gb|BG789656.1|BG789656
EST:     CTCTGCATGATGCATTGTCAATTGTCAAGAGAACTCTTGAATCAAATACG                         GTGGTAGCTGGTGGAGGTGCTGTTGAGGCAGCATTATCAGTTTATTTAGAG
genomic: CTCTGCATGATGCATTGTCAATTGTCAAGAGAACTCTTGAATCAAATACGgtatcctgca ... taaaattcagGTGGTAGCTGGTGGAGGTGCTGTTGAGGCAGCATTATCAGTTTATTTAGAG
EST: gi|193444629|gb|FK407491.1|FK407491
EST:     CTCTGCATGATGCATTGTCAATTGTCAAGAGAACTCTTGAATCAAATACG                         GTGGTAGCTGGTGGAGGTGCTGTTGAGGCA
genomic: CTCTGCATGATGCATTGTCAATTGTCAAGAGAACTCTTGAATCAAATACGgtatcctgca ... taaaattcagGTGGTAGCTGGTGGAGGTGCTGTTGAGGCA
EST: gi|58017859|gb|CX704601.1|CX704601
EST:     CTCTGCATGATGCATTGTCAATTGTCAAGAGAACTCTTGAATCAAATACG                         GTGGTAGCTGGTGGAGGTGCTGTTGAGGCAGCATTATCAGTTTATTTAGAG
genomic: CTCTGCATGATGCATTGTCAATTGTCAAGAGAACTCTTGAATCAAATACGgtatcctgca ... taaaattcagGTGGTAGCTGGTGGAGGTGCTGTTGAGGCAGCATTATCAGTTTATTTAGAG
EST: gi|15200044|gb|BI424143.1|BI424143
EST:     CTCTGCATGATGCATTGTCAATTGTCAAGAGAACTCTTGAATCAAATACG                         GTGGTAGCTGGTGGAGGTGCTGTTGAGGCAGCATTATCAGTTTATTTAGAG
genomic: CTCTGCATGATGCATTGTCAATTGTCAAGAGAACTCTTGAATCAAATACGgtatcctgca ... taaaattcagGTGGTAGCTGGTGGAGGTGCTGTTGAGGCAGCATTATCAGTTTATTTAGAG
EST: gi|18040540|gb|BM308834.1|BM308834
EST:     CTCTGCATGATGCATTGTCAATTGTCAAGAGAACTCTTGAATCAAATACG                         GTGGTAGCTGGTGGAGGTGCTGTTGAGGCAGCATTATCAGTTTATTTGGAG
genomic: CTCTGCATGATGCATTGTCAATTGTCAAGAGAACTCTTGAATCAAATACGgtatcctgca ... taaaattcagGTGGTAGCTGGTGGAGGTGCTGTTGAGGCAGCATTATCAGTTTATTTAGAG
EST: gi|51335203|gb|CO979069.1|CO979069
EST:     CTCTGCATGATGCATTGTCAATTGTCAAGAGAACTCTTGAATCAAATACG                         GTGGTAGCTGGTGGAGGTGCTGTTGAGGCAGCATTATCAGTTTATTTGGAG
genomic: CTCTGCATGATGCATTGTCAATTGTCAAGAGAACTCTTGAATCAAATACGgtatcctgca ... taaaattcagGTGGTAGCTGGTGGAGGTGCTGTTGAGGCAGCATTATCAGTTTATTTAGAG
EST: gi|58019703|gb|CX706445.1|CX706445
EST:     CTCTGCATGATGCATTGTCAATTGTCAAGAGAACTCTTGAATCAAATACG                         GTGGTAGCTGGTGGAGGTGCTGTTGAGGCAGCATTATCAGTTTATTTAGAG
genomic: CTCTGCATGATGCATTGTCAATTGTCAAGAGAACTCTTGAATCAAATACGgtatcctgca ... taaaattcagGTGGTAGCTGGTGGAGGTGCTGTTGAGGCAGCATTATCAGTTTATTTAGAG
EST: gi|151398434|gb|EV268305.1|EV268305
EST:     CTCTGCATGATGCATTGTCAATTGTCAAGAGAACTCATGAATCAAATACG                         GTGGTAGCTGGTGGAGGTGCTGTTGAGGCAGCATTATCAGTTTATTTAGAG
genomic: CTCTGCATGATGCATTGTCAATTGTCAAGAGAACTCTTGAATCAAATACGgtatcctgca ... taaaattcagGTGGTAGCTGGTGGAGGTGCTGTTGAGGCAGCATTATCAGTTTATTTAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtctttttatttttccttccttgtgctttattttttatatatataaaattcagGTGGTAGCTGGTGGAGGTGCTGTTGAGGCAGCATTATCAGTTTATTTAGAGTACCTTGCTACAACTTTAGGATCTCGGGAGCAGTTGGCTATAGCAGAAT
                  ttccttgtgctttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcctgcatacatagctttcatcctactttggttgaaatcaaaattttgctttagattaagtttttcaaatgaagtctttttatttttccttccttgtgctttattttttatatatataaaattcagGTGGTAGCTGGTGGAGGTGCTGTTGAGGCAGCATTATCAGTTTATTTAGAGTACCTTGCTACAACTTTAGGATCTCGGGAGCAGTTGGCTATAGCAGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG