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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtatttagttaaatatcaacagttgttgacttcaagatatagcttccttcttatacagctgtctgagctataagttttatttttttcccagTTTGCAACTGAAGCTGCTATTACCATCCTTCGAATTGATGACATGATCAAGCTTGTCAAGGATGAAAGTCAAAATGAGGATTAAAGTATAACTGAATCTA

Basic information

species Glycine max
transcript GLYMA05G29870.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G29870.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv15s0021g02230.t01 (Vitis vinifera), 3'ss of exon 16
gtatgtatttagttaaatatcaacagttgttgac-ttcaagatatagcttccttcttatacagctgtctgagctataagttttatttttttcccagTTTGCAACTGAAGCTGCTATTACCATCCTTCGAATTGATGACATGATCAAGCTTGTCAAGGATGAAAGTCAAAATGAGGA---TTAAAGTATAACTGAATCTA
|| ||| | | | || | || | |||| | ||| || | | || |||| || || | | | ||||||||||| ||||| || || || || ||||||||||| |||||||||||||||||||| ||||||| ||| ||||| || ||| || | | | | |
-----------gtaaaagctgcaaaacaattaatatttatgataaaacttggtttcaaaagag----tccagctgaaatttctggtgtg----cagTTTGCAACAGAAGCAGCCATAACAATTCTTCGAATTGACGACATGATCAAGCTTGTCAAAGATGAAACTCAGAATGAAGAAGATTAGAGGAGAGCAGCCT---

upper sequence: GLYMA05G29870.1 (Glycine max), 3'ss of exon 16
lower sequence: PP1S200_112V6.2 (Physcomitrella patens), 3'ss of exon 16
---------------------------------------------------------gtatgtatttagttaaatatcaacagttgttgacttcaagata----tagcttccttcttatacagctgtctgagct----------ataagttttatttttttcccagTTTGCAACTGAAGCTGCTATTACCATCCTTCGAATTGATGACATGATCAAGCTTGTCAAGGATGAAAGTCAAAATGAG-GATTAAAGTATAACTGAATCTA
|||||| | | | | | ||||| | | | | || | | | | | | || | || | | | | | ||||| |||||||||||||||||||| ||||| ||||| |||||||||||||||||||| || ||||||| ||| | || | || | | | | |||
gtaagaaacatgtgcttttgaaagattcccttttaatatatgaagattttttgacagatatgtactgtctcgtttctggatcattgttctttgtatgttgaggttaattgctctggtgtgtgggggtgtaagatcatgcctgatgtgacatcggtattttttgcagTTTGCAACTGAAGCTGCAATTACAATCCTACGAATTGATGACATGATCAAACTGTTCAAGGAGGAAGATGGTGATCGGTGACATCACTTTCGCAGAAGGA-
















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|7589251|gb|AW705029.1|AW705029
EST:     TGGAGGCCGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAG                         TTTGCAACTGAAGCTGCTATTACCATCCTTCGAATTGATGACATGATCAAG
genomic: TGGAGGCCGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAGgtatgtattt ... tttttcccagTTTGCAACTGAAGCTGCTATTACCATCCTTCGAATTGATGACATGATCAAG
EST: gi|57575315|gb|CX548290.1|CX548290
EST:     TGGAGGCCGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAG                         TTTGCAACTGAAGCTGCTATTACCATCCTTCGAATTGATGACATGATCAAG
genomic: TGGAGGCCGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAGgtatgtattt ... tttttcccagTTTGCAACTGAAGCTGCTATTACCATCCTTCGAATTGATGACATGATCAAG
EST: gi|193550064|gb|FK505547.1|FK505547
EST:     GGCCGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAG                         TTTGCAACTGAAGCTGCTATTACCATCCTTCGAATTGATGACATGATCAAG
genomic: GGCCGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAGgtatgtattt ... tttttcccagTTTGCAACTGAAGCTGCTATTACCATCCTTCGAATTGATGACATGATCAAG
EST: gi|192324819|gb|FK018795.1|FK018795
EST:     AGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAG                         TTTGCAACTGAAGCTGCTATTACCATCCTTCGAATTGATGACATGATCAAG
genomic: AGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAGgtatgtattt ... tttttcccagTTTGCAACTGAAGCTGCTATTACCATCCTTCGAATTGATGACATGATCAAG
EST: gi|23727410|gb|BU761735.1|BU761735
EST:     TGGAGGCCGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAG                         TTTGCAACTGAAGCTGCTATTACCATCCTTCGAATTGATGACATGATCAAG
genomic: TGGAGGCCGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAGgtatgtattt ... tttttcccagTTTGCAACTGAAGCTGCTATTACCATCCTTCGAATTGATGACATGATCAAG
EST: gi|57575079|gb|CX548054.1|CX548054
EST:     TGGAGGCCGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAG                         TTTGCAACTGAAGCTGCTATTACCATCCTTCGAATTGATGACATGATCAAG
genomic: TGGAGGCCGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAGgtatgtattt ... tttttcccagTTTGCAACTGAAGCTGCTATTACCATCCTTCGAATTGATGACATGATCAAG
EST: gi|22932667|gb|BU549806.1|BU549806
EST:     TGGAGGCCGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAG                         TTTGCAACTGAAGCTGCTATTACCATCCTTCGAATTGATGACATGATCAAG
genomic: TGGAGGCCGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAGgtatgtattt ... tttttcccagTTTGCAACTGAAGCTGCTATTACCATCCTTCGAATTGATGACATGATCAAG
EST: gi|7589348|gb|AW705124.1|AW705124
EST:     TGGAGGCCGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAG                         TTTGCAACTGAAGCTGCTATTACCATCCTTCGAATTGATGACATGATCAAG
genomic: TGGAGGCCGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAGgtatgtattt ... tttttcccagTTTGCAACTGAAGCTGCTATTACCATCCTTCGAATTGATGACATGATCAAG
EST: gi|31473682|gb|CD415710.1|CD415710
EST:     GTAAAAATTATTCAG                         TTTGCAACTGAAGCTGCTATTACCATCCTTCGAATTGATGACATGATCAAG
genomic: GTAAAAATTATTCAGgtatgtattt ... tttttcccagTTTGCAACTGAAGCTGCTATTACCATCCTTCGAATTGATGACATGATCAAG
EST: gi|151401732|gb|EV271545.1|EV271545
EST:     AGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAG                         TTTGCAACTGAAGCTGCTATTACCATCCTTCGAATTGATGACATGATCAAG
genomic: AGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAGgtatgtattt ... tttttcccagTTTGCAACTGAAGCTGCTATTACCATCCTTCGAATTGATGACATGATCAAG
EST: gi|58018371|gb|CX705113.1|CX705113
EST:     TGGAGGCCGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAG                         TTTGCAACTGAAGCTGCTATTACCATCCTTCGAATTGATGACATGATCAAG
genomic: TGGAGGCCGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAGgtatgtattt ... tttttcccagTTTGCAACTGAAGCTGCTATTACCATCCTTCGAATTGATGACATGATCAAG
EST: gi|58016681|gb|CX703423.1|CX703423
EST:     TGGAGGCCGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAG                         TTTGCAACTGAAGCTGCTATTACCATCCTTCGAATTGATGACATGATCAAG
genomic: TGGAGGCCGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAGgtatgtattt ... tttttcccagTTTGCAACTGAAGCTGCTATTACCATCCTTCGAATTGATGACATGATCAAG
EST: gi|298170514|gb|HO019138.1|HO019138
EST:     TGGAGGCCGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAG                         TTTGCAACTGAAGCTGCTATTACCATCCTTCGAATTGATGACATGATCAAG
genomic: TGGAGGCCGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAGgtatgtattt ... tttttcccagTTTGCAACTGAAGCTGCTATTACCATCCTTCGAATTGATGACATGATCAAG
EST: gi|58016928|gb|CX703670.1|CX703670
EST:     TGGAGGCCGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAG                         TTTGCAACTGAAGCTGCTATTACCATCCTTCGAATTGATGACATGATCAAG
genomic: TGGAGGCCGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAGgtatgtattt ... tttttcccagTTTGCAACTGAAGCTGCTATTACCATCCTTCGAATTGATGACATGATCAAG
EST: gi|254334340|gb|GR844125.1|GR844125
EST:     TGGAGGCCGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAG                         TTTGCAACTGAAGCTGCTATTACCATCCTTCGAATTGATGACATGATCAAG
genomic: TGGAGGCCGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAGgtatgtattt ... tttttcccagTTTGCAACTGAAGCTGCTATTACCATCCTTCGAATTGATGACATGATCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatagcttccttcttatacagctgtctgagctataagttttatttttttcccagTTTGCAACTGAAGCTGCTATTACCATCCTTCGAATTGATGACATGATCAAGCTTGTCAAGGATGAAAGTCAAAATGAGGATTAAAGTATAACTGAATCTA
                                      ttttatttttttccc  CT-rich tract
 agctataagttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtatttagttaaatatcaacagttgttgacttcaagatatagcttccttcttatacagctgtctgagctataagttttatttttttcccagTTTGCAACTGAAGCTGCTATTACCATCCTTCGAATTGATGACATGATCAAGCTTGTCAAGGATGAAAGTCAAAATGAGGATTAAAGTATAACTGAATCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT