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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaaaataatcctttatgactaccatgctgatttaaatgatttgttttgctggatatctgttcatttaacattatctatttgttattagATTTGAAACATGTTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGGATCTTGAGAAAGCTGGTATTACTGTCATCCAGATTGATGAGGCTGCTCTA

Basic information

species Glycine max
transcript GLYMA04G30350.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G30350.1 (Glycine max), 3'ss of exon 10
lower sequence: AT5G20980.1 (Arabidopsis thaliana), 3'ss of exon 10
gtatgaaaataatcctttatgactaccatgctgatttaaatgatttgttttgctggatatctgttcatttaacattatctatttgttattagATTTGAAACATGTTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGGATCTTGAGAAAGCTGGTATTACTGTCATCCAGATTGATGAGGCTGCTCTA
                 | ||||  | | ||   | | || | ||  ||| |||| ||     | ||||| ||  | |||  |||||  |||   ||| ||||||| ||| |||||  | || ||||| |||||||||||||| ||||| || |||||| | ||||| |||||||||||||| |||||  ||
----------------gtgtgacatctaagcc--tctcaa-gcttcctttcgctgtatggtattccatttcaccat-tcttgttgtttgtagGCATGAGACATGTTTCCAAATTGCACTTGCCATCAAAGATGAGGTTGAGGACCTTGAAAAGGCTGGTGTCACTGTTATCCAGATTGATGAAGCTGCATTA

upper sequence: GLYMA04G30350.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv06s0009g01080.t01 (Vitis vinifera), 3'ss of exon 10
gtatgaaaat--aatcctttatgactaccat-gctgatttaaatgatttgttttgctggatatctgttcatttaacattatctatttgttattagATTTGAAACATGTTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGGATCTTGAGAAAGCTGGTATTACTGTCATCCAGATTGATGAGGCTGCTCTA
||| ||||||  |  |    |   ||| |   |  |||||  | |||    |||| |  | ||   |  || |||   | | ||  || | ||||||| || || || || |||||||||||||| ||||| || ||||||||||||||||| | ||| ||||||||||||||||||||||||||||||||||||
gtaagaaaatcaagccaaccaaatctatctcagtcgatttctacgat----tttgttata-atgattgaatctaatgct-tttacctgatcttagATTCGAGACTTGCTATCAGATTGCTTTGGCCATCAAAGACGAGGTTGAGGATCTTGAAAGAGCAGGTATTACTGTCATCCAGATTGATGAGGCTGCTCTA
















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|192312936|gb|FK003616.1|FK003616
EST:     GGCCCTGTTACTATTCTGAACTGGTCCTTTGTTAGAGATGACCAACCAAG                         ATTTGAAACATGTTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGGA
genomic: GGCCCTGTTACTATTCTGAACTGGTCCTTTGTTAGAGATGACCAACCAAGgtatgaaaat ... ttgttattagATTTGAAACATGTTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGGA
EST: gi|209721377|gb|BW654573.1|BW654573
EST:     GGCCCTGTTACTATTCTGAACTGGTCCTTTGTTAGAGATGACCAACCAAG                         ATTTGAAACATGTTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGGA
genomic: GGCCCTGTTACTATTCTGAACTGGTCCTTTGTTAGAGATGACCAACCAAGgtatgaaaat ... ttgttattagATTTGAAACATGTTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGGA
EST: gi|105634473|gb|DW247563.1|DW247563
EST:     GGCCCTGTTACTATTCTGAACTGGTCCTTTGTTAGAGATGACCAACCAAG                         ATTTGAAACATGTTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGGA
genomic: GGCCCTGTTACTATTCTGAACTGGTCCTTTGTTAGAGATGACCAACCAAGgtatgaaaat ... ttgttattagATTTGAAACATGTTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGGA
EST: gi|193328415|gb|FK295990.1|FK295990
EST:     GGCCCTGTTACTATTCTGAACTGGTCCTTTGTTAGAGATGACCAACCAAG                         ATTTGAAACATGTTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGG
genomic: GGCCCTGTTACTATTCTGAACTGGTCCTTTGTTAGAGATGACCAACCAAGgtatgaaaat ... ttgttattagATTTGAAACATGTTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGG
EST: gi|208070328|gb|GD870865.1|GD870865
EST:     GGCCCTGTTACTATTCTGAACTGGTCCTTTGTTAGAGATGACCAACCAAG                         ATTTGAAACATGTTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGGA
genomic: GGCCCTGTTACTATTCTGAACTGGTCCTTTGTTAGAGATGACCAACCAAGgtatgaaaat ... ttgttattagATTTGAAACATGTTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGGA
EST: gi|254341544|gb|GR852681.1|GR852681
EST:     GGCCCTGTTACTATTCTGAACTGGTCCTTTGTTAGAGATGACCAACCAAG                         ATTTGAAACATGTTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGGA
genomic: GGCCCTGTTACTATTCTGAACTGGTCCTTTGTTAGAGATGACCAACCAAGgtatgaaaat ... ttgttattagATTTGAAACATGTTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGGA
EST: gi|16348382|gb|BI973977.1|BI973977
EST:     GGCCCTGTTACTATTCTGAACTGGTCCTTTGTTAGAGATGACCAACCAAG                         ATTTGAAACATGTTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGGA
genomic: GGCCCTGTTACTATTCTGAACTGGTCCTTTGTTAGAGATGACCAACCAAGgtatgaaaat ... ttgttattagATTTGAAACATGTTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatgatttgttttgctggatatctgttcatttaacattatctatttgttattagATTTGAAACATGTTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGGATCTTGAGAAAGCTGGTATTACTGTCATCCAGATTGATGAGGCTGCTCTA
                             atttaac  putative branch site (score: 3)
                                        tctattt  putative PPT
                          ttcatttaacattatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaaaataatcctttatgactaccatgctgatttaaatgatttgttttgctggatatctgttcatttaacattatctatttgttattagATTTGAAACATGTTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGGATCTTGAGAAAGCTGGTATTACTGTCATCCAGATTGATGAGGCTGCTCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT