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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agattagggaatatttgttcttctcatttaggaagttcttttcctggcgttattggtgtccataattgtttgatctacaattgctgcatattatttgtagGATCCTTTAAATTCAATGGTGATATTATGCGATGCAAAGCTTCAAGAGCTACTTGGATGTGAAAGCATTTCTGCTTTAGGAATACCAGAGATGTTAGCAC

Basic information

species Glycine max
transcript GLYMA17G01230.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G01230.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s0187g00240.t01 (Vitis vinifera), 3'ss of exon 4
agattagggaatatttgttcttctcatt--taggaagttcttttcctggcgtt---attggtgtccataattgtttgatctacaat----tgctgcatattatttgtagGATCCTTTAAATTCAATGGTGATATTATGCGATGCAAAGCTTCAAGAGCTACTTGGATGTGAAAGCATTTCTGCTTTAGGAATACCAGAGATGTTAGCAC
           | ||| || || |   |   ||    || || |   |   ||    || |||   | | ||  |||   |  ||     |  ||  | | | || ||||||||| ||||||||||||  ||| |||| |||||||||||||  |||||  ||||||||||||| ||||||||  | ||  || | |||||||||||||
---------tctgtttatttttttgggtggcagcctatttttatttagaaattccagttagtgaaaaaagttcattggcttttaaggtggttttgtttgtcacttttagGATCCTCTAAATTCAATGGCAATACTATGTGATGCAAAGCTTCGGGAGCTCTTTGGATGTGAAAGTATTTCTGCACTGGGGGTATCTGAGATGTTAGCAC

upper sequence: GLYMA17G01230.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s0187g00190.t01 (Vitis vinifera), 3'ss of exon 4
agattagggaatatttgttcttctcatt--taggaagttcttttcctggcgtt---attggtgtccataattgtttgatctacaat----tgctgcatattatttgtagGATCCTTTAAATTCAATGGTGATATTATGCGATGCAAAGCTTCAAGAGCTACTTGGATGTGAAAGCATTTCTGCTTTAGGAATACCAGAGATGTTAGCAC
           | ||| || || |   |  |||    || || |   |   ||    || |||   | | |   |||   |  ||     |  ||  | | | || ||||||||| ||||||| ||||  ||| |||| |||||||||||||| |||||  ||||||||||||| ||||||||  | ||  || | ||||||||||| |
---------tctgtttatttttttgggtggtagcctattattatttagaaattccagttagtgaaaaaagtgcattggcttttaaggtggttttgtttgtcacttttagGATCCTCTAAATTCGATGGCAATACTATGTGATGCAAAGCTTCAGGAGCTCTTTGGATGTGAAAGTATTTCTGCACTGGGGGTATCTGAGATGTTAGCGC
















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|208101134|gb|GD900551.1|GD900551
EST:     GGGAGTACATCAAGCTTCACCATTTGGAG                         GATCCTTTAAATTCAATGGTGATATTATGCGATGCAAAGCTTCAAGAGCTA
genomic: GGGAGTACATCAAGCTTCACCATTTGGAGgtgtgtagtc ... ttatttgtagGATCCTTTAAATTCAATGGTGATATTATGCGATGCAAAGCTTCAAGAGCTA
EST: gi|208320363|gb|GE120432.1|GE120432
EST:     GACTTGTTTGGGAGTACTATTCAAGCTTCACCATTTGGAG                         GATCCTTTAAATTCAATGGTGATATTATGCGATGCAAAGCTTCAAGAGCTA
genomic: GACTTGTTTGGGAGTAC-A-TCAAGCTTCACCATTTGGAGgtgtgtagtc ... ttatttgtagGATCCTTTAAATTCAATGGTGATATTATGCGATGCAAAGCTTCAAGAGCTA
EST: gi|193729793|gb|FK664739.1|FK664739
EST:     CTTCACCATTTGGAG                         GATCCTTTAAATTCAATGGTGATATTATGCGATGCAAAGCTTCAAGAGCTA
genomic: CTTCACCATTTGGAGgtgtgtagtc ... ttatttgtagGATCCTTTAAATTCAATGGTGATATTATGCGATGCAAAGCTTCAAGAGCTA
EST: gi|193533094|gb|FK490590.1|FK490590
EST:     CTGAAGCCATAAGACTTGTTTGGGAGTACATCAAGCTTCACCATTTGGAG                         GATCCTTTAAATTCAATGGTGATATTATGCGATGCAAAGCTTCAAGAGCTA
genomic: CTGAAGCCATAAGACTTGTTTGGGAGTACATCAAGCTTCACCATTTGGAGgtgtgtagtc ... ttatttgtagGATCCTTTAAATTCAATGGTGATATTATGCGATGCAAAGCTTCAAGAGCTA
EST: gi|308098720|gb|HO760461.1|HO760461
EST:     ACATCAAGCTTCACCATTTGGAG                         GATCCTTTAAATTCAATGGTGATATTATGCGATGCAAAGCTTCAAGAGCTA
genomic: ACATCAAGCTTCACCATTTGGAGgtgtgtagtc ... ttatttgtagGATCCTTTAAATTCAATGGTGATATTATGCGATGCAAAGCTTCAAGAGCTA
EST: gi|208074637|gb|GD868274.1|GD868274
EST:     CTGAAGCCATAAGACTTGTTTGGGAGTACATCAAGCTTCACCATTTGGAG                         GATCCTTTAAATTCAATGGTGATATTATGCGATGCAAAGCTTCAAGAGCTA
genomic: CTGAAGCCATAAGACTTGTTTGGGAGTACATCAAGCTTCACCATTTGGAGgtgtgtagtc ... ttatttgtagGATCCTTTAAATTCAATGGTGATATTATGCGATGCAAAGCTTCAAGAGCTA
EST: gi|208088930|gb|GD887788.1|GD887788
EST:     CTGAGGCCATAAGACTTGTTTGGGAGTACATCAAGCTACACCATTTGGAG                         GATCCTTTAAATTC
genomic: CTGAAGCCATAAGACTTGTTTGGGAGTACATCAAGCTTCACCATTTGGAGgtgtgtagtc ... ttatttgtagGATCCTTTAAATTC
EST: gi|192314884|gb|FK010702.1|FK010702
EST:     AAGACTTGTTTGGGAGTACATCAAGCTTCACCATTTGGAG                         GATCCTTTAAATTCAATGGTGATATTATGCGATGCAAAGCTTCAAGAGCTA
genomic: AAGACTTGTTTGGGAGTACATCAAGCTTCACCATTTGGAGgtgtgtagtc ... ttatttgtagGATCCTTTAAATTCAATGGTGATATTATGCGATGCAAAGCTTCAAGAGCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcgttattggtgtccataattgtttgatctacaattgctgcatattatttgtagGATCCTTTAAATTCAATGGTGATATTATGCGATGCAAAGCTTCAAGAGCTACTTGGATGTGAAAGCATTTCTGCTTTAGGAATACCAGAGATGTTAGCAC
                      gtttgat  putative branch site (score: 5)
                                          atattatttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agattagggaatatttgttcttctcatttaggaagttcttttcctggcgttattggtgtccataattgtttgatctacaattgctgcatattatttgtagGATCCTTTAAATTCAATGGTGATATTATGCGATGCAAAGCTTCAAGAGCTACTTGGATGTGAAAGCATTTCTGCTTTAGGAATACCAGAGATGTTAGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - -tggtgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgctgc