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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagacatgtagaatcaatgttacttgtgaataacttgttaaaatttcaaattgtaattttgttacagctaattttctaacgaataccattagctatttgacaaaccttaaagtgttcttgtacctctggaactgcagGTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAAT

Basic information

species Glycine max
transcript GLYMA08G43230.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G43230.3 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g72205.1 (Oryza sativa), 3'ss of exon 3
------------------gtagacatgtagaatcaatgttacttgtgaataacttgttaaaatttcaaattgtaattttgttacagctaattttctaacgaataccattagctatttgacaaa-ccttaaagtgttcttgta---------cctctggaac----------------tgcagGTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAAT
                  | | || | ||        |||  || | ||| ||     | | |   | |||| |   |  |||   ||  |||| |  | |  |   || | |  ||  |    ||||    || | || ||         |   ||  ||                | ||| | || || || ||||| |||   ||    | | | |||||  ||||| |||| |||||||| |||||||| || |||||||||||||
gtaagcagcttaagctccgaacacttttaagggttcagttcattataaattac--accacactagtatattgcagcatgcttatctctttttttttcccaataatgctttgatgcttatctgctccttgtgatgatattatatggatatgccaattgatacatgatgttgacatactttcagATTGCTAACCACCTTGATCGTGCTGTTAGTAGCTTGGGAAGGGATCCTTTGAAAGTTTTGGTACAAGTAAACACTAGTGGAGAAGAAT
















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|208172293|gb|GD968910.1|GD968910
EST:     TGGGTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAG                         GTAGCAAATCATCTTGACTGTATGGTATCAACCCTTGGAAGAAATCCTCTG
genomic: TGGGTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAGgtagacatgt ... ggaactgcagGTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG
EST: gi|298199617|gb|HO043494.1|HO043494
EST:     GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAG                         GTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG
genomic: GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAGgtagacatgt ... ggaactgcagGTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG
EST: gi|209708248|gb|BW678618.1|BW678618
EST:     GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAG                         GTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG
genomic: GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAGgtagacatgt ... ggaactgcagGTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG
EST: gi|120530250|gb|EH258384.1|EH258384
EST:     GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAG                         GTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG
genomic: GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAGgtagacatgt ... ggaactgcagGTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG
EST: gi|20498376|gb|BQ273306.1|BQ273306
EST:     GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAG                         GTAACAAATCATCTTGACCGAATGGTATCAACCCTTGGAAGAAATCCTCTG
genomic: GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAGgtagacatgt ... ggaactgcagGTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG
EST: gi|31473950|gb|CD415978.1|CD415978
EST:     GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAG                         GTAGCAAATCATCTTGACCGTATGGTATCA
genomic: GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAGgtagacatgt ... ggaactgcagGTAGCAAATCATCTTGACCGTATGGTATCA
EST: gi|209728275|gb|BW658487.1|BW658487
EST:     GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAG                         GTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG
genomic: GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAGgtagacatgt ... ggaactgcagGTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG
EST: gi|21285679|gb|BQ473550.1|BQ473550
EST:     GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAG                         GTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG
genomic: GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAGgtagacatgt ... ggaactgcagGTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG
EST: gi|298165006|gb|HO011055.1|HO011055
EST:     GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAG                         GTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG
genomic: GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAGgtagacatgt ... ggaactgcagGTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG
EST: gi|208064645|gb|GD865921.1|GD865921
EST:     GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAG                         GTAGCAAATCATCTTGACTGTATGGTATCAACCCTTGGAAGAAATCCTCTG
genomic: GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAGgtagacatgt ... ggaactgcagGTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG
EST: gi|13180762|gb|BG352102.1|BG352102
EST:     GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAG                         GTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG
genomic: GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAGgtagacatgt ... ggaactgcagGTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG
EST: gi|208156781|gb|GD957287.1|GD957287
EST:     GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAG                         GTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG
genomic: GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAGgtagacatgt ... ggaactgcagGTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG
EST: gi|20207929|gb|BQ134018.1|BQ134018
EST:     GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAG                         GTAACAAATCATCTTGACCGAATGGTATCAACCCTTGGAAGAAATCCTCTG
genomic: GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAGgtagacatgt ... ggaactgcagGTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG
EST: gi|298163042|gb|HO011775.1|HO011775
EST:     GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAG                         GTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG
genomic: GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAGgtagacatgt ... ggaactgcagGTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG
EST: gi|298179673|gb|HO024888.1|HO024888
EST:     GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAG                         GTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG
genomic: GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAGgtagacatgt ... ggaactgcagGTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG
EST: gi|193664931|gb|FK610891.1|FK610891
EST:     GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAG                         GTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG
genomic: GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAGgtagacatgt ... ggaactgcagGTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG
EST: gi|15664325|gb|BI701696.1|BI701696
EST:     GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAG                         GTAACAAATCATCTTGACCGAATGGTATCAACCCTTGGAAGAAATCCTCTG
genomic: GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAGgtagacatgt ... ggaactgcagGTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG
EST: gi|193353738|gb|FK319422.1|FK319422
EST:     GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAG                         GTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG
genomic: GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAGgtagacatgt ... ggaactgcagGTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG
EST: gi|209705383|gb|BW668013.1|BW668013
EST:     GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAG                         GTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG
genomic: GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAGgtagacatgt ... ggaactgcagGTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG
EST: gi|7926422|gb|AW832448.1|AW832448
EST:     GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAG                         GTAGCAAATCATCTTGACCGTATGGTATCGACCCTTGGAAGAAATCCTCTG
genomic: GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAGgtagacatgt ... ggaactgcagGTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG
EST: gi|207845177|gb|GD816202.1|GD816202
EST:     GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAG                         GTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG
genomic: GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAGgtagacatgt ... ggaactgcagGTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG
EST: gi|21993868|gb|BQ785396.1|BQ785396
EST:     GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAG                         GTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG
genomic: GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAGgtagacatgt ... ggaactgcagGTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG
EST: gi|15337855|gb|BI498511.1|BI498511
EST:     GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAG                         GTAACAAATCATCTTGACCGAATGGTATCAACCCTTGGAAGAAATCCTCTG
genomic: GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAGgtagacatgt ... ggaactgcagGTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG
EST: gi|17401932|gb|BM178714.1|BM178714
EST:     GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAG                         GTAACAAATCATCTTGACCGAATGGTATCAACCCTTGGAAGAAATCCTCTG
genomic: GTGGAGTTCCAAATCTGGCCATGGTCCAGAGTGTGGACAATCAGAAGgtagacatgt ... ggaactgcagGTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataccattagctatttgacaaaccttaaagtgttcttgtacctctggaactgcagGTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAAT
            atttgac  putative branch site (score: 4)
           tatttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagacatgtagaatcaatgttacttgtgaataacttgttaaaatttcaaattgtaattttgttacagctaattttctaacgaataccattagctatttgacaaaccttaaagtgttcttgtacctctggaactgcagGTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA