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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaaatggttgttttagtttctccatttgtgcatattatattgatggttttcacaaccaatagtccgttccttattatttcgtgatttgtgatgagatagACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTATTACCACAGCTCAG

Basic information

species Glycine max
transcript GLYMA01G36880.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G36880.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G17800.2 (Arabidopsis thaliana), 3'ss of exon 5
--acaaatggttgttttagtttctccatttgtgcatattatattgatggttttcacaaccaatagtccgttccttattatttcgtgatttgtgatga--gatagACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTATTACCACAGCTCAG
     ||   | |   |  | |||  ||  ||  | |   || |  |  |  | |  |    | ||| | | |||||  ||| ||| ||  | ||    |  ||| ||||||||||| || ||||||| ||||||||| ||||| || ||||| ||||| || ||||||
tgcttaactttcggcctgctgtctg-atccgtctagacc-tacttttaatagttatgagtt-tcgtctggtgcttat-gttttgtgtttcatcatatatgccagATCTTCGGGATGACAAACAGTTCTTCATTGACCACCCTGGCGCTGTACCAATTACTACTGCTCAG

upper sequence: GLYMA01G36880.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 5
acaaatggttgttttagtttctccatttgtgcatattatattgatggttttcacaaccaatagtccgttccttattatttcgtgatttgtgatgagatagACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTATTACCACAGCTCAG
  ||||   |        ||  |  |  | | |  |||| |      || | | ||  || |     ||  |   |  ||    || |    |||| |||| |||||||| || |||||||||| ||| |||||||||||||| || || ||  |  ||||||||
ctaaattagtagaaggaatttgcagtaggagtaggttatttatggttttgtgataattaacaaattttttttgtctgattttcaatgttaattgagctagATCTTCGGGAAGACAAGCAGTTCTTCATAGACCATCCTGGTGCTGTGCCCATCTCTGCAGCTCAG
















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|6746963|gb|AW317419.1|AW317419
EST:     TGGTTGGCAC-TATCTTG                         ACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTA
genomic: TGGTTGGCACAAAGCTTGgtaagcttat ... gatgagatagACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTA
EST: gi|9819855|gb|BE555431.1|BE555431
EST:     CTCCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTG                         ACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTA
genomic: CTCCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTGgtaagcttat ... gatgagatagACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTA
EST: gi|26268044|gb|CA819107.1|CA819107
EST:     GAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTG                         ACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTA
genomic: GAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTGgtaagcttat ... gatgagatagACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTA
EST: gi|26057126|gb|CA800040.1|CA800040
EST:     GAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTG                         ACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTA
genomic: GAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTGgtaagcttat ... gatgagatagACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTA
EST: gi|298166464|gb|HO009903.1|HO009903
EST:     GAAGCGTTATGCTCCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTG                         ACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTA
genomic: GAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTGgtaagcttat ... gatgagatagACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTA
EST: gi|31455813|gb|CD397841.1|CD397841
EST:     GAAGCATGATGCTCCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTG                         ACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTA
genomic: GAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTGgtaagcttat ... gatgagatagACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTA
EST: gi|19452394|gb|BM953804.1|BM953804
EST:     GAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTG                         ACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTA
genomic: GAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTGgtaagcttat ... gatgagatagACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTA
EST: gi|5175630|gb|AI759963.1|AI759963
EST:     GAAGCATTATGCTCCTGGTGTCCGCATTATTCTGGTTGGCACAAAGCTTG                         ACCTTCAGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTA
genomic: GAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTGgtaagcttat ... gatgagatagACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTA
EST: gi|10843808|gb|BF067063.1|BF067063
EST:     AAGCATTATGCTCGCTG-TGTCCCCATTATTCTGGTTGGCACGAAGCTTG                         ACCTTCGGGATGATAAGCAGTTCTGCCTCGACCCTCCTGGTGCCGTACCTA
genomic: AAGCATTATGCTC-CTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTGgtaagcttat ... gatgagatagACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTA
EST: gi|31306633|gb|CD391836.1|CD391836
EST:     GAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTTGGCACCAAGCTTG                         ACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTA
genomic: GAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTGgtaagcttat ... gatgagatagACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTA
EST: gi|17964056|gb|BM270797.1|BM270797
EST:     GAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTG                         ACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTA
genomic: GAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTGgtaagcttat ... gatgagatagACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTA
EST: gi|7925509|gb|AW831535.1|AW831535
EST:     GAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTG                         ACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTA
genomic: GAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTGgtaagcttat ... gatgagatagACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTA
EST: gi|5688224|gb|AI941239.1|AI941239
EST:     GAAGCATTATGCTCCTGGTGTCCNCATTATTCTGGTTGGCACAAAGCTTG                         ACCTTCGGGATGATAAGCAGTTCTGCATTGACCATTCTGGTGCCGTACCTA
genomic: GAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTGgtaagcttat ... gatgagatagACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTA
EST: gi|31469737|gb|CD411765.1|CD411765
EST:     GAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTG                         ACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTA
genomic: GAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTGgtaagcttat ... gatgagatagACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTA
EST: gi|37995833|gb|CF807422.1|CF807422
EST:     GAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTG                         ACCTTCGGGATGATAAGCAGTTCTG
genomic: GAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTGgtaagcttat ... gatgagatagACCTTCGGGATGATAAGCAGTTCTG
EST: gi|17519189|gb|BM188231.1|BM188231
EST:     GAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTG                         ACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTA
genomic: GAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTGgtaagcttat ... gatgagatagACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTA
EST: gi|14991554|gb|BI317227.1|BI317227
EST:     GAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTG                         ACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTA
genomic: GAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTGgtaagcttat ... gatgagatagACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTA
EST: gi|31309981|gb|CD395184.1|CD395184
EST:     GAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTTGGCACCAAGCTTG                         ACNTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTA
genomic: GAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTGgtaagcttat ... gatgagatagACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTA
EST: gi|31458682|gb|CD400710.1|CD400710
EST:     GAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTG                         ACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTA
genomic: GAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTGgtaagcttat ... gatgagatagACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTA
EST: gi|17964054|gb|BM270795.1|BM270795
EST:     GAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTG                         ACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCT
genomic: GAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTGgtaagcttat ... gatgagatagACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttttcacaaccaatagtccgttccttattatttcgtgatttgtgatgagatagACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTATTACCACAGCTCAG
                          ttattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaaatggttgttttagtttctccatttgtgcatattatattgatggttttcacaaccaatagtccgttccttattatttcgtgatttgtgatgagatagACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTATTACCACAGCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA