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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtgttgattgcagattcctcatttgaagttgaaacaaataatattccttttctttttttgaaagttgaaagaaataatactctttctttcctttgaagTAACAATGCAGGGGTGATGGCGACTCCATTCACACTTTCCCAAGACAATATTGAATTGCAGTTCGCAACCAATCATTTAG

Basic information

species Glycine max
transcript GLYMA05G37720.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G37720.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0025g03380.t01 (Vitis vinifera), 3'ss of exon 2
atgtgttgattgcaga-ttcctcatttgaagttgaa-acaaataatatt--ccttttctttttttgaaagttgaaagaaataatactctttctttcctttgaagTAACAATGCAGGGGTGATGGCGACTCCATTCACACTTTCCCAAGACAATATTGAATTGCAGTTCGCAACCAATCATTTAG
        |   |||  ||  ||  ||  | ||| | ||| |||   |   |   |  || |||||||| || |   |    ||  ||||| |||  || ||||||||||||||||||| ||||| |||||||||   |||||||| ||||| || ||  ||||||| |||||||| |||||||
----ccctaccacaggctttttctcttacacttgcacacacatagcttctgctcctctttcttttgaaaattcaggaatgacattgtctttttttatttggaagTAACAATGCAGGGGTTATGGCCACTCCATTCCTGCTTTCCCATGACAACATAGAGCTGCAGTTTGCAACCAACCATTTAG
















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|37995130|gb|CF806719.1|CF806719
EST:     AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAAT                         TAACAATGCAGGGGTGATGGCGACTCCATTCACACTTTCCCAAGACAATAT
genomic: AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAATgtaagaactt ... tcctttgaagTAACAATGCAGGGGTGATGGCGACTCCATTCACACTTTCCCAAGACAATAT
EST: gi|209729809|gb|BW658614.1|BW658614
EST:     AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAAT                         TAACAATGCAGGGGTGATGGCGACTCCATTCACACTTTCCCAAGACAATAT
genomic: AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAATgtaagaactt ... tcctttgaagTAACAATGCAGGGGTGATGGCGACTCCATTCACACTTTCCCAAGACAATAT
EST: gi|192308671|gb|FG999738.1|FG999738
EST:     AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAAT                         TAACAATGCAGGGGTGATGGCGACTCCATTCACACTTTCCCAAGACAATAT
genomic: AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAATgtaagaactt ... tcctttgaagTAACAATGCAGGGGTGATGGCGACTCCATTCACACTTTCCCAAGACAATAT
EST: gi|17963402|gb|BM270151.1|BM270151
EST:     AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAAT                         TAACAATGCAGGGGTGATGGCGACTCCATTCACACTTTCCCAAGACAATAT
genomic: AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAATgtaagaactt ... tcctttgaagTAACAATGCAGGGGTGATGGCGACTCCATTCACACTTTCCCAAGACAATAT
EST: gi|254319860|gb|GR830884.1|GR830884
EST:     AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAAT                         TAACAATGCAGGGGTGATGGCGACTCCATTCACACTTTCCCAAGACAATAT
genomic: AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAATgtaagaactt ... tcctttgaagTAACAATGCAGGGGTGATGGCGACTCCATTCACACTTTCCCAAGACAATAT
EST: gi|21256750|gb|BQ453638.1|BQ453638
EST:     AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAAT                         TAACAATGCAGGGGTGATGGCGACTCCATTCACACTTTCCCAAGACAATAT
genomic: AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAATgtaagaactt ... tcctttgaagTAACAATGCAGGGGTGATGGCGACTCCATTCACACTTTCCCAAGACAATAT
EST: gi|19269548|gb|BM885804.1|BM885804
EST:     AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAAT                         TAACAATGCAGGGGTGATGGCGACTCCATTCACACTTTCCCAAGACAATAT
genomic: AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAATgtaagaactt ... tcctttgaagTAACAATGCAGGGGTGATGGCGACTCCATTCACACTTTCCCAAGACAATAT
EST: gi|18040854|gb|BM309148.1|BM309148
EST:     AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAAT                         TAACAATGCAGGGGTGATGGCGACTCCATTCACACTTTCCCAAGACAATAT
genomic: AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAATgtaagaactt ... tcctttgaagTAACAATGCAGGGGTGATGGCGACTCCATTCACACTTTCCCAAGACAATAT
EST: gi|192300987|gb|FG988902.1|FG988902
EST:     AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAAT                         TAACAATGCAGGGGTGATGGCGACTCCATTCACACTTTCCCAAGACAATAT
genomic: AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAATgtaagaactt ... tcctttgaagTAACAATGCAGGGGTGATGGCGACTCCATTCACACTTTCCCAAGACAATAT
EST: gi|7924361|gb|AW830387.1|AW830387
EST:     AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAAT                         TAACAATGCAGGGGTGATGGCGACTCCATTCACACTTTCCCAAGACAATAT
genomic: AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAATgtaagaactt ... tcctttgaagTAACAATGCAGGGGTGATGGCGACTCCATTCACACTTTCCCAAGACAATAT
EST: gi|6070718|gb|AW100105.1|AW100105
EST:     AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAAT                         TAACAATGCAGGGGTGATGGCGACTCCATTCACACTTTCCCAAGACAATAT
genomic: AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAATgtaagaactt ... tcctttgaagTAACAATGCAGGGGTGATGGCGACTCCATTCACACTTTCCCAAGACAATAT
EST: gi|7924863|gb|AW830889.1|AW830889
EST:     AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAAT                         TAACAATGCAGGGGTGAT
genomic: AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAATgtaagaactt ... tcctttgaagTAACAATGCAGGGGTGAT
EST: gi|16348712|gb|BI974307.1|BI974307
EST:     AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAAT                         TAACAATGCAGGGGTGATGGCGACTCCATTCACACTTTCCCAAGACAATAT
genomic: AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAATgtaagaactt ... tcctttgaagTAACAATGCAGGGGTGATGGCGACTCCATTCACACTTTCCCAAGACAATAT
EST: gi|16348170|gb|BI973765.1|BI973765
EST:     AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAAT                         TAACAATGCAGGGGTGATGGCGACTCCATTCACACTTTCCCAAGACAATAT
genomic: AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAATgtaagaactt ... tcctttgaagTAACAATGCAGGGGTGATGGCGACTCCATTCACACTTTCCCAAGACAATAT
EST: gi|7285547|gb|AW598034.1|AW598034
EST:     AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAAT                         TAACAATGCAGGGGTGATGGCGACTCCATTCACACTTTCCCAAGACAATAT
genomic: AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAATgtaagaactt ... tcctttgaagTAACAATGCAGGGGTGATGGCGACTCCATTCACACTTTCCCAAGACAATAT
EST: gi|27426481|gb|CA938001.1|CA938001
EST:     AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAAT                         TAACAATGCAGGGGTGATGGCGACTCCATTCACACTTTCCCAAGACAATAT
genomic: AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAATgtaagaactt ... tcctttgaagTAACAATGCAGGGGTGATGGCGACTCCATTCACACTTTCCCAAGACAATAT
EST: gi|10848080|gb|BF070633.1|BF070633
EST:     AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAAT                         TAACAATGCAGGGGTGATGGCGACTCCATTCACACTTTCCCAAGACAATAT
genomic: AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAATgtaagaactt ... tcctttgaagTAACAATGCAGGGGTGATGGCGACTCCATTCACACTTTCCCAAGACAATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccttttctttttttgaaagttgaaagaaataatactctttctttcctttgaagTAACAATGCAGGGGTGATGGCGACTCCATTCACACTTTCCCAAGACAATATTGAATTGCAGTTCGCAACCAATCATTTAG
                                  tactctttctttcctt  CT-rich tract
         tttttttgaaagttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtgttgattgcagattcctcatttgaagttgaaacaaataatattccttttctttttttgaaagttgaaagaaataatactctttctttcctttgaagTAACAATGCAGGGGTGATGGCGACTCCATTCACACTTTCCCAAGACAATATTGAATTGCAGTTCGCAACCAATCATTTAG

- - - tgattgc
- - - - - - - - - - - - - - - - -aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaagaaa