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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttattgaattagcatggtaacaaaactaaattctagtttcagtagcactaattaaatgttcactcggatcatgaccgcaatgctatgattttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGGTATGTCACAGCTGTGGTGGAGGAAGGAGGAATCCAGGTGGACCAGGTGT

Basic information

species Glycine max
transcript GLYMA01G37360.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G37360.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0023g03040.t01 (Vitis vinifera), 3'ss of exon 2
gtttattgaattagcatggtaacaaaactaaattctagtttcagtagcactaattaaatgttcactcggatcatgaccgca-atgctatgattttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGGTATGTCACAGCTGTGGTGGAGGAAGGAGG---AATCCAGGTGGACCAGGTGT
        || ||  | | ||| || |   ||   || | ||        |  | ||||  |   |  |   |  || | | |||  ||   | ||  |||||||||||||| | | |||| ||||||||| || |||| | |||||||||||| || ||||| ||||||||||| |  |     | | ||||||| ||||   
------gtaagtattacg-taataagaacgaaga-taatctc--------tcttgaaattctttttgagcagagaactgaacatgggattgctgtgaacagTGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGGTACGTGACAGCAGTGGTGGAGGACGACGATGCGAACAAGGTGGATCAGG---
















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|298197845|gb|HO039384.1|HO039384
EST:     TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGAGATGAGG
genomic: TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
EST: gi|298184592|gb|HO029805.1|HO029805
EST:     TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
genomic: TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
EST: gi|298175182|gb|HO014985.1|HO014985
EST:     TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
genomic: TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
EST: gi|298197732|gb|HO045211.1|HO045211
EST:     TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
genomic: TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
EST: gi|193346384|gb|FK313362.1|FK313362
EST:     AAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
genomic: AAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
EST: gi|298163484|gb|HO012217.1|HO012217
EST:     TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
genomic: TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
EST: gi|193425422|gb|FK387855.1|FK387855
EST:     AAGAAAGGCCTATAAATCCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
genomic: AAGAAAGGCCTATAAAT-CCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
EST: gi|208050692|gb|GD848561.1|GD848561
EST:     TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGT
genomic: TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGT
EST: gi|298176803|gb|HO023276.1|HO023276
EST:     TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
genomic: TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
EST: gi|151396245|gb|EV266122.1|EV266122
EST:     TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
genomic: TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
EST: gi|209696524|gb|BW672839.1|BW672839
EST:     TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
genomic: TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
EST: gi|298181079|gb|HO022518.1|HO022518
EST:     TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
genomic: TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
EST: gi|151396015|gb|EV265892.1|EV265892
EST:     TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
genomic: TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
EST: gi|298169316|gb|HO020676.1|HO020676
EST:     TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
genomic: TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
EST: gi|298171711|gb|HO021303.1|HO021303
EST:     TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
genomic: TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
EST: gi|298179760|gb|HO024975.1|HO024975
EST:     TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
genomic: TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
EST: gi|193495895|gb|FK458125.1|FK458125
EST:     TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
genomic: TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
EST: gi|298190002|gb|HO032123.1|HO032123
EST:     TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
genomic: TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
EST: gi|298171512|gb|HO016544.1|HO016544
EST:     TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
genomic: TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
EST: gi|11688030|gb|BF595706.1|BF595706
EST:     TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGANG
genomic: TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
EST: gi|298170156|gb|HO018780.1|HO018780
EST:     TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
genomic: TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
EST: gi|151398990|gb|EV268861.1|EV268861
EST:     TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
genomic: TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
EST: gi|298183829|gb|HO029042.1|HO029042
EST:     TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
genomic: TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
EST: gi|208204779|gb|GE005680.1|GE005680
EST:     TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
genomic: TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
EST: gi|151393466|gb|EV263341.1|EV263341
EST:     TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
genomic: TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
EST: gi|298178113|gb|HO027496.1|HO027496
EST:     TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
genomic: TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
EST: gi|192325713|gb|FK015070.1|FK015070
EST:     TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
genomic: TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
EST: gi|298179747|gb|HO024962.1|HO024962
EST:     TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
genomic: TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
EST: gi|298170749|gb|HO015725.1|HO015725
EST:     TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAG                         TGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG
genomic: TGAATGAAGAAAGGCCTATAAATCCCAAGGACAACCATATCTCATTCCAGgtaactaggc ... ttttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcactaattaaatgttcactcggatcatgaccgcaatgctatgattttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGGTATGTCACAGCTGTGGTGGAGGAAGGAGGAATCCAGGTGGACCAGGTGT
  cactaat  putative branch site (score: 2)
     taattaaatgttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttattgaattagcatggtaacaaaactaaattctagtttcagtagcactaattaaatgttcactcggatcatgaccgcaatgctatgattttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGGTATGTCACAGCTGTGGTGGAGGAAGGAGGAATCCAGGTGGACCAGGTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - -gcatggt
- - - - - - - - - - aacaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caatgct