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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGTTGAGCTTGAGCTGAGAAAGCTAGAGGGAGCAGTAAGAGGCCATCCATGAGAATTTGCTCTATCTTAAGGGCAGgtaattccaatcacatcaatatctccccctataaatagtttatttcaatttttttttaaaaaaacttttcatatgtttaatttttggtttttgggtttcag

Basic information

species Glycine max
transcript GLYMA08G13470.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G13470.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv12s0034g01440.t01 (Vitis vinifera), 5'ss of exon 3
GGAGTTGAGCTTGAGCTGAGAAAGCTAGAGGGAGCAGTAAGAGGCCATCCATGAGAATTTGCTCTATCTTAAGGGCAGgtaattccaatcacatcaat---atctccccctataaatagtttatttcaatttttttttaaaaaaacttttcatatgtttaatttttggtttttgggtttcag------
|| |||||||||||| ||||||| || || ||||||||  |||||||||||||||||| | |||||||| ||| || |||||||   ||    | | |   | |  |  |||    |  |  ||| | | |   ||  |  | | |  ||   || |||      |  |||| |  ||| |       
GGTGTTGAGCTTGAGTTGAGAAAACTTGAAGGAGCAGTG-GAGGCCATCCATGAGAATCTACTCTATCTCAAGAGCCGgtaatttttatggttttagttggaacagcatctaatgtttttgcattgctaatcaattagatcataccagttaccatttttctcccatttttttggacttttactcacag
















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|151394340|gb|EV264211.1|EV264211
EST:     AGGGAGCAGTA-GAGGCCATCCATGAGAATTTGCTCTATCTTAAGGGCAG                         GGAAGCTGAGATGAGGATTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
genomic: AGGGAGCAGTAAGAGGCCATCCATGAGAATTTGCTCTATCTTAAGGGCAGgtaattccaa ... tgggtttcagGGAAGCTGAGATGAGGATTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
EST: gi|208099775|gb|GD900326.1|GD900326
EST:     AGAGGCCATCCATGAGAATTTGCTCTATCTTAAGGGCAG                         GGAAGCTGAGATGAGGATTGTGAGTG-AAAAACAAATGGCAGAGTGGCATG
genomic: AGAGGCCATCCATGAGAATTTGCTCTATCTTAAGGGCAGgtaattccaa ... tgggtttcagGGAAGCTGAGATGAGGATTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
EST: gi|207683875|gb|GD666634.1|GD666634
EST:     AGAGGCCATCCATGAGAATTTGCTCTATCTTAAGGGCAG                         GGAAGCTGAGATGAGGATTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
genomic: AGAGGCCATCCATGAGAATTTGCTCTATCTTAAGGGCAGgtaattccaa ... tgggtttcagGGAAGCTGAGATGAGGATTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
EST: gi|193688522|gb|FK634457.1|FK634457
EST:     AGGGAGCAGT-AGAGGCCATCCATGAGAATTTGCTCTATCTTAAGGGCAG                         GGAAGCTGAGATGAGGATTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
genomic: AGGGAGCAGTAAGAGGCCATCCATGAGAATTTGCTCTATCTTAAGGGCAGgtaattccaa ... tgggtttcagGGAAGCTGAGATGAGGATTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
EST: gi|151394089|gb|EV263960.1|EV263960
EST:     AGGGAGCAGTA-GAGGCCATCCATGAGAATTTGCTCTATCTTAAGGGCAG                         GGAAGCTGAGATGAGGATTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
genomic: AGGGAGCAGTAAGAGGCCATCCATGAGAATTTGCTCTATCTTAAGGGCAGgtaattccaa ... tgggtttcagGGAAGCTGAGATGAGGATTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
EST: gi|193628652|gb|FK574548.1|FK574548
EST:     CATCCATGAGAATTTGCTCTATCTTAGGGGCAG                         GGAAGCTGAGATGAGGATTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
genomic: CATCCATGAGAATTTGCTCTATCTTAAGGGCAGgtaattccaa ... tgggtttcagGGAAGCTGAGATGAGGATTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
EST: gi|209708754|gb|BW683778.1|BW683778
EST:     AGGGAGCAGTA-GAGGCCATCCATGAGAATTTGCTCTATCTTAAGGGCAG                         GGAAGCTGAGATGAGGATTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
genomic: AGGGAGCAGTAAGAGGCCATCCATGAGAATTTGCTCTATCTTAAGGGCAGgtaattccaa ... tgggtttcagGGAAGCTGAGATGAGGATTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
EST: gi|193686122|gb|FK625473.1|FK625473
EST:     AGGGAGCAGT-AGAGGCCATCCATGAGAATTTGCTCTATCTTAAGGGCAG                         GGAAGCTGAGATGAGGATTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
genomic: AGGGAGCAGTAAGAGGCCATCCATGAGAATTTGCTCTATCTTAAGGGCAGgtaattccaa ... tgggtttcagGGAAGCTGAGATGAGGATTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
EST: gi|208050941|gb|GD848964.1|GD848964
EST:     ATGAGAATTTGCTCTATCTTAAGGGCAG                         GGAAGCTGAGATGAGGATTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
genomic: ATGAGAATTTGCTCTATCTTAAGGGCAGgtaattccaa ... tgggtttcagGGAAGCTGAGATGAGGATTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
EST: gi|207689114|gb|GD673467.1|GD673467
EST:     AGGGAGCAGT-AGAGGCCATCCATGAGAATTTGCTCTATCTTAAGGGCAG                         GGAAGCTGAGATGAGGATTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
genomic: AGGGAGCAGTAAGAGGCCATCCATGAGAATTTGCTCTATCTTAAGGGCAGgtaattccaa ... tgggtttcagGGAAGCTGAGATGAGGATTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
EST: gi|298170194|gb|HO018818.1|HO018818
EST:     AGGGAGCAGTA-GAGGCCATCCATGAGAATTTGCTCTATCTTAAGGGCAG                         GGAAGCTGAGATGAGGATTGTGAGTGA
genomic: AGGGAGCAGTAAGAGGCCATCCATGAGAATTTGCTCTATCTTAAGGGCAGgtaattccaa ... tgggtttcagGGAAGCTGAGATGAGGATTGTGAGTGA
EST: gi|208328123|gb|GE124661.1|GE124661
EST:     AGGGAGCAGT-AGAGGCCATCCATGAGAATTTGCTCTATCTTAAGGGCAG                         GGAAGCTGAGATGAGGATTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
genomic: AGGGAGCAGTAAGAGGCCATCCATGAGAATTTGCTCTATCTTAAGGGCAGgtaattccaa ... tgggtttcagGGAAGCTGAGATGAGGATTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
EST: gi|209708781|gb|BW683779.1|BW683779
EST:     AGGGAGCAGT-AGAGGCCATCCATGAGAATTTGCTCTATCTTAAGGGCAG                         GGAAGCTGAGATGAGGATTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
genomic: AGGGAGCAGTAAGAGGCCATCCATGAGAATTTGCTCTATCTTAAGGGCAGgtaattccaa ... tgggtttcagGGAAGCTGAGATGAGGATTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
EST: gi|208251434|gb|GE050585.1|GE050585
EST:     AGGGAGCAGT-AGAGGCCATCCATGAGAATTTGCTCTATCTTAAGGGCAG                         GGAAGCTGAGATGAGGATTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
genomic: AGGGAGCAGTAAGAGGCCATCCATGAGAATTTGCTCTATCTTAAGGGCAGgtaattccaa ... tgggtttcagGGAAGCTGAGATGAGGATTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
EST: gi|298164598|gb|HO014243.1|HO014243
EST:     AGGGAGCAGTA-GAGGCCATCCATGAGAATTTGCTCTATCTTAAGGGCAG                         GGAAGCTGAGATGAGGATTGTGAG
genomic: AGGGAGCAGTAAGAGGCCATCCATGAGAATTTGCTCTATCTTAAGGGCAGgtaattccaa ... tgggtttcagGGAAGCTGAGATGAGGATTGTGAG
EST: gi|31474639|gb|CD416667.1|CD416667
EST:     AGGGAGCAGTA-GAGGCCATCCATGAGAATTTGCTCTATCTTAAGGGCAG                         GGAAGCTGAGATGAGGATTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
genomic: AGGGAGCAGTAAGAGGCCATCCATGAGAATTTGCTCTATCTTAAGGGCAGgtaattccaa ... tgggtttcagGGAAGCTGAGATGAGGATTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
EST: gi|192306630|gb|FG998056.1|FG998056
EST:     AGGGAGCAGT-AGAGGCCATCCATGAGAATTTGCTCTATCTTAAGGGCAG                         GGAAGCTGAGATGAGGATTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
genomic: AGGGAGCAGTAAGAGGCCATCCATGAGAATTTGCTCTATCTTAAGGGCAGgtaattccaa ... tgggtttcagGGAAGCTGAGATGAGGATTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
EST: gi|207847367|gb|GD820408.1|GD820408
EST:     AGAGGCCATCCTATGAGTAATTTGCTCTATCTTAAGGGCAG                         GGAAGCTGAGATGAGGATTGTGAGTG-AAAAAC-AATGGCAGAGTGGCATG
genomic: AGAGGCCATCC-ATGAG-AATTTGCTCTATCTTAAGGGCAGgtaattccaa ... tgggtttcagGGAAGCTGAGATGAGGATTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
EST: gi|208059371|gb|GD856939.1|GD856939
EST:     AGAGGCCATCCATGAGAATTTGCTCTATCTTAAGGGCAG                         GGAAGCTGAGATGAGGATTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
genomic: AGAGGCCATCCATGAGAATTTGCTCTATCTTAAGGGCAGgtaattccaa ... tgggtttcagGGAAGCTGAGATGAGGATTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
EST: gi|208328580|gb|GE132160.1|GE132160
EST:     TATCTTAAGGGCAG                         GGAAGCTGGGATGAGGATTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
genomic: TATCTTAAGGGCAGgtaattccaa ... tgggtttcagGGAAGCTGAGATGAGGATTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGTTGAGCTTGAGCTGAGAAAGCTAGAGGGAGCAGTAAGAGGCCATCCATGAGAATTTGCTCTATCTTAAGGGCAGgtaattccaatcacatcaatatctccccctataaatagtttatttcaatttttttttaaaaaaacttttcatatgtttaatttttggtttttgggtttcag

- - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - AAGAGG