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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATCCGACGTCGTTGCAGTTATAATGGCTCCATTCAGCGGCGATGAGACGGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCTgtaattcaatccctaatttctcaattagatctatgctcgtattttcttgatctcttttgaatttcactttatcaggaaattttaatgttcgatgcgcaat...

Basic information

species Glycine max
transcript GLYMA12G04090.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G04090.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os11g06890.2 (Oryza sativa), 5'ss of exon 1
CAATCCGACGTCGTTGCAGTTATAATGGCTCCATTCAGCGGCGATGAGACGGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCTgtaattcaatccctaatttctcaattagatctatgctcgtattttcttg-atctcttttgaatttcactttatcaggaaattttaatgttcgatgcgcaat
  |   |     |  |||   ||   | |    |||||||||||||||||||| || || ||||||||||| || |||||  | |||||| ||||||| ||||||     || |   |  ||   |    |    |  |   ||   || |      |  | |||  |      | |      |  | |||  | | | | 
GGAGAAGGAAGAGGAGCAAAGATGTCGTCGGTGTTCAGCGGCGATGAGACGGCGCCCTTCTTCGGCTTCCTCGGCGCCGCCTCCGCCCTCATCTTCTCATgtaatctccgccatccctcttcctcttcccccgatcaagcgattaggtgtagaaagctccagtttttccaatcaaagtcgccatctttttctttccccca-

upper sequence: GLYMA12G04090.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os05g01560.1 (Oryza sativa), 5'ss of exon 1
CAATCCGACGTCGTTGCAGTTATAATGGC----TCCA--TTCAGCGGCGATGAGACGGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCTgtaattcaatccctaatttctcaattagatctatgctcgtattttcttgatctcttttgaatttcactttat-caggaaattttaatgttcgatgcgcaat
     ||||| ||  ||    |  ||| |    ||||  ||||||||||||||||| || || || ||||||||||| || |||||  | |||||||| |||||||||||       || ||| |  |  ||   | |   ||||      |  |||||  | |||  |    || |  || ||    |  | |             
-----CGACGGCGA-GCGACCACCATGTCCTCCTCCACCTTCAGCGGCGATGAGACCGCCCCTTTCTTCGGCTTCCTCGGCGCCGCCTCCGCCCTCGTATTCTCCTgtaa----gctcccaatcttccccttcacttt---ctcgggg---ccagatctgatctgagatgaggttgacacacgacgcatgcaag-------------

upper sequence: GLYMA12G04090.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G177005_T01 (Zea mays), 5'ss of exon 1
CAATCCGACGTCGTTG-CAGTTATAATGGCTCCATTCAGCGGCGATGAGACGGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCTgta-attcaatcccta--atttctcaattagatctatgctcgtattttcttgatctcttttgaatttcactttatcagga---aattttaatgttcgatgcgcaat
 ||   || | ||  | |    ||   | |    |||||||||||||||||||| || || ||||||||||| || ||||| || |||||||||||||| |||   |||     | |  ||    |  ||  |  |   | |  ||    ||     ||      | |   ||| || |||   | |||  || ||  |        
-AACAGGAAGCCGGAGGCGAAGATGTCGTCGGTGTTCAGCGGCGATGAGACGGCCCCCTTCTTCGGCTTCCTCGGCGCCGCCGCCGCCCTCGTCTTCTCATgttcgttccccttcgaccatcctccttttccacttgctcgctcatgcgattccgtactcaaagctctagttttttccggataaagtttggatttttcacc------

upper sequence: GLYMA12G04090.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM5G893252_T01 (Zea mays), 5'ss of exon 1
-CAATCCGACGTCGTTGCAGTTATAATGGCTCCATTCAGCGGCGATGAGACGGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCTgtaattcaatccctaatttctcaattagatctatgctcgtattttcttgatctcttttgaatttcactttatcaggaa-attttaatgttcgatgcgcaat
 ||   | || ||    || |        |  | ||||||||||| |||||||| || || ||||||||||| || ||||| || || |||||||||||||||||        |  || || |         | |     | |||       |   |   |   ||  ||  |||     ||      |   | |||  |  
CCACCTCCACCTCCACCCA-TGGCGGCCTCCACCTTCAGCGGCGACGAGACGGCGCCCTTCTTCGGCTTCCTCGGCGCCGCCGCCGCGCTCGTCTTCTCCTgtaagcacccatcagatctccctccctcccttctctgtctctttcaccagccggatccaaccatccattcctcactcccatcacctcggctggtgcctag-

upper sequence: GLYMA12G04090.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G101020_T01 (Zea mays), 5'ss of exon 1
CAATCCGACGTCGTTGCAGTTATAATGGCTCCATTCAGCGGCGATGAGACGGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCTgtaattcaatccctaatttctcaattagatctatgctcgtattttcttgatctcttttgaatttcactttatcaggaaattttaatgttcgatgcgcaat
     |  |      |  |  ||   | |  | ||||||||||||||||| || || || |||||||||||||| ||| | ||||| ||||||||||| ||||  |    | |    |  ||     |   ||| ||     || | |  | |||||   | ||    |    |  |  ||  |         |  |  |
AGCGGCAGCAGTAAGGGGGAGATGTCGTCGGCGTTCAGCGGCGATGAGACCGCCCCTTTCTTCGGCTTCCTTGGCGCCTCCGCTGCGCTCGTCTTCTCATgtacgtgcgccgcctcctcgtcctcacgtgttatactttcggttgcattgtttctttccgaatttgagtggggaaaaggttggagccgatcccgtccttt

upper sequence: GLYMA12G04090.1 (Glycine max), 5'ss of exon 1
lower sequence: AC216067.3_FGT002 (Zea mays), 5'ss of exon 1
CAATCCGACGTCGTTGCAGTTATAATGGCTCCATTCAGCGGCGATGAGACGGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCTgtaattc---aatcccta-atttctcaattagatctatgctcgtattttcttgatctct---tttgaatttcactttatcaggaaattttaatgttcgatgcgcaat
                     ||   | |    |||||||||||||||||||| || || ||||| ||||| || ||||| || |||||||||||||| |||   ||     |||| | | | |||    |     | |||||     |   |  | |     |  | |||   ||| ||  |||  |  |   |  | | |     
---------------------ATGTCGTCGGTGTTCAGCGGCGATGAGACGGCCCCCTTCTTCGGTTTCCTCGGCGCCGCCGCCGCCCTCGTCTTCTCATgttcgtcccgcttccccatactcctcttccactcgcacgctcgagcgattccgtacccgaagctctagtttttttttttcccgaa--tagagcttctgtttc-----

upper sequence: GLYMA12G04090.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv03s0038g00790.t01 (Vitis vinifera), 5'ss of exon 1
--CAATCCGACGTCGTTGCAGTTATAATGGCTCCATTCAGCGGCGATGAGACGGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCTgtaattcaatccctaatttctcaattagatctatgctcgtattttcttgatctcttttgaatttcactttatcaggaaattttaatgttcgatgcgcaat--
  |  | |     |  |  |  || |||| || |||||||||||||||| ||||||||||||||||| ||||| || ||||| ||||||||||||||||||||||  |||| |||||||| ||| ||| | |   |  ||    | |||  ||   |||  | ||| ||  |         |  | |    |     | ||   
GTCGTTTCAGATCCACT--ATCTAAAATGTCTACATTCAGCGGCGATGAAACGGCACCGTTTTTCGGATTCCTCGGCGCCGCTGCTGCCCTCGTCTTCTCCTgta-ctcaaaccctaatt-ctctattcgcttcgttttcacgctatctccattcttttccatttttacgctgcgtttggttcctgagaaaccgcatgaaaata

upper sequence: GLYMA12G04090.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S45_97V6.1 (Physcomitrella patens), 5'ss of exon 1
---CAATCCGACGTCGTTGCAGTTATAATGGCTCCATTCAGCGGCGATGAGACGGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCTgtaattcaatccctaatt--tctcaattagatctatgctcgtattttcttgatctcttttgaatttcactttatcaggaaattt--taatgt-tcgatgcgcaat
    || ||| || | |  |          |||   |||| ||| ||||||   || || || ||||||||| ||||||| |||||||| ||||||||||| ||||  |  |  |  | |   |||| |   |||||   |  | | |   | | |   | |||  | || ||| ||   |   |||  | |||  ||| ||  |   
ATCGAAGCCGGCGCCATGTCGACCT---CTGCTGTGTTCAACGGAGATGAGGTCGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCATgta--tggactctcactcactctcgacc-gatctggcccagaagtggttcgtttgttcttgggtgtcgcttcattttggggtttggtgatggatcgttggacc--

upper sequence: GLYMA12G04090.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S1_66V6.1 (Physcomitrella patens), 5'ss of exon 1
---CAATCCGACGTCGTTGCAGTTATAATGGCTCCATTCAGCGGCGATGAGACGGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCTgtaattcaatccctaatttctcaattagatctatgctcgtattttcttgatctcttttgaatttcactttatcagg-aaatttt---aatgttcgatgcgcaat---
   | ||||| || | |  |         ||     ||||  || ||||||   || || || ||||||||| | |||||||||||||||||||||||||| ||||   ||||  |      |   ||    | ||   |||  | |  ||| |      ||  ||||    ||| ||    |||||   || |   | | ||   |   
ATTCGATCCGGCGCCATGTCGACCTCGGCGG---TGTTCAATGGGGATGAGGTCGCTCCTTTCTTCGGCTTCATCGGAGCCGCAGCTGCCCTCGTCTTCTCATgta-cgcaatgtccg--cccctgatgtagtttagaatcgggtctatttggtg----atgggtttcgtggtattagatggatttttggaaggagtgctacgtccttga

upper sequence: GLYMA12G04090.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S45_100V6.1 (Physcomitrella patens), 5'ss of exon 1
CAATCCGAC-GTCGTTGCAGTTATAATGGCTCCATTCAGCGGCGATGAGACGGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCTgta---attcaatccctaatttctcaattagatctatgctcgtattttcttgatctcttttgaatttcactttatcaggaaattttaatgttcgatgcgcaat-
 || | |   | |         |     |||   |||| ||| ||||||   || || ||||| |||||| ||||||| |||||||||||||| ||||| ||||   |||  || | | | || |   |  |||         |||||  |     | || ||||   || ||      | | ||      |  |  | |   | 
-AACCTGCTAGACACCATGTCCACTGCTGCTGTGTTCAACGGGGATGAGGTCGCCCCCTTTTTTGGCTTCATTGGAGCTGCAGCTGCCCTCGTTTTCTCATgtatgcattggattcgttactt-tggttgcgattgggaggattatttgatgtgggtattgtgaa---catttggggtcggacttgagtcatgtggggagatgtg

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|13181084|gb|BG352424.1|BG352424
EST:     -GCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCT                         GTATGGGAGCTGCCTATGGCACAGCGAAGAGTGGCGTGGGCGTGGCTTCGA
genomic: GGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCTgtaattcaat ... atggaggaagGTATGGGAGCTGCCTATGGCACAGCGAAGAGTGGCGTGGGCGTGGCTTCGA
EST: gi|213607640|gb|DB958659.1|DB958659
EST:     GGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCT                         GTATGGGAGCTGCCTATGGCACAGCGAAGAGTGGCGTGGGCGTGGCTTCGA
genomic: GGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCTgtaattcaat ... atggaggaagGTATGGGAGCTGCCTATGGCACAGCGAAGAGTGGCGTGGGCGTGGCTTCGA
EST: gi|213593065|gb|DB966058.1|DB966058
EST:     GGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCT                         GTATGGGAGCTGCCTATGGCACAGCGAAGAGTGGCGTGGGCGTGGCTTCGA
genomic: GGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCTgtaattcaat ... atggaggaagGTATGGGAGCTGCCTATGGCACAGCGAAGAGTGGCGTGGGCGTGGCTTCGA
EST: gi|209710992|gb|BW681342.1|BW681342
EST:     GGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCT                         GTATGGGAGCTGCCTATGGCACAGCGAAGAGTGGCGTGGGCGTGGCTTCGA
genomic: GGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCTgtaattcaat ... atggaggaagGTATGGGAGCTGCCTATGGCACAGCGAAGAGTGGCGTGGGCGTGGCTTCGA
EST: gi|298188080|gb|HO032037.1|HO032037
EST:     GGCACCGTTTTTCGGCTTCCTTGGAGCCACAGCTGCCCTCGTCTTCTCCT                         GTATGGGAGCTGCTTATGGCACAGCGAAGAGTGGCGTGGGCGTGGCTTCGA
genomic: GGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCTgtaattcaat ... atggaggaagGTATGGGAGCTGCCTATGGCACAGCGAAGAGTGGCGTGGGCGTGGCTTCGA
EST: gi|192330761|gb|FK022346.1|FK022346
EST:     GGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCT                         GTATGGGAGCTGCCTATGGCACAGCGAAGAGTGGCATGGGCGTGGCTTCGA
genomic: GGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCTgtaattcaat ... atggaggaagGTATGGGAGCTGCCTATGGCACAGCGAAGAGTGGCGTGGGCGTGGCTTCGA
EST: gi|213595089|gb|DB972023.1|DB972023
EST:     GGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCT                         GTATGGGAGCTGCCTATGGCACAGCGAAGAGTGGCGTGGGCGTGGCTTCGA
genomic: GGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCTgtaattcaat ... atggaggaagGTATGGGAGCTGCCTATGGCACAGCGAAGAGTGGCGTGGGCGTGGCTTCGA
EST: gi|23726185|gb|BU761076.1|BU761076
EST:     GGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCT                         GTATGGGAGCTGCCTATGGCACAGCGAAGAGTGGCGTGGGCGTGGCTTCGA
genomic: GGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCTgtaattcaat ... atggaggaagGTATGGGAGCTGCCTATGGCACAGCGAAGAGTGGCGTGGGCGTGGCTTCGA
EST: gi|208242482|gb|GE037882.1|GE037882
EST:     GGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCT                         GTATGGGAGCTGCCTATGGCACAGCGAAGAGTGGCGTTGGCGTGGCTTCGA
genomic: GGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCTgtaattcaat ... atggaggaagGTATGGGAGCTGCCTATGGCACAGCGAAGAGTGGCGTGGGCGTGGCTTCGA
EST: gi|209704615|gb|BW656634.1|BW656634
EST:     GGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCT                         GTATGGGAGCTGCCTATGGCACAGCGAAGAGTGGCGTGGGCGTGGCTTCGA
genomic: GGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCTgtaattcaat ... atggaggaagGTATGGGAGCTGCCTATGGCACAGCGAAGAGTGGCGTGGGCGTGGCTTCGA
EST: gi|213593648|gb|DB971670.1|DB971670
EST:     GGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCT                         GTATGGGAGCTGCCTATGGCACAGCGAAGAGTGGCGTGGGCGTGGCTTCGA
genomic: GGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCTgtaattcaat ... atggaggaagGTATGGGAGCTGCCTATGGCACAGCGAAGAGTGGCGTGGGCGTGGCTTCGA
EST: gi|6482619|gb|AW201864.1|AW201864
EST:     GGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCT                         GTATGGGAGCTGCCTATGGCACAGCGAAGAGTGGCGTGGGCGTGGCTTCGA
genomic: GGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCTgtaattcaat ... atggaggaagGTATGGGAGCTGCCTATGGCACAGCGAAGAGTGGCGTGGGCGTGGCTTCGA
EST: gi|151403459|gb|EV273269.1|EV273269
EST:     GGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCT                         GTATGGGAGCTGCCTATGGCACAGCGAAGAGTGGCGTGGGCGTGGCTTCGA
genomic: GGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCTgtaattcaat ... atggaggaagGTATGGGAGCTGCCTATGGCACAGCGAAGAGTGGCGTGGGCGTGGCTTCGA
EST: gi|18040823|gb|BM309117.1|BM309117
EST:     GGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCT                         GTATGGGAGCTGCCTATGGCACAGCGAAGAGTGGCGTGGGCGTGGCTTCGA
genomic: GGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCTgtaattcaat ... atggaggaagGTATGGGAGCTGCCTATGGCACAGCGAAGAGTGGCGTGGGCGTGGCTTCGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAATCCGACGTCGTTGCAGTTATAATGGCTCCATTCAGCGGCGATGAGACGGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCTgtaattcaatccctaatttctcaattagatctatgctcgtattttcttgatctcttttgaatttcactttatcaggaaattttaatgttcgatgcgcaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC