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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCACAGGAAATATTTGGCCACACCTTGGAGTCTCTTCGTGGAATTAAATATTTGTACAAgtaagtcaagctggatatttttccctcactctccccaaccctctgattgggtgaagatgtgaagtatagaacctaaacttttcgtttacttgcaaattgt...

Basic information

species Glycine max
transcript GLYMA03G07890.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G07890.1 (Glycine max), 5'ss of exon 12
lower sequence: LOC_Os06g03760.2 (Oryza sativa), 5'ss of exon 12
TCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCACAGGAAATATTTGGCCACACCTTGGAGTCTCTTCGTGGAATTAAATATTTGTACAAgtaagt------caagc-------tggatatttttccctcactctccccaaccctctgattgggtgaagatg-tgaagtatagaacctaaacttttcgtttacttgcaaattgt-----------------
||||  ||||||| ||||| || ||||| |||||||||||||| ||||| || |||||||||||  || | ||||| ||||||||||| ||| | |||||||| ||      || ||       | |  | ||| |  |   |  | | ||    |||  |   |  |  || || |   | || | | ||  ||| |   |  | |  ||| |                 
TCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAACTGCAGCTCAGGAGATCTTTGGCCACACACTGCAATCTCTCCGTGGAATTAAGTATCTCTACAAgtatgtatctagcatgcaaatccatagtcagtttacagttgtttgctcgaataagctggatatatccatgtggtggatattggagcatcaaacttttgaaaatgttctgattttaacatctgaatatgcag

upper sequence: GLYMA03G07890.1 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM2G012284_T01 (Zea mays), 5'ss of exon 10
TCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCACAGGAAATATTTGGCCACACCTTGGAGTCTCTTCGTGGAATTAAATATTTGTACAAgtaagtcaagctgg-atatttttccctcactctccccaaccctctgattgggtgaagat-gtgaagtatagaacctaaacttttcgtttacttgcaaattgt----
||||  |||| || ||||||||||| || |||||||||||||| || || |||||||||||||| ||| | || |||||||||||||| ||| | ||||||| ||||   |      |        | | |  | |       | | |   ||  | ||  | || | | ||   ||  ||  || |||||   ||||   |    
TCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGCAGCTCAAGAGATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgttagtctcccaaatgaagagcagatttagttgctctgttttacaggtgttgtagacattattaaatttcgactgtattctgatcctttacc-acaaaacatgcag

upper sequence: GLYMA03G07890.1 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM5G871262_T01 (Zea mays), 5'ss of exon 1
TCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCACAGGAAATATTTGGCCACACCTTGGAGTCTCTTCGTGGAATTAAATATTTGTACAAgtaagtca-agctggatattt--ttccctcactctccccaaccctctgattgggtgaagatgtgaagtatagaacctaaacttttcgtttacttgcaaattgt----
||||  |||| || |||||||| ||||| ||||||||||| || || || || ||||||||||| ||| | || |||||||||||||| ||| | ||||||| ||||  |  || | | |    |   |  || |    |    | |   ||  || | || | ||   | |||| ||   |  |  || |    ||||   |    
TCTGTGCCACGGCTTTTGCCTATTATGCACAAGCAACTGCTGCTCAAGAGATCTTTGGCCACACATTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgtgagtctcaaatgaagagtgaaattagttgctttgtttacaggtattgctg--tggatatttaaaactt-gaacgtactttgatacttgaaccacaaaacatgcag

upper sequence: GLYMA03G07890.1 (Glycine max), 5'ss of exon 12
lower sequence: AT5G01460.1 (Arabidopsis thaliana), 5'ss of exon 12
TCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCACAGGAAATATTTGGCCACACCTTGGAGTCTCTTCGTGGAATTAAATATTTGTACAAgtaagtcaagctggatatttttccctcactctccccaaccctctgattgggtgaagatgtgaagtatagaacctaaacttttcgtttacttgcaaattgt
||||| |||| |||||||  || ||||||||||| || || || ||||| |||||||||||||| ||| |||| ||||| || ||||| ||  | ||||||||||| |    || | |||     | |   || |        ||  |   | |   ||   |  ||    |||   ||| ||| |  ||| ||      
TCTGCGCCACTGCATTTGGATATTATGCTCAAGCCACCGCCGCTCAGGAGATATTTGGCCACACTTTGCAGTCCCTTCGCGGTATTAAGTACCTCTACAAgtaagtaatatcgggtttttgcaaataaaggtctca-----cttgtgtacataagactgatgataatcttcccttt-cttatcggtatctttcag-----

upper sequence: GLYMA03G07890.1 (Glycine max), 5'ss of exon 12
lower sequence: AT3G08930.1 (Arabidopsis thaliana), 5'ss of exon 12
TCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCACAGGAAATATTTGGCCACACCTTGGAGTCTCTTCGTGGAATTAAATATTTGTACAAgtaagtcaagctggatatttttccctcactctccccaaccctctgattgggtgaagatgtgaagtatagaacctaaacttttcgtttacttgcaaattgt
| ||  |||| |||||||  || || |||||||| ||||| || ||||| |||||||||||||| ||| |||| ||| | |||||||| ||  | |||||||||||  |  |||           | ||      ||  | | || |        |||| |   ||| ||   |  |  ||||                 
TTTGTGCCACTGCATTTGGATATTACGCTCAAGCCACTGCTGCCCAGGAGATATTTGGCCACACATTGCAGTCCCTTAGAGGAATTAAGTACCTTTACAAgtaagtagaagtgg---------tataacatatagcagtcatatgctatatccgtgatgcgtcttattgaggttttatatttcag---------------

upper sequence: GLYMA03G07890.1 (Glycine max), 5'ss of exon 12
lower sequence: Vv08s0007g02270.t01 (Vitis vinifera), 5'ss of exon 12
TCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCACAGGAAATATTTGGCCACACCTTGGAGTCTCTTCGTGGAATTAAATATTTGTACAAgtaagtcaagctggatatttttccctcactctccccaaccctctgattgggtgaa-gatgtgaagtatagaacctaaacttttcgtttacttgcaaattgt
||||| ||||||||||||  |||||||||||||||||||| |||||||||||||||||||||||  |||| |||||    |||||||||||||| |||||||  || |   | | |  | |   || |           |||||||||||    | | |    | |        ||  |   | ||| |  ||||      
TCTGCGCCACAGCATTTGGTTACTATGCTCAAGCAACTGCTGCACAGGAAATATTTGGCCACACACTGGAATCTCTCAAAGGAATTAAATATTTATACAAgtcggtaacaattgttcatgtctactgat--------gtcctctgattggagatatggtactgatttggttgtgtatgcccattgttgaactgcag-----

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|18730359|gb|BM525833.1|BM525833
EST:     ATATTTGGCCACACCTTGGAGTCTCTTCGTGGAATTAAATATTTGTACAA                         GTACAACGTCTTTCAGATTGCATTCGTTGCATTGGCTGGATTGACTTTTGT
genomic: ATATTTGGCCACACCTTGGAGTCTCTTCGTGGAATTAAATATTTGTACAAgtaagtcaag ... cacatcacagGTACAACGTCTTTCAGATTGCATTCGTTGCATTGGCTGGATTGACTTTTGT
EST: gi|58025422|gb|CX712163.1|CX712163
EST:     ATATTTGGCCACACCTTGGAGTCTCTTCGTGGAATTAAATATTTGTACAA                         GTACAACGTCTTTCAGATTGCATTCGTTGCATTGGCTGGATTGACTTTTGT
genomic: ATATTTGGCCACACCTTGGAGTCTCTTCGTGGAATTAAATATTTGTACAAgtaagtcaag ... cacatcacagGTACAACGTCTTTCAGATTGCATTCGTTGCATTGGCTGGATTGACTTTTGT
EST: gi|58015128|gb|CX701870.1|CX701870
EST:     ATATTTGGCCACACCTTGGAGTCTCTTCGTGGAATTAAATATTTGTACAA                         GTACAACGTCTTTCAGATTGCATTCGTTGCATTGGCTGGATTGACTTTTGT
genomic: ATATTTGGCCACACCTTGGAGTCTCTTCGTGGAATTAAATATTTGTACAAgtaagtcaag ... cacatcacagGTACAACGTCTTTCAGATTGCATTCGTTGCATTGGCTGGATTGACTTTTGT
EST: gi|192326624|gb|FK018496.1|FK018496
EST:     ATATTTGGCCACACCTTGGAGTCTCTTCGTGGAATTAAATATTTGTACAA                         GTACAACGTCTTTCAGATTGCATTCGTTGCATTGGCTGGATTGACTTTTGT
genomic: ATATTTGGCCACACCTTGGAGTCTCTTCGTGGAATTAAATATTTGTACAAgtaagtcaag ... cacatcacagGTACAACGTCTTTCAGATTGCATTCGTTGCATTGGCTGGATTGACTTTTGT
EST: gi|209705585|gb|BW673566.1|BW673566
EST:     ATATTTGGCCACACCTTGGAGTCTCTTCGTGGAATTAAATATTTGTACAA                         GTACAACGTCTTTCAGATTGCATTCGTTGCATTGGCTGGATTGACTTTTGT
genomic: ATATTTGGCCACACCTTGGAGTCTCTTCGTGGAATTAAATATTTGTACAAgtaagtcaag ... cacatcacagGTACAACGTCTTTCAGATTGCATTCGTTGCATTGGCTGGATTGACTTTTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCACAGGAAATATTTGGCCACACCTTGGAGTCTCTTCGTGGAATTAAATATTTGTACAAgtaagtcaagctggatatttttccctcactctccccaaccctctgattgggtgaagatgtgaagtatagaacctaaacttttcgtttacttgcaaattgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttccctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgggtg