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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATCGCGTTCAGAACCAAATCAGAGCTTGAGATCATGGATGATGGATACAAGTGGAGGAAGTACGGCAAGAAGTCTGTGAAGAGCAATCCCAATCTAAGgtaaaaaaaaaatattactaatagtattaatgaagtaagatattatttattgacgtacttttttgcactttgaaccttcttattttaaaataactgttat...

Basic information

species Glycine max
transcript GLYMA05G31800.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G31800.2 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os05g09020.2 (Oryza sativa), 5'ss of exon 2
GGATCGCGTTCAGAACCAAATCAGAGCTTGAGATCATGGATGATGGATACAAGTGGAGGAAGTACGGCAAGAAGTCTGTGAAGAGCAATCCCAATCTAAGgtaaaaaaaaaatattactaatagtatta-atgaagtaagatattatttattgacgtacttttttgcactttgaaccttcttattttaaaataactgttat
|||||| |||||| || |  || ||| | |||||  | |||||||| | ||||||||||||||||||||||||  |||| |||| ||  || |||| |||||| |  || | |      | |   | ||     | |  | ||| | |  |          |    ||  || || |  ||   || |  |     ||| |
GGATCGGGTTCAGGACGAGGTCGGAGGTGGAGATTCTTGATGATGGCTTCAAGTGGAGGAAGTACGGCAAGAAAGCTGTCAAGAACAGCCCAAATCCAAGgtacacgaatattgacgtcactgccactatgcccatttggctatcaatcttaattaattagtaccacaagtttaatca-ctagcttaattactggcgttct

upper sequence: GLYMA05G31800.2 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G163054_T02 (Zea mays), 5'ss of exon 2
GGATCGCGTTCAGAACCAAATCAGAGCTTGAGATCATGGATGATGGATACAAGTGGAGGAAGTACGGCAAGAAGTCTGTGAAGAGCAATCCCAATCTAAGgtaaaaaaaaaatattactaatagtattaatgaagtaagatattatt-tattgacgtacttttttgcactttgaaccttcttattttaaaat-aactgttat-----------------------------------------------------------
|||||| ||||||||| | ||||||| | |||||| |||| ||||||| ||| ||||||||||| ||||||||| |||| ||||| |  || |||| |||||| |   | |   | ||    | |||   | || |||  |   |    ||  | | |       | |     |        |  |  |||  || ||  ||                                                           
GGATCGGGTTCAGAACGAGATCAGAGGTGGAGATCTTGGACGATGGATTCAAATGGAGGAAGTATGGCAAGAAGGCTGTCAAGAGTAGCCCAAATCCAAGgtacacccatatgttcacctggaatatagttaaaataaattcccagaacatgaaagcaacaagcagaaaagcaacgaagaagaaatagaaacgaaatggaatgtttactggatcgatgctgatggatatataattgtgcatgcacacgtacgtacgtgcag

upper sequence: GLYMA05G31800.2 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM5G863420_T01 (Zea mays), 5'ss of exon 2
GGATCGCGTTCAGAACCAAATCAGAGCTTGAGATCATGGATGATGGATACAAGTGGAGGAAGTACGGCAAGAAGTCTGTGAAGAGCAATCCCAATCTAAGgtaaaaaaaaa---atattac-taat------------agtattaatgaagtaaga-tattatttattgacgtactt-----ttttgcactttgaaccttcttattttaaaataactgttat-------------------------------
||||||||||| | || |  || ||| | |||||| |||| || || ||||||||||||||||||||||||||||| || |||| ||  ||||| | |||||||  |  ||    || ||| | ||            |||| ||   |  || || ||  | |  | | || | ||     | |||||      | |    | | | ||    | ||| |                                
GGATCGCGTTCCGGACGAGGTCGGAGATCGAGATCCTGGACGACGGCTACAAGTGGAGGAAGTACGGCAAGAAGTCCGTCAAGAACAGCCCCAACCCAAGgtaactagtaatctgtagtacatgatcacaattactccagtactagctagctaggagtagcactagtaggcgcatttcgcgatattgcagcagctagccatctctctcaatcacagtgtcacacatgacatgcgtggtggtgcgcgcccgcag

upper sequence: GLYMA05G31800.2 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G057116_T01 (Zea mays), 5'ss of exon 2
GGATCGCGTTCAGAACCAAATCAGAGCTTGAGATCATGGATGATGGATACAAGTGGAGGAAGTACGGCAAGAAGTCTGTGAAGAGCAATCCCAATCTAAGgtaaaaaaaaaatattactaatagtattaatgaagtaagatattatttattgacgtacttttttgcactttgaaccttcttattttaaaataactgttat---------------------------------------------------------------------------------
|||||| ||||||||| |  |||||| | |||||| |||| || |||| |||||||||||||||||| |||||| | || |||| ||  || |||| ||||||  |  | | ||  || ||||  |      || ||| | |  |  ||  |    | |         |   | ||     |     ||| |  ||   |                                                                                 
GGATCGGGTTCAGAACGAGGTCAGAGGTGGAGATCTTGGACGACGGATTCAAGTGGAGGAAGTACGGGAAGAAGGCCGTCAAGAACAGCCCAAATCCAAGgtactactatactac-acaaata-cacatgcaaattaatagagcagcta--gctaaattcccccaacatgaaagccaagacaagagcaaagagatgaattaatcctcgcaaaacgaaacaaaaataaaaaaagaaatgtttacttcgtcgatgctgatggcttgtgcacatgcccatgtag

upper sequence: GLYMA05G31800.2 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G137802_T01 (Zea mays), 5'ss of exon 2
GGATCGCGTTCAGAACCAAATCAGAGCTTGAGATCATGGATGATGGATACAAGTGGAGGAAGTACGGCAAGAAGTCTGTGAAGAGCAATCCCAATCTAAGgtaaaaaaaaaatattactaatagtattaatgaagtaagatattatttattgacgtacttttttgcactttgaaccttcttattttaaaataactgttat-----
||||||||||| | || |  || ||| | ||| || |||| || || ||||||||||||||||||||||||||||| || |||| ||  ||||| | ||||||              ||||  ||         ||  |     |||||       ||     || |||   | |   || | || |  | ||||||| |     
GGATCGCGTTCCGGACGAGGTCGGAGGTCGAGGTCCTGGACGACGGCTACAAGTGGAGGAAGTACGGCAAGAAGTCCGTCAAGAACAGCCCCAACCCAAGgtag-------------ctaactgt---------gtgcgtcccaatttacaacaccacacgactggactgctagcgcactcacttcacgacaactgttctgtcag

upper sequence: GLYMA05G31800.2 (Glycine max), 5'ss of exon 2
lower sequence: Vv07s0031g01710.t01 (Vitis vinifera), 5'ss of exon 2
GGATCGCGTTCAGAACCAAATCAGAGCTTGAGATCATGGATGATGGATACAAGTGGAGGAAGTACGGCAAGAAGTCTGTGAAGAGCAATCCCAATCTAAGgtaaaaaaaaaatattactaatagtattaatgaagtaagatattatttattgacgtacttttttgcactttgaaccttcttattttaaaataactgttat-
|| | || ||||  || ||||| ||  | ||||||||||||||||| |  |||||||||||||| || ||||| || ||||||| ||  ||||||| |||||||||  |  ||  |||  ||  ||||||   | |    |    ||||      |     |||  ||     |     ||| || ||    |   | |  
GGGTTGCCTTCAAGACGAAATCGGATTTGGAGATCATGGATGATGGGTTTAAGTGGAGGAAGTATGGGAAGAAATCAGTGAAGAACAGCCCCAATCCAAGgtaaaatgatcatcatacatatcatattaagtcatttttttccattttaaaattattaccgtttaaacccacgatgga-ttaattaaattggatcatgagt

upper sequence: GLYMA05G31800.2 (Glycine max), 5'ss of exon 2
lower sequence: PP1S235_126V6.1 (Physcomitrella patens), 5'ss of exon 2
GGATCGCGTTCAGAACCAAATCAGAGCTTGAGATCATGGATGATGGATACAAGTGGAGGAAGTACGGCAAGAAGTCTGTGAAGAGCAATCCCAATCTAAGgtaaaaaaaaaatattactaatagtattaatgaa---gtaagatattatttattgac-gtacttttttgcactttgaaccttcttattttaaaataactgttat
|   |||| | | |||||   | ||   |||  | ||||||||||| ||||||||||||||||| ||  ||||| |||| || |  |  ||  | |  |||||   ||    | ||    | | | | |   ||   |  || | ||  || | |   ||   |  |||| ||   |||   ||    | |||  |     |  
GCTACGCGATTAAAACCAGGACTGATACTGATGTAATGGATGATGGTTACAAGTGGAGGAAGTATGGACAGAAGGCTGTCAAAAAAAGCCCTCACCCCAGgtactgaact--ttttcaagaaaatctcaggaaacgtggtaggtttttcttgtcgttagtgtctccttgcgctac-aactgcctgcagtcaaatcaggaactc-

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|120494077|gb|EH222244.1|EH222244
EST:     AAGTGGAGGAAGTACGGCAAGAAGTCTGTGAAGAGCAATCCCAATCTAAG                         GAACTACTACAAATGTTCAAGTGGAGGATGCAGTGTGAAGAAAAGGGTGGA
genomic: AAGTGGAGGAAGTACGGCAAGAAGTCTGTGAAGAGCAATCCCAATCTAAGgtaaaaaaaa ... atgatgacagGAACTACTACAAATGTTCAAGTGGAGGATGCAGTGTGAAGAAAAGGGTGGA
EST: gi|151407252|gb|EV277067.1|EV277067
EST:     AAGTGGAGGAAGTACGGCAAGAAGTCTGTGAAGAGCAATCCCAATCTAAG                         GAACTACTACAAATGTTCAAGTGGAGGATGCAGTGTGAAGAAAAGGGTGGA
genomic: AAGTGGAGGAAGTACGGCAAGAAGTCTGTGAAGAGCAATCCCAATCTAAGgtaaaaaaaa ... atgatgacagGAACTACTACAAATGTTCAAGTGGAGGATGCAGTGTGAAGAAAAGGGTGGA
EST: gi|151402817|gb|EV272630.1|EV272630
EST:     AAGTGGAGGAAGTACGGCAAGAAGTCTGTGAAGAGCAATCCCAATCTAAG                         GAACTACTACAAATGTTCAAGTGGAGGATGCAGTGTGAAGAAAAGGGTGGA
genomic: AAGTGGAGGAAGTACGGCAAGAAGTCTGTGAAGAGCAATCCCAATCTAAGgtaaaaaaaa ... atgatgacagGAACTACTACAAATGTTCAAGTGGAGGATGCAGTGTGAAGAAAAGGGTGGA
EST: gi|192321467|gb|FK012859.1|FK012859
EST:     AAGTGGAGGAAGTACGGCAAGAAGTCTGTGAAGAGCAATCCCAATCTAAG                         GAACTACTACAAATGTTCAAGTGGAGGATGCAGTGTGAAGAAAAGGGTGGA
genomic: AAGTGGAGGAAGTACGGCAAGAAGTCTGTGAAGAGCAATCCCAATCTAAGgtaaaaaaaa ... atgatgacagGAACTACTACAAATGTTCAAGTGGAGGATGCAGTGTGAAGAAAAGGGTGGA
EST: gi|151398026|gb|EV267904.1|EV267904
EST:     AAGTGGAGGAAGTACGGCAAGAAGTCTGTGAAGAGCAATCCCAATCTAAG                         GAACTACTACAAATGTCCAAGTGGAGGATGCAGTGTGAAGAAAAGGGTGGA
genomic: AAGTGGAGGAAGTACGGCAAGAAGTCTGTGAAGAGCAATCCCAATCTAAGgtaaaaaaaa ... atgatgacagGAACTACTACAAATGTTCAAGTGGAGGATGCAGTGTGAAGAAAAGGGTGGA
EST: gi|120494237|gb|EH222404.1|EH222404
EST:     AAGTGGAGGAATTACGGCAAGAAGTCTGTGAAGAGCAATCCCAATTTAAG                         GAACTACTACAAATGTTCAAGTGGAGGATGCAGTGTGAAGAAAAGGGTGGA
genomic: AAGTGGAGGAAGTACGGCAAGAAGTCTGTGAAGAGCAATCCCAATCTAAGgtaaaaaaaa ... atgatgacagGAACTACTACAAATGTTCAAGTGGAGGATGCAGTGTGAAGAAAAGGGTGGA
EST: gi|192321468|gb|FK012860.1|FK012860
EST:     AAGTGGAGGAAGTACGGCAAGAAGTCTGTGAAGAGCAATCCCAATCTAAG                         GAACTACTACAAATGTTCAAGTGGAGGATGCAGTGTGAAGAAAAGGGTGGA
genomic: AAGTGGAGGAAGTACGGCAAGAAGTCTGTGAAGAGCAATCCCAATCTAAGgtaaaaaaaa ... atgatgacagGAACTACTACAAATGTTCAAGTGGAGGATGCAGTGTGAAGAAAAGGGTGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATCGCGTTCAGAACCAAATCAGAGCTTGAGATCATGGATGATGGATACAAGTGGAGGAAGTACGGCAAGAAGTCTGTGAAGAGCAATCCCAATCTAAGgtaaaaaaaaaatattactaatagtattaatgaagtaagatattatttattgacgtacttttttgcactttgaaccttcttattttaaaataactgttat

- - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaat