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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAGCCATCCAATGAGAAGTCAGATGTTTACAGCTTTGGTGTCATCTTGTGGGAGATCGCAACATTGCAACAGCCTTGGAGTAATTTGAATCCACCACAGgtttgttgtataactttgatatatttcagtgtgcttatgcttagattttccaatacgattatattgctttgatttttatgaaagattctttaagatctga...

Basic information

species Glycine max
transcript GLYMA19G37570.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G37570.2 (Glycine max), 5'ss of exon 14
lower sequence: LOC_Os02g32610.2 (Oryza sativa), 5'ss of exon 14
CGAGCCATCCAATGAGAAGTCAGATGTTTACAGCTTTGGTGTCATCTTGTGGGAGATCGCAACATTGCAACAGCCTTGGAGTAATTTGAATCCACCACAGgtttgttgtataactttgatatatttcagtgtgcttatgcttagattttccaatacgattatattgctttgatttttatgaaagattctttaagatctga--
 |||||||| ||||||||||| ||||| |||||||||||||| ||| | |||||| ||   ||||||||||| || ||||||| |||||||||| | |||||||||     | ||    | |  ||||      | |  |  | |||||||||     ||     |   ||| ||  |  ||   | | |    |  ||   
TGAGCCATCAAATGAGAAGTCTGATGTCTACAGCTTTGGTGTTATCCTATGGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAGgtttgt-----atctcctgttttcttca------tcacacggatattttccaac----ttcggacgaactgaattgaacaaagtctacctgttcacttgcag

upper sequence: GLYMA19G37570.2 (Glycine max), 5'ss of exon 14
lower sequence: GRMZM2G059671_T02 (Zea mays), 5'ss of exon 8
CGAGCCATCCAATGAGAAGTCAGATGTTTACAGCTTTGGTGTCATCTTGTGGGAGATCGCAACATTGCAACAGCCTTGGAGTAATTTGAATCCACCACAGgtttgttgtataactttgatatatttcagtgtg------------cttatgcttagattttcc-----aatacgattat--attgctttgatttttatgaaagattctttaagatctga-------
|||||| || ||||||||||| |||||||||||||| ||||| ||||| |||||| |    |||||||| ||||| ||||||||||| |||||| | ||||||||      |   || ||  ||  |||| |               ||   |||||| | ||      | |  ||  |  | | || |  ||||| | ||| | |   ||  || | |       
CGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatctcatgctttatgcatcacagtatcacattgacgttttctagctttagatataccccatggagaaaatccttaagttctctcttttttgttaaaaaatacgtacaattttacttgcag

upper sequence: GLYMA19G37570.2 (Glycine max), 5'ss of exon 14
lower sequence: AT5G03730.1 (Arabidopsis thaliana), 5'ss of exon 13
CGAGCCATCCAATGAGAAGTCAGATGTTTACAGCTTTGGTGTCATCTTGTGGGAGATCGCAACATTGCAACAGCCTTGGAGTAATTTGAATCCACCACAGgtttgttgtataactttgatatatttcagtgtgcttatgcttagattttccaatacgat-tatattgctttgatttttatgaaagattctttaagatctga------------------
 ||||| || ||||| ||||||||||| |||||||| || ||||||||||||||| | || ||||||||||| || ||| |||| || |||||  | |||||   ||     ||| | | | || |||   |  | ||| |   ||||| || |  ||  |   |  || |   ||| || | |   | | || ||||  |                  
TGAGCCGTCTAATGAAAAGTCAGATGTGTACAGCTTCGGGGTCATCTTGTGGGAGCTTGCTACATTGCAACAACCATGGGGTAACTTAAATCCGGCTCAGgtactttcc---actctaa-acatctcaa-ataataatgatattattttgcatttggaagtccctcactctacatttcataacatgctatatatgatcatacaaaaaaatgttccatag

upper sequence: GLYMA19G37570.2 (Glycine max), 5'ss of exon 14
lower sequence: Vv08s0007g03910.t01 (Vitis vinifera), 5'ss of exon 13
CGAGCCATCCAATGAGAAGTCAGATGTTTACAGCTTTGGTGTCATCTTGTGGGAGATCGCAACATTGCAACAGCCTTGGAGTAATTTGAATCCACCACAGgtttgttgtataactttgatatatttcagtgtgcttatgcttagattttccaatacgattat-attgctttgattttt-atgaaagattctttaagatctga
 ||| |||| ||||| ||||||||  | || ||||||||| | |||||||||||  | |||||||||||||| |||||||||||||| |||||| |||||||||||  | | |  ||     ||   ||||   | ||    |||      |    | | || |||   ||  | ||| | |  ||||  |  ||    |  
TGAGGCATCAAATGAAAAGTCAGACATATATAGCTTTGGTATAATCTTGTGGGAACTTGCAACATTGCAACAACCTTGGAGTAATTTAAATCCAGCACAGgtttgtcttctgaagttatgtaatgcaagtgaaatcattgaaagaagagagagattgttgatgattatatttttctttgaagggagatgatgcaattctt--

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|208336673|gb|GE135105.1|GE135105
EST:     GGGAGATCGCAACATTGCAACAGCCTTGGAGTAATTTGAATCCACCACAG                         GTTGTGGCAGCTGTTGGCTTTAAGGGAAAAAGACTTGAGATACCACGTGAT
genomic: GGGAGATCGCAACATTGCAACAGCCTTGGAGTAATTTGAATCCACCACAGgtttgttgta ... tgttttgtagGTTGTGGCAGCTGTTGGCTTTAAGGGAAAAAGACTTGAGATACCACGTGAT
EST: gi|208074644|gb|GD868281.1|GD868281
EST:     GGGAGATCGCAACATTGCAACAGCCTTGGAGTAATTTGAATCCACCACAG                         GTTGTGGCAGCTGTTGGCTTTAAGGGAAAAAGACTTGAGATACCACGTGAT
genomic: GGGAGATCGCAACATTGCAACAGCCTTGGAGTAATTTGAATCCACCACAGgtttgttgta ... tgttttgtagGTTGTGGCAGCTGTTGGCTTTAAGGGAAAAAGACTTGAGATACCACGTGAT
EST: gi|207781788|gb|GD751791.1|GD751791
EST:     GGGAGATCGCAACATTGCAACAGCCTTGGAGTAATTTGAATCCACCACAG                         GTTGTGGCAGCTGTTGGCTTTAAAGGGAAAAAGACTTGAGATACCACGTGA
genomic: GGGAGATCGCAACATTGCAACAGCCTTGGAGTAATTTGAATCCACCACAGgtttgttgta ... tgttttgtagGTTGTGGCAGCTGTTGGCTTTAA-GGGAAAAAGACTTGAGATACCACGTGA
EST: gi|208260829|gb|GE059837.1|GE059837
EST:     GGGAGATCGCAACATTGCAACAGCCTTGGAGTAATTTGAATCCACCACAG                         GTTGTGGCAGCTGTTGGCTTTAAGGGAAAAAGACTTGAGATACCACGTGAT
genomic: GGGAGATCGCAACATTGCAACAGCCTTGGAGTAATTTGAATCCACCACAGgtttgttgta ... tgttttgtagGTTGTGGCAGCTGTTGGCTTTAAGGGAAAAAGACTTGAGATACCACGTGAT
EST: gi|208280179|gb|GE075477.1|GE075477
EST:     GGGAGATCGCAACATTGCAACAGCCTTGGAGTAATTTGAATCCACCACAG                         GTTGTGGCAGCTGTTG
genomic: GGGAGATCGCAACATTGCAACAGCCTTGGAGTAATTTGAATCCACCACAGgtttgttgta ... tgttttgtagGTTGTGGCAGCTGTTG
EST: gi|208104845|gb|GD907342.1|GD907342
EST:     GGGAGATCGCAACATTGCAACAGCCTTGGAGTAATTTGAATCCACCACAG                         GTTGTGGCAGCTGTTGGCTTTAAGGGAAAA-GACTTGAGATACCACGTGAT
genomic: GGGAGATCGCAACATTGCAACAGCCTTGGAGTAATTTGAATCCACCACAGgtttgttgta ... tgttttgtagGTTGTGGCAGCTGTTGGCTTTAAGGGAAAAAGACTTGAGATACCACGTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGAGCCATCCAATGAGAAGTCAGATGTTTACAGCTTTGGTGTCATCTTGTGGGAGATCGCAACATTGCAACAGCCTTGGAGTAATTTGAATCCACCACAGgtttgttgtataactttgatatatttcagtgtgcttatgcttagattttccaatacgattatattgctttgatttttatgaaagattctttaagatctga

- - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG