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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTCGAAGGGTCCACGCTGCCCAGAAAGATGATGACATGCCTCCAATAGAAGCAATTCTTGCTCCTTTGGAAGCTGAACTCAAGCTTGCTCGGCAAGAGgtattaccttgttcttggagttcatattgtaatcccctggagaaagagctgatggaaggacttaaactggcttaaaatgagtaattttttgatttgtacttccatttattccttgcag

Basic information

species Glycine max
transcript GLYMA02G09390.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G09390.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os02g50320.2 (Oryza sativa), 5'ss of exon 4
TCTTCGAAGGGTCCACGCTGCCCAGAAAGATGATGACATGCCTCCAATAGAAGCAATTCTTGCTCCTTTGGAAGCTGAACTCAAGCTTGCTCGGCAAGAGgtattaccttgttcttggagt------------tcatattgta--atcccctggagaaagagctgatggaagga------cttaaactggcttaaaatgag----taattttttgatttgtacttccatttattccttgcag-------------------------------------------------------
||| ||||| || || || ||||| ||||||||||| ||||| || || ||||| |||||||||||  | ||||||||||| ||||||||||| ||||||||| |||  ||||  |  | |             |||||| ||   | |  |       | | ||||   |  |      || | |||   ||| | |  |    |   ||    | |  || ||| | || | | || ||                                                        
TCTGCGAAGAGTGCATGCAGCCCAAAAAGATGATGATATGCCACCTATTGAAGCTATTCTTGCTCCACTTGAAGCTGAACTAAAGCTTGCTCGTCAAGAGgtaatactgtgttactcaaatggccaggcatggccatattttattgttcattttgtttggtgttgatattacaatattttctcacacttatttagattttgcctcttgcttccatagtcctaattcaacttctccattccaccacatgcatgttcactataattgtctaaagaataagatttgctttttttcttcag

upper sequence: GLYMA02G09390.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os12g44340.1 (Oryza sativa), 5'ss of exon 4
TCTTCGAAGGGTCCACGCTGCCCAGAAAGATGATGACATGCCTCCAATAGAAGCAATTCTTGCTCCTTTGGAAGCTGAACTCAAGCTTGCTCGGCAAGAGgtattaccttgttcttggagttcatattgtaatcccctggagaaagagctgatggaaggacttaaactggcttaaaatgagtaattttttgatttgtacttccatttattccttgcag
 ||||||||||| || || || ||||| |||||||||||||| || || || || |||||||| || |||||||||||||| || || ||||| || ||||||||      |  |   |||  |||     || | ||          ||     |        ||    ||| |    |    | |||   |    |       ||           
ACTTCGAAGGGTTCATGCAGCACAGAAGGATGATGACATGCCCCCTATTGAGGCCATTCTTGCGCCATTGGAAGCTGAACTGAAACTAGCTCGTCATGAGgtatt------tcatccaagtgtatacctggattctctttcttcttttctttccaatcagtaccaatgttcttcatgc-atcggtctttgtgtcaagatgcttgctt-----------

upper sequence: GLYMA02G09390.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os06g14080.1 (Oryza sativa), 5'ss of exon 4
TCTTCGAAGGGTCCACGCTGCCCAGAAAGATGATGACATGCCTCCAATAGAAGCAATTCTTGCTCCTTTGGAAGCTGAACTCAAGCTTGCTCGGCAAGAGgtattaccttgttcttggagttcatattgta-atcccctggagaaagagctgatggaaggacttaaactggcttaaaa-----tgagtaattt-----tttgatttgt----acttccatttattccttgcag--------------------------------------------------------------------
| | || || || || || ||||| || |||||||||||||| ||||| ||||| ||||| || ||  | |||||||| || ||||||||||||||||||||   || ||||||    |   |  ||| |  |||   | |     |   || |  ||   ||||  ||  | ||| |     ||| || |||     | || ||||     ||  | | ||| |      ||                                                                    
TTTGCGGAGAGTACATGCAGCCCAAAAGGATGATGACATGCCACCAATTGAAGCCATTCTCGCACCGCTTGAAGCTGAGCTAAAGCTTGCTCGGCAAGAGgtgaaactttgttcacccatcccccattttctatcattttgtttgtg---tggtttaatttcttatgctttcctaacagttactgattattttcatcctctggtttgcctaaacggctaattagttgccttagtttcttttcattggtttgtgtattttctatgatcaaataagatgaccagttaacttggttcactttag

upper sequence: GLYMA02G09390.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G008556_T01 (Zea mays), 5'ss of exon 4
TCTTCGAAGGGTCCACGCTGCCCAGAAAGATGATGACATGCCTCCAATAGAAGCAATTCTTGCTCCTTTGGAAGCTGAACTCAAGCTTGCTCGGCAAGAGgtattaccttgttcttggagttcatattgtaatcccctggagaaagagctgatggaaggacttaaactggcttaaaatgagtaattttttgatttgtacttccatt-tattccttgcag----------------------------------------------------------------------
| | ||||| || || || ||||||||||||||||||||||| ||||| ||||| |||||||| ||  | |||||||| || |||||| |||| ||||||||| ||| | ||  ||     | |  ||||  |    | | |   | || ||||      ||||   |    | | ||  | || | ||| |    | |   ||   ||   | |  |                                                                       
TTTGCGAAGAGTACATGCAGCCCAGAAAGATGATGACATGCCACCAATTGAAGCCATTCTTGCACCGCTTGAAGCTGAGCTAAAGCTTTCTCGCCAAGAGgtaatacttagtattttatagtta-gttgttctttatttgtgtttgtgcagatgttttt-cttaggtttctgttacatttgcaaatattttacacctccagtcaccctagatcatctaactacccttttcccaatttgtcatgtatttcctgtggagaaagtgtatgataagttaaaccttgttttcag

upper sequence: GLYMA02G09390.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G039325_T01 (Zea mays), 5'ss of exon 4
TCTTCGAAGGGTCCACGCTGCCCAGAAAGATGATGACATGCCTCCAATAGAAGCAATTCTTGCTCCTTTGGAAGCTGAACTCAAGCTTGCTCGGCAAGAGgtattaccttgt-tcttggagttcatattgtaatcccctggagaaagagctgatggaaggacttaaactggctt--aaaatgagtaattttttgatttgtact------tccatttattccttgcag--------------------------------------------------------
| | || || || || || ||||||||||||||||||||||| ||||| ||||| |||||||| ||  | |||||||| || |||||| |||| || |||||| ||| | || | ||   |||  |  | || |    |      |||  |  |  |  |  ||  | |   ||   ||||   | |    |  | |    ||      || | |||  | || |                                                          
TTTGCGGAGAGTACATGCAGCCCAGAAAGATGATGACATGCCACCAATTGAAGCCATTCTTGCACCACTTGAAGCTGAGCTAAAGCTTTCTCGCCAGGAGgtaatacttagtcttttatggttggttctttatttgtgtttgtgcagatgtctttcataggtttctattacatttgcaaatattttacgcctccagtcaccctcgatgatctaattacccttttccaatttgtcatgtatttcctgcggatgaagtgtatgacaagttaaatcttgttttcag

upper sequence: GLYMA02G09390.1 (Glycine max), 5'ss of exon 4
lower sequence: AT1G68060.1 (Arabidopsis thaliana), 5'ss of exon 4
TCTTCGAAGGGTCCACGCTGCCCAGAAAGATGATGACATGCCTCCAATAGAAGCAATTCTTGCTCCTTTGGAAGCTGAACTCAAGCTTGCTCGGCAAGAGgtattaccttgttc--ttggagttcatattgtaatcccctggagaaagagctgatggaaggacttaaactggcttaaaatgagtaattttttgatttgtacttccatttattccttgcag
  |  |||||||||| ||||| || || |||||||| |||||||| || ||||| ||||| ||||| ||||||||||| || ||||| |||||    |||||||    ||  ||  ||| ||| || |||    ||  || |  ||   | |  |  ||    | |   |    | ||                                          
CTTAAGAAGGGTCCATGCTGCTCAAAAGGATGATGATATGCCTCCGATTGAAGCCATTCTAGCTCCATTGGAAGCTGAGCTTAAGCTAGCTCGCTCTGAGgtat-gttttactcatttgaagtccaaatt----tctacttgcaaatcggatatt--aatttatgatgtttctgtgaag-----------------------------------------

upper sequence: GLYMA02G09390.1 (Glycine max), 5'ss of exon 4
lower sequence: AT1G24764.1 (Arabidopsis thaliana), 5'ss of exon 4
TCTTCGAAGGGTCCACGCTGCCCAGAAAGATGATGACATGCCTCCAATAGAAGCAATTCTTGCTCCTTTGGAAGCTGAACTCAAGCTTGCTCGGCAAGAGgtattaccttgttcttggagttcata-ttgtaatcccctggagaaagagctgatggaaggacttaaactggcttaaaatgagtaattttttg-atttgtacttccatttattccttgcag
| |  |||| ||||| ||||| || || ||||||||||||||||| || ||||| || |||||||| || ||||||||||| |||||||| ||   ||||||||    |  || |  |  |   |  |||   |   ||     | | | |  || |||    | |  |  || |  |     ||| | ||| || |||                     
TTTAAGAAGAGTCCATGCTGCTCAAAAGGATGATGACATGCCTCCTATTGAAGCCATCCTTGCTCCATTAGAAGCTGAACTTAAGCTTGCACGATCAGAGgtatattgtcattttaagtctaactgcttgctgtttactttcatatgggatattgaaagtttatgaggtcactgatca-----aatctcttgtatctgtgtag-----------------

upper sequence: GLYMA02G09390.1 (Glycine max), 5'ss of exon 4
lower sequence: AT1G14840.2 (Arabidopsis thaliana), 5'ss of exon 4
TCTTCGAAGGGTCCACGCTGCCCAGAAAGATGATGACATGCCTCCAATAGAAGCAATTCTTGCTCCTTTGGAAGCTGAACTCAAGCTTGCTCGGCAAGAGgtattaccttgttcttggagttcatattgtaatcccctggagaaagagctgatggaaggacttaaactggcttaaaatgagtaattttttgatttgtacttccatttattccttg-cag
|||||| ||||| || ||||| || || |||||||||||||||||||| ||||| |||||||| ||||| ||||||||||| || ||| |  | ||||| |||||  | | | ||| ||      |||     ||  || | |       |||  ||  |||||  | ||   | | | |  |  ||| | || ||   || ||| | ||  |||  ||
TCTTCGTAGGGTTCATGCTGCTCAAAAGGATGATGACATGCCTCCAATTGAAGCTATTCTTGCCCCTTTAGAAGCTGAACTGAAACTTTCGAGACAAGAAgtattttcct-tcctttgaaccagaatta----cctttgtatagc---tcgattcaacaactta--cggg---acatttaacagctttctcatatgggtttacatgttttgattggtag

upper sequence: GLYMA02G09390.1 (Glycine max), 5'ss of exon 4
lower sequence: AT2G01750.2 (Arabidopsis thaliana), 5'ss of exon 5
TCTTCGAAGGGTCCACGCTGCCCAGAAAGATGATGACATGCCTCCAATAGAAGCAATTCTTGCTCCTTTGGAAGCTGAACTCAAGCTTGCTCGGCAAGAGgtatt--accttgttct--tggagttcatattgtaatcccctggagaaagagctgatggaaggacttaaactggcttaaaatgagtaattttttgatttgtacttccatttattccttgcag
|||||||||||| || ||||| || || ||||| || |||||||| || ||||| ||||| |||||||| || |||||||||||| | ||  | || || |||||  || |  ||    |  | |  || |  || | || ||   |  ||| |  |||||    || || |  ||    ||   |   || || |||||||                    
TCTTCGAAGGGTTCATGCTGCTCAAAAGGATGACGATATGCCTCCTATTGAAGCTATTCTCGCTCCTTTAGAGGCTGAACTCAAGTTGGCGAGACATGAAgtattttacttcctttcaatcaactatatctcttatttccttgcttattgag-tcttggaacctttttaa-taactgggcat---tgcattcttcatttgtag-------------------

upper sequence: GLYMA02G09390.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 5'ss of exon 4
TCTTCGAAGGGTCCACGCTGCCCAGAAAGATGATGACATGCCTCCAATAGAAGCAATTCTTGCTCCTTTGGAAGCTGAACTCAAGCTTGCTCGGCAAGAGgtattaccttgttcttggagttcatattgtaatcccctggagaaagagctgatggaaggacttaaactggcttaaaatgagtaattttttgatt-tgtacttccatttattccttgcag
|||| ||||||| || ||||| ||||| ||||| || |||||||| || ||||| |||||||| || ||||| ||||| ||||||||||||||||| |||||| |   |||    |||  || | | | | |    |           || |  | |  |||     | | | | ||  |||| || | ||||| | |   |  |||  ||| || |||
TCTTAGAAGGGTTCATGCTGCGCAGAAGGATGACGATATGCCTCCCATTGAAGCGATTCTTGCACCGTTGGAGGCTGAGCTCAAGCTTGCTCGGCAGGAGgtagt-tattgcatgtggcctttaaacttttaatgac---gattctttctcaaagtaaaactcctcatagatgataaatagtagttatatgattgtttggctgtattggttcttttcag

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|254322365|gb|GR837779.1|GR837779
EST:     AAGCAATTCTTGCTCCTTTGGAAGCTGAACTCAAGCTTGCTCGGCAAGAG                         ATTGCTAAACTACAAGATGATAACAAAGCTTTAGATCGTCTTACCAAATCT
genomic: AAGCAATTCTTGCTCCTTTGGAAGCTGAACTCAAGCTTGCTCGGCAAGAGgtattacctt ... ttccttgcagATTGCTAAACTACAAGATGATAACAAAGCTTTAGATCGTCTTACCAAATCT
EST: gi|14990947|gb|BI316620.1|BI316620
EST:     GCAATTCTTGCTCCTTTGGAAGCTGAACTCAAGCTTGCTCGGCAAGAG                         ATTGCTAAACTACAAGATGATAACAAAGCTTTAGATCGTCTTACCAAATCT
genomic: GCAATTCTTGCTCCTTTGGAAGCTGAACTCAAGCTTGCTCGGCAAGAGgtattacctt ... ttccttgcagATTGCTAAACTACAAGATGATAACAAAGCTTTAGATCGTCTTACCAAATCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTCGAAGGGTCCACGCTGCCCAGAAAGATGATGACATGCCTCCAATAGAAGCAATTCTTGCTCCTTTGGAAGCTGAACTCAAGCTTGCTCGGCAAGAGgtattaccttgttcttggagttcatattgtaatcccctggagaaagagctgatggaaggacttaaactggcttaaaatgagtaattttttgatttgtacttccatttattccttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA