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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatcctcatattttctcacactgacatctttaaatacattcaatgttaaaagagtttctagctgatccttcatccttgtgctgatgattcagGGTCACTGTGGTTCTTGTTGGGCATTTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTT

Basic information

species Glycine max
transcript GLYMA03G38520.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G38520.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g24550.1 (Oryza sativa), 3'ss of exon 4
gtgatcctcatattttctcacactgacatctttaaatacattcaatgttaaaa--gagtttctagctgatccttcatccttgt-gctgatgattcagGGTCACTGTGGTTCTTGTTGGGCATTTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTT
|| | |  |         || |     ||  ||||   |||      ||| ||   |   | ||   | |  |   || | || |   ||||  |||||||||||||| || |||||||||||||||||||| || |   |    ||||| || |||||||||||  |  | 
gtaaactacgcgcaccaccataa----attgttaatcccatgagggtttagaatgcaagatataataggtattatgtcttggttgacaatga--cagGGTCACTGTGGCTCGTGTTGGGCATTTGGTGCTGTGGAGTGTCTCCAGGATCGTTTCTGCATTCATTTCAACATG

upper sequence: GLYMA03G38520.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G108849_T04 (Zea mays), 3'ss of exon 5
-gtgatcctcatattttctcacactgacatctttaaatacatt--caatgt-taaaagagt--ttctagctgatcct----tcatccttgtgctgatgatt-cagGGTCACTGTGGTTCTTGTTGGGCATTTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTT
  | ||   || ||    | |     |||   |   ||| |||   | ||  ||||||||   | | |  || |  |    | ||   |   |||||||   |||||||||||||| ||||||||||| ||||||||||| || |   |    || || |||||||||||  |  |  | 
cttcatgagcagatcaagtaagttcaacagtctagcatatattattagtgcctaaaagagcgatgcaacatgcttgtagtataatgtcttgtctgatgacAACAGGGTCACTGTGGCTCTTGTTGGGCTTTTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATG

upper sequence: GLYMA03G38520.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G02300.1 (Arabidopsis thaliana), 3'ss of exon 4
---------------gtgatcctcatattttctcacactgacatctttaaatac--attcaatgttaaaagagtttctagctga-tccttcatccttgtgctgatgattcagGGTCACTGTGGTTCTTGTTGGGCATTTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTT------------------------------------------------
                |      ||   | |||  || | ||    | |  |||  | ||    |       ||||| |  |   ||| || |  |||  || | ||| ||||   |   |  ||    ||| |    |  |  | |||||  ||       ||   |   |  | | |||   |||                                                
gtcggttttaatctcttagcttccactatctctgtcattaacccaatgatttactgactcttcttatgttttgtttcaaattatctccctctttattgcactaaagat-caggtgaaacatcatttcatttgagTGGGTTATA-TATTGAACAATGTGTTACTCTGGTCGACGATAACTTTATGGTTTTGGTTTCTTTTGGGTCATTGTGGTTCTTGCTGGGCATTTGGTGCTGT

upper sequence: GLYMA03G38520.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G01610.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgatcctcatattttct---cacactgacatctttaaatacattcaatgttaaaagagtttctagctgatccttcatccttgtgctgatgattcagGGTCACTGTGGTTCTTGTTGGGCATTTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTT
|| |       || || |    |   ||  |  |||| ||   |  |  |  | ||  | || ||   |||         ||||| |  || || |||| || ||||||||||| |||||||||||||||||||||||| | |||||| | || || || || ||||   | 
gtaaattatcaatcttttgtgtatcttgtaacttttagatttgtctagaggaataaatggttttatgagatt--------ttgtggttttggtttagGGACATTGTGGTTCTTGCTGGGCATTTGGTGCTGTTGAATCACTATCAGATAGATTCTGTATCCAATTTGGCATG

upper sequence: GLYMA03G38520.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G01610.2 (Arabidopsis thaliana), 3'ss of exon 4
----------------------------------------------------------------------------------------------------------gtgatcctcatattttct---cacactgacatctttaaatacattcaatgttaaaagagtttctagctgatccttcatccttgtgctgatgattcagGGTCACTGTGGTTCTTGTTGGGCATTTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTT
                                                                                                          || |       || || |    |   ||  |  |||| ||   |  |  |  | ||  | || ||   |||         ||||| |  || || |||| || ||||||||||| |||||||||||||||||||||||| | |||||| | || || || || ||||   | 
gttttatgcttttagctttttcctcacaattttagtgttcaattgcatttcgttattaactcttggtttttgtgtgtgtgtgttgactgctctatgaacagatcaggtaaattatcaatcttttgtgtatcttgtaacttttagatttgtctagaggaataaatggttttatgagatt--------ttgtggttttggtttagGGACATTGTGGTTCTTGCTGGGCATTTGGTGCTGTTGAATCACTATCAGATAGATTCTGTATCCAATTTGGCATG

upper sequence: GLYMA03G38520.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G02305.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgatcctcatattttctcacactgacatctttaaatacattcaatgttaaaagagtttctagctgatcctt-catccttgtgctgatg-attcagGGTCACTGTGGTTCTTGTTGGGCATTTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTT
               |  || |       ||| |  |  ||      | ||  |  | ||   | |||     |||  | ||  || |   || ||||||||||||||||||| ||||| |||||||||||||||||| |||| ||  | || |||||  | | | |  | 
--------------gtaacagatcatttacttgagttttatattgcat-aatgggttctcagacagatataaacattttggttttggtttgtttagGGTCACTGTGGTTCTTGCTGGGCCTTTGGTGCTGTTGAATCACTGTCTGACAGATTCTGCATCAAATATAACATG

upper sequence: GLYMA03G38520.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0005g02820.t01 (Vitis vinifera), 3'ss of exon 4
-----gtgatcctcatattttctcacactgacatctt-taaatacattc--aatgttaaaagagtt---tctagctgatccttcatccttgtgctgatgattcagGGTCACTGTGGTTCTTGTTGGGCATTTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTT
      || |   ||| || | |  |  || |    | |||||  ||    |||  | | | | ||   | ||  |  |  || ||  || |  |  | | ||||||||| ||||| ||||||||||| |||||||||||||||||  |||||||||| ||||| || |||||||   | 
gtaacttggtttgcattttatttagcgttgtccctatataaatgaatgaggaattctcagaaatttgggtttatttatttatttatttttattttt-taaatcagGGTCATTGTGGCTCTTGTTGGGCTTTTGGTGCTGTTGAATCGCTGTCAGATCGTTTTTGTATCCATTTTGGCATG

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|192323979|gb|FK015700.1|FK015700
EST:     TTGGAAGAATTCTAGATCAG
genomic: TTGGAAGAATTCTAGATCAG
EST: gi|192329589|gb|FK021903.1|FK021903
EST:     TTGGAAGAATTCTAGATCAG
genomic: TTGGAAGAATTCTAGATCAG
EST: gi|151398613|gb|EV268484.1|EV268484
EST:     TTGGAAGAATTCTAGATCAG
genomic: TTGGAAGAATTCTAGATCAG
EST: gi|19346536|gb|BM891416.1|BM891416
EST:     TTGGAAGAATTCTAGATCAG
genomic: TTGGAAGAATTCTAGATCAG
EST: gi|120532302|gb|EH260435.1|EH260435
EST:     TTGGAAGAATTCTAGATCAG
genomic: TTGGAAGAATTCTAGATCAG
EST: gi|6134067|gb|AW132396.1|AW132396
EST:     TTGGAAGAATTCTAGATCAG
genomic: TTGGAAGAATTCTAGATCAG
EST: gi|18713013|gb|BM522699.1|BM522699
EST:     TTGGAAGAATTCTAGATCAG
genomic: TTGGAAGAATTCTAGATCAG
EST: gi|192308925|gb|FK002149.1|FK002149
EST:     TTGGAAGAATTCTAGATCAG
genomic: TTGGAAGAATTCTAGATCAG
EST: gi|151411964|gb|EV281775.1|EV281775
EST:     TTGGAAGAATTCTAGATCAG
genomic: TTGGAAGAATTCTAGATCAG
EST: gi|6666111|gb|AW277570.1|AW277570
EST:     TTGGAAGAATTCTAGATCAG
genomic: TTGGAAGAATTCTAGATCAG
EST: gi|207761165|gb|GD733298.1|GD733298
EST:     TTGGAAGAATTCTAGATCAG
genomic: TTGGAAGAATTCTAGATCAG
EST: gi|10238899|gb|BE807795.1|BE807795
EST:     TTGGAAGAATTCTAGATCAG
genomic: TTGGAAGAATTCTAGATCAG
EST: gi|9986530|gb|BE660638.1|BE660638
EST:     TTGGAAGAATTCTAGATCAG
genomic: TTGGAAGAATTCTAGATCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcaatgttaaaagagtttctagctgatccttcatccttgtgctgatgattcagGGTCACTGTGGTTCTTGTTGGGCATTTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTT
                                         tgctgat  putative branch site (score: 3)
     atgttaaaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatcctcatattttctcacactgacatctttaaatacattcaatgttaaaagagtttctagctgatccttcatccttgtgctgatgattcagGGTCACTGTGGTTCTTGTTGGGCATTTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT