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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaccattccagtttcgtaattttattgaaacaagcatatcttacataatccttactaaaaactcttctaccaactttggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGGACAGTGTATGGATTAATTGTCTCTCAATATAGAGATATAGAGGACCCAC

Basic information

species Glycine max
transcript GLYMA08G21540.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G21540.1 (Glycine max), 3'ss of exon 21
lower sequence: LOC_Os06g36090.2 (Oryza sativa), 3'ss of exon 17
gtgagtaccattccagtttcgtaattttattgaaacaagcatatcttacataatccttactaaaaactcttctaccaactttggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGGACAGTGTATGGATTAATTGTCTCTCAATATAGAGATATAGAG-GACCCAC
||||||    ||  | |       |||  |||||      ||   |     ||     |   ||   | || | |    |||    |||||||  ||||| ||||||||| | ||||| |||||| |||| ||| |||||||||||||||||||  | || ||  | || ||| ||||  ||||   |  || 
gtgagttttcttgga-tcaaaccgtttctttgaactttttattcttcttggaagatcaaagtaatggtgttattcatgtttta---tttcagAGGATTCCCAAATGGTGGATCTGGTACTACTGGCTTTGCCCATTGGCATGGACAGTGTATGGGCTCATAGTGACACAGTATGGAGACCTAGAACAAATCA-

upper sequence: GLYMA08G21540.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G366146_T01 (Zea mays), 3'ss of exon 17
-------gtgagtaccatt-ccagtttcgtaattttattgaaacaagcatatcttacataatccttactaaaaactcttctaccaactttggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGGACAGTGTATGGATTAATTGTCTCTCAATATAGAGATATAGAGGACCCAC
       ||   | | ||  ||  |  ||| ||  | ||    |      ||   | ||||| ||||        | ||   | |   ||    ||||||| |||||||| ||||||| | ||||| ||||||||||| ||| |||||||||||||||||||  | || ||  | |||||  ||||  |  | |||||  
gttagttgtttcttcaatcacctttaccgtgatcctttt----ctgtaggattaaaaataatgcttat--gttgttttttctctattctta---tttcagAGAATTCCTAGATGGTGGATCTGGTACTACTGGATTTGCCCATTGGCATGGACAGTGTATGGGCTCATCGTGACACAATACGGAGACCTGCAAGACCCCA

upper sequence: GLYMA08G21540.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G029506_T01 (Zea mays), 3'ss of exon 21
gtgagt-accattccagtttcgtaattttattgaaacaagcatatcttacataatccttactaaaaactc---ttctaccaactttggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGGACAGTGTATGGATTAATTGTCTCTCAATATAGAGATATAGAGGACCCAC
|| |||     || || |  |   ||      ||  |        | |  |  ||    |   |  ||||   || |  |    ||    ||||||| |||||||  ||||||| | ||||| ||||||||||| ||| |||||||||||||||||||  | || ||  | |||||  ||||  | || ||||   
gtcagttgttgtttcaat--caccatccctgcgatccttttcctacctgtaggattaa-atagaggactcatgttttttctctattcctgtttcagAGAATTCCTGGATGGTGGATCTGGTACTACTGGATTTGCCCACTGGCATGGACAGTGTATGGGCTCATCGTGACACAATACGGAGACCTGGAAGACCTCA

upper sequence: GLYMA08G21540.1 (Glycine max), 3'ss of exon 21
lower sequence: AT3G16340.1 (Arabidopsis thaliana), 3'ss of exon 18
gtgagtaccattccagtttc--gtaattttattgaaaca--agcatatcttacataatccttactaaaaactcttctaccaactttggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGGACAGTGTATGGATTAATTGTCTCTCAATATAGAGATATAGAGGACCCAC
|| |||     |    ||||  | ||      ||||||   |    ||  |  ||      ||  | || ||  | |    |||||    || |||| |||||| ||||||||| | |||||||||||||| ||||||||||| ||||| ||||||||||| ||||| || || ||  | ||  | |||||  |  
gttagtgttggttacttttctggcaagaaagctgaaaccctaaatgattctctattgattctatcataagctggtttt---actttcctcttgcagAGAATTCCGAAATGGTGGATATGGTATTACTGGATCTGTCCAGTGGCTTGGACTGTGTATGGATTGATTGTTTCGCAGTACGGTGACGTGGAGGATACGA

upper sequence: GLYMA08G21540.1 (Glycine max), 3'ss of exon 21
lower sequence: Vv09s0002g03570.t01 (Vitis vinifera), 3'ss of exon 4
gtgagtaccattcc---agtttcgtaa----ttttattgaaacaagcatatcttacataatccttactaaaa-actcttctaccaac-tttggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGGACAGTGTATGGATTAATTGTCTCTCAATATAGAGATATAGAGGACCCAC
|| ||| |  || |   |||  | ||     ||| ||     | | |  | || |   | | |  |||||   |  | || |  ||  |||    |||||||||||||| || |||||| | ||||| || |||||||| ||| | ||||||||||| || ||  | || || || |||||| ||||  | |||||| || 
gtaagttcattttcctcagtggcatagccactttcatgccttccaaccaacctcatccactacaaactaactcaaacctccattaatgtttaaaatttcagAAAATTCCCAAGTGGTGGATCTGGTACTATTGGATTTGCCCACTAGCATGGACAGTTTACGGGCTGATCGTATCGCAATATGGAGACTTGGAGGACACAA

upper sequence: GLYMA08G21540.1 (Glycine max), 3'ss of exon 21
lower sequence: Vv09s0002g03640.t01 (Vitis vinifera), 3'ss of exon 20
gtgagtaccattcc---agtttcgtaa----ttttattgaaacaagcatatcttacataatccttactaaaa-actcttctaccaac-tttggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGGACAGTGTATGGATTAATTGTCTCTCAATATAGAGATATAGAGGACCCAC
|| ||| |  || |   |||  | ||     ||| ||     | | |  | || |   | | |  |||||   |  | || |  ||  |||    |||||||||||||| || |||||| | ||||| || |||||||| ||||| ||||||||||| || ||  | || || || |||||| ||||  | |||||| || 
gtaagttcattttcctcagtggcatagccactttcatgccttccaaccaacctcatccactacaaactaactcaaacctccattaatgtttaaaatttcagAAAATTCCCAAGTGGTGGATCTGGTACTATTGGATTTGCCCAGTAGCATGGACAGTTTACGGGCTGATCGTATCGCAATATGGAGACTTGGAGGACACAA

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|120493864|gb|EH222031.1|EH222031
EST:     CATTCTATGGACTCTTTAATCTCTTCTCTGGTTTCTTTATCCCAAGACCG                         AAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGG
genomic: CATTCTATGGACTCTTTAATCTCTTCTCTGGTTTCTTTATCCCAAGACCGgtgagtacca ... ggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGG
EST: gi|254319129|gb|GR828857.1|GR828857
EST:     CATTCTATGGACTCTTTAATCTCTTCTCTGGTTTCTTTATCCCAAGACCG                         AAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGG
genomic: CATTCTATGGACTCTTTAATCTCTTCTCTGGTTTCTTTATCCCAAGACCGgtgagtacca ... ggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGG
EST: gi|16283012|gb|BI945322.1|BI945322
EST:     TTTAATCTCTTCTCTGGTTTCTTTATCCCAAGACCG                         AAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGG
genomic: TTTAATCTCTTCTCTGGTTTCTTTATCCCAAGACCGgtgagtacca ... ggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGG
EST: gi|22525652|gb|BU084463.1|BU084463
EST:     CATTCTATGGACTCTTTAATCTCTTCTCTGGTTTCTTTATCCCAAGACCG                         AAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGG
genomic: CATTCTATGGACTCTTTAATCTCTTCTCTGGTTTCTTTATCCCAAGACCGgtgagtacca ... ggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGG
EST: gi|214009273|gb|DB988582.1|DB988582
EST:     CATTCTATGGACTCTTTAATCTCTTCTCTGGTTTCTTTATCCCAAGACCG                         AAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGG
genomic: CATTCTATGGACTCTTTAATCTCTTCTCTGGTTTCTTTATCCCAAGACCGgtgagtacca ... ggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcatatcttacataatccttactaaaaactcttctaccaactttggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGGACAGTGTATGGATTAATTGTCTCTCAATATAGAGATATAGAGGACCCAC
                    tactaaa  putative branch site (score: 1)
                                               cttttc  putative PPT
                   ttactaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtaccattccagtttcgtaattttattgaaacaagcatatcttacataatccttactaaaaactcttctaccaactttggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGGACAGTGTATGGATTAATTGTCTCTCAATATAGAGATATAGAGGACCCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA