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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgcttgcatgaggtgacatcagctttctgcttttatttcttcttactgtttcttgttaattttgttaaaattttcttgtgtcagAACCTCTACTGGGCTGATAGTGGTGATCTAGTGACGATTGCTAGTGATACATCATTCTATATCCTGAAGTACAAT

Basic information

species Glycine max
transcript GLYMA07G03890.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 13
gtaagtgcttgcatgaggtgacatcagctttctgcttttatttcttcttactgtt-tcttgttaattttgttaaaattttcttgtgtcagAACCTCTACTGGGCTGATAGTGGTGATCTAGTGACGATTGCTAGTGATACATCATTCTATATCCTGAAGTACAAT
|| |||  ||   |     ||  | |  ||| |  |     |  ||   | | || |  || ||| |  | |    |||  |  |   |||| ||||| ||||| |||||||||||| ||||||| ||||| ||||| || |||||||| ||  |||||||||||
gtgagtaattttgttcctggatttaaatttttttttgcgtgtcatttggaatattatgatgctaaataggatctgctttcttatttgtagAATCTCTATTGGGCCGATAGTGGTGATTTAGTGACAATTGCAAGTGACACCTCATTCTACATTTTGAAGTACAAT

upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 4
gtaagtgcttgcatgaggtgacatcagctttctgcttttatttcttcttactgtttcttgttaattttgttaaaattttcttgtgtcagAACCTCTACTGGGCTGATAGTGGTGATCTAGTGACGATTGCTAGTGATACATCATTCTATATCCTGAAGTACAAT
|| |||  ||   |     ||    |  ||  |     | |   ||   |   | |  || ||| |  | |    |||  |  |   |||| ||||| ||||| |||||||||||| ||||||| ||||| ||||| || |||||||| ||  |||||||||||
gtgagtaattttgttcatggattcaaatttattttgcgtgtcatttggaatattatgatgctaaataggatccgctttcttatttgtagAATCTCTATTGGGCCGATAGTGGTGATTTAGTGACAATTGCAAGTGACACCTCATTCTACATTTTGAAGTACAAT

upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 13
gtaagt--gcttgcatgaggtgacatc---agctttctgcttttattt--cttcttactgtttcttgttaattttgttaaaattttcttgtgtcagAACCTCTACTGGGCTGATAGTGGTGATCTAGTGACGATTGCTAGTGATACATCATTCTATATCCTGAAGTACAAT
|| |||    |   ||    ||| ||    || ||  | ||||||      ||| |||||    |   || |||||| |   | || ||     ||||||| || ||||||||||| ||||| |||||  | || || ||||||||||||||||| || ||||||||||| 
gtgagtcaaatattatctattgatatttatagattgatacttttaacgaatttcatactgaaa-taactagttttgtcactgtattttt-----agAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC

upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 13
gtaagtgcttgcatgaggtgacatcagctttctgcttttatttcttcttact---gtttcttgttaattttgttaaaattttcttgtgtcagAACCTCTACTGGGCTGATAGTGGTGATCTAGTGACGATTGCTAGTGATACATCATTCTATATCCTGAAGTACAAT
      |   |    | ||   ||      |  | |   | || |   |      ||||  | ||||  || |    ||  | |  |   ||||  | |||||||||||||||||||| |||||  | || || ||||||||||||||||| ||||| |||||||||
------gtgagtcaaaagtattatttttccttgggtggaaattttgtatgtatgagtttaatattaaccttttgtttatcatgtgtttatagAATGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAAT

upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 12
-----gtaagtgcttgcatgaggtgacatcagctttctgcttttatttcttcttactgtttcttgttaattttgttaaaattttcttgtgtcagAACCTCTACTGGGCTGATAGTGGTGATCTAGTGACGATTGCTAGTGATACATCATTCTATATCCTGAAGTACAAT
       ||||  |    |    ||   |     || ||  | ||     | | |  ||||  | ||||  || |    ||  |    |   ||||| | |||||||||||||||||||| |||||  | || || ||||||||||||||||| ||||| |||||||||
gtgaatcaagtattattttttcttgg-gtggaaattttgtatgtaaaatgtatga--gtttactattaaccttttctttatcatgcatttatagAACGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAAT

upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 13
gtaagtgcttgcatgaggtgacatcagctttctgcttttatttc-ttcttactgtttct--tgttaattttgttaaaa----ttttcttgtgtcagAACCTCTACTGGGCTGATAGTGGTGATCTAGTGACGATTGCTAGTGATACATCATTCTATATCCTGAAGTACAAT
||||  |  |   | |  |   || |  |     ||||| || | ||| | |  |||    ||||       | ||||    |||  |||||| |||| || ||||||||||| ||||||||| |||| || ||||| |||||||| |||||||| ||  |||| || |||
gtaatggaatttgttacct--tattatttcaaacctttttttacattcatgccatttgaaatgttgtgccactcaaaacatgtttctttgtgt-agAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT

upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 13
---------------------------gtaagtgcttgcatgaggtgacatcagctttctgcttttatttcttcttactgtttct--tgttaattttgttaaaa----ttttcttgtgtcagAACCTCTACTGGGCTGATAGTGGTGATCTAGTGACGATTGCTAGTGATACATCATTCTATATCCTGAAGTACAAT
                            ||| | |   | ||   |  |||   |  | ||    || |     ||    |||    ||||       | || |    |||  |||||| |||| || ||||||||||| ||||||||| |||| || ||||| |||||||| |||||||| ||  |||| || |||
gtaatgacatttgacatttgttgccttataatttcaaacctggttttgcatttccaatgtgaaggtaatggcatttgacatttgaaatgttgtgccactgaagacatgtttctttgtgt-agAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT

upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 2
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 17
-------------------------------------------------------------------------------------------------gtaagtgcttgcatgaggt--gacatcagctttctgcttttatttctt-cttactgtttcttgttaattttgttaaaattttcttgtgtcagAACCTCTACTGGGCTGATAGTGGTGATCTAGTGACGATTGCTAGTGATACATCATTCTATATCCTGAAGTACAAT
                                                                                                   |  | |||   |||  |   |   ||         |  || | ||  |||| |   | ||     ||||||| |   ||   ||| |||||| || || ||||| || ||||||||||||||  | ||||| ||||||||||||||||| ||||| |||| ||||
gtaagtgcttatataccagaagtagatccattagtttctacaagaaaatagtttataggttacgttttcagtaatatttttattggagaaatacaaaagagttccttatctgaaatttaaacgcaaaagcagattggtactgctcgcttattcacttttaacgtttttgttta---ttcaatgtttcagAATCTTTATTGGGCGGACAGTGGTGATCTAGTTGCAATTGCCAGTGATACATCATTCTACATCCTTAAGTTCAAT

upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 2
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 13
----------------------------------------------------gtaagtgcttgcatgaggtgacatca--gctttctgcttttatttcttcttact-gtttcttgttaattttgt--taaaattttcttgtgt---cagAACCTCTACTGGGCTGATAGTGGTGATCTAGTGACGATTGCTAGTGATACATCATTCTATATCCTGAAGTACAAT
                                                     |  |   | |    |  | | ||||  || ||| | ||    || | ||   | ||||||| |  | |||||  |     |   |   ||   ||||| || || |||||||| ||||||||| ||||  | ||||||||||| ||||||||||| ||| |||| | ||| 
gtatcccagttaacttggctcagtttattgtaagaagtttacttcaagacatatttggaatagtggaaactaatatcattgccttcagtttgaggttttcctcgtttgtttcttctctaatttgtagtgttgctacataacgtttgcagAATCTATATTGGGCTGACAGTGGTGATTTAGTAGCCATTGCTAGTGACACATCATTCTACATCTTGAAATTCAAC

upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 2
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
---------------------------gtaagt--gcttgcatgaggtgacatcagctttctgcttttatttcttctt---------actgtttc--ttgttaattttgttaaaatttt-cttgtgt----------cagAACCTCTACTGGGCTGATAGTGGTGATCTAGTGACGATTGCTAGTGATACATCATTCTATATCCTGAAGTACAAT
                             ||||  || | ||| |  |     ||  | | |  ||  ||||  | ||           |||  |  ||  |   |||  |||   ||| ||    |          ||||| || || |||||||| ||||||||| ||||  | |||||||||||||| |||||||| ||| |||||||||||
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagttgaaagttgtcccaattagtgtctttactaactctttactcccatgaaaaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT

upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 13
gtaagtgcttgcatgaggtgacatcagctttc-------tgcttttatttcttcttac--------------tgtttcttgttaattttgttaaaattttcttgtgtcagAACCTCTACTGGGCTGATAGTGGTGATCTAGTGACGATTGCTAGTGATACATCATTCTATATCCTGAAGTACAAT
|||||  ||  ||||| |     |  |||  |       || ||| ||  |    | |              |||| ||| ||  |||| ||    |||   | | |||||||||||| |||||||||||||| ||| | ||| | ||||| |||||||||||||| || |||||||||||||||
gtaagcactaacatgatggcctgttggctaccgtggtattgttttcatgccacactgcaggaattgattaaatgttccttttttcttttctttttttttcactatttcagAACCTCTATTGGGCTGATAGTGGGGATTTGGTGGCCATTGCCAGTGATACATCATTTTACATCCTGAAGTACAAT

upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 13
gtaagtgcttgcatgaggtgacatca-gctttctgcttttatttcttcttactgtttcttgttaattttgttaaa--attttcttgtgtcagAACCTCTACTGGGCTGATAGTGGTGATCTAGTGACGATTGCTAGTGATACATCATTCTATATCCTGAAGTACAAT
| | || ||   |  || | || |||   || |    |||    |          |  | ||| ||||  ||      |||   | | |||||| || || |||||||||||||||||| ||||| | ||||| |||||| ||||||| || ||| | |||||||||
gcatgttctca-aaaagcttacttcacaattaccaggttttggccacagagaaactaatagttcatttctttgggtggtttcaatatttcagAATCTTTATTGGGCTGATAGTGGTGATTTAGTGGCAATTGCAAGTGATTCATCATTTTACATCTTAAAGTACAAT

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|254341657|gb|GR852794.1|GR852794
EST:     ATGATTGGGCTGAATGCAGGTTGATTCGTCGTATTGATGTTAATGTTAAA                         AACCTCTACTGGGCTGATAGTGGTGATCTAGTGACGATTGCTAGTGATACA
genomic: ATGATTGGGCTGAATGCAGGTTGATTCGTCGTATTGATGTTAATGTTAAAgtaagtgctt ... cttgtgtcagAACCTCTACTGGGCTGATAGTGGTGATCTAGTGACGATTGCTAGTGATACA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttatttcttcttactgtttcttgttaattttgttaaaattttcttgtgtcagAACCTCTACTGGGCTGATAGTGGTGATCTAGTGACGATTGCTAGTGATACATCATTCTATATCCTGAAGTACAAT
                                         ttttcttgt  CT-rich tract
                   tttcttgttaattttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgcttgcatgaggtgacatcagctttctgcttttatttcttcttactgtttcttgttaattttgttaaaattttcttgtgtcagAACCTCTACTGGGCTGATAGTGGTGATCTAGTGACGATTGCTAGTGATACATCATTCTATATCCTGAAGTACAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG