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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctactatatagatttaactggagtggaatttcaatgcattttttctctgaattctctgcatttgatgcacaatgttcatactttggacccctttgcagGAACGGGATACCTGACAGCATGCTTTGCCTTGATGGTTGGACCCCAAGGCCGTGCTATTGGCGTGGAACATATTCCTGAGTTGGTTTCTTTTTCAATCGA

Basic information

species Glycine max
transcript GLYMA05G02810.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G02810.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G100315_T01 (Zea mays), 3'ss of exon 2
------------------tgctactatatagatttaactgg--agtggaatttcaatgcatt-ttttctctgaattctctgcatttgatgcacaatgttcatac-tttggacccctttgcagGAACGGGATACCTGACAGCATGCTTTGCCTTGATGGTTGGACCCCAAGGCCGTGCTATTGGCGTGGAACATATTCCTGAGTTGGTTTCTTTTTCAATCGA
                   || | |    ||     |   |  | |  ||  | ||   |    || |||  | || | |   | | |   |        || | ||     | | ||  ||| |  || ||||||||||| || |||||| |||||||||||||  ||||||||||  | ||  | |||||  |||| ||| | ||| ||| |||  | ||
gtctgttgctgatacttcagccatttgcaagtgcccatcagcaattacaagctgaacaaacagcttgctcaaatttttttctgtctaactgatgccacaaatgcattcatgtcacgttatagGTAGTGGCTACCTGACAGCTTGTTTTGCCATGATGGTTGGACCAGAAGGCCGTGCAGTGGGAATTGAACACGTTCCCGAGATCGTTGCTTCTTCTGTTGA

upper sequence: GLYMA05G02810.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G423027_T05 (Zea mays), 3'ss of exon 3
-----tgctactatatagatttaactggagtggaatttcaatgcattttttctctgaattctctgcatttgatgcacaatgttcatactttggacccctttgcagGAACGGGATACCTGACAGCATGCTTTGCCTTGATGGTTGGACCCCAAGGCCGTGCTATTGGCGTGGAACATATTCCTGAGTTGGTTTCTTTTTCAATCGA
      ||   |||     |  |    |   | |    | ||      | | | |   ||  || |||||         ||||  |  |||       |||||||| || |||||||| || || ||||||||  |||||||||||||  |||| || ||  |||| || |||||||| || ||||||||| ||  ||| |  ||
tgccaggcagttatcccagtccacgaagcaagcaggccctatattagatatttgttgtttaact-cattttgcctgtt-tgtttctgattta---ttttttgcagGCACTGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGAAGGGCGAGCAGTTGGTGTCGAACATATCCCAGAGTTGGTTGCTACTTCTACTGA

upper sequence: GLYMA05G02810.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G48330.1 (Arabidopsis thaliana), 3'ss of exon 2
tgctactatatagatttaactggagtggaatttcaatgcattttttctctgaattctctgcatttgatgcacaatgttcatactttggacccctttgcagGAACGGGATACCTGACAGCATGCTTTGCCTTGATGGTTGGACCCCAAGGCCGTGCTATTGGCGTGGAACATATTCCTGAGTTGGTTTCTTTTTCAATCGA
                        ||    |||   | |  || ||   | | || | | ||||            ||   |  |        ||   ||| || || ||| | || || ||||||||  | ||||||||| || |||| ||||||||||| ||||||||||||||||| |||||  ||| |||  |  |
------------------------gtttgttttactttctcttcttgaattagttttgtacattcttcttcttgcttttgaatatgatgaattttgatagGGACCGGGTACTTAACTGCTTGCTTTGCGGTTATGGTTGGAACCGAAGGGCGTGCTATTGGTGTGGAACATATTCCTGAATTGGTGGCTTCTTCTGTTAA

upper sequence: GLYMA05G02810.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv17s0000g09690.t01 (Vitis vinifera), 3'ss of exon 2
tgctactatatagatttaactggagtg---gaatttcaatgcattttttctctgaattctctgcatttgatgcacaatgttcatactttggacccctttgcagGAACGGGATACCTGACAGCATGCTTTGCCTTGATGGTTGGACCCCAAGGCCGTGCTATTGGCGTGGAACATATTCCTGAGTTGGTTTCTTTTTCAATCGA
| |    ||  | ||    ||| |||    | |||         ||| |   | ||   |||  |||   ||  || | ||  |  |||        ||  ||||||||| ||  ||||||| ||||||||  ||||||||||||| |||||  ||||  |||| || ||||| || |||||||||||| ||| ||||||| |
tacagaaatgcaaatcct-ctgcagtttctggattctgcatttctttgtgattaaagattctatattacctgaccatttttttttttttt--ttaaattttagGAACGGGGTATTTGACAGCCTGCTTTGCACTGATGGTTGGACCACAAGGTTGTGCAGTTGGAGTAGAACACATACCTGAGTTGGTTGCTTCTTCAATCAA

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|151406312|gb|EV276127.1|EV276127
EST:     GCTTGAGAAGAATTTGCAACCTGGAATGCGTGTTCTTGACGTTGGCTCCG                         GAACGGGATACCTGACAGCATGCTTTGCCTTGATGGTTGGACCCCAAGGCC
genomic: GCTTGAGAAGAATTTGCAACCTGGAATGCGTGTTCTTGACGTTGGCTCCGgtatagttca ... ccctttgcagGAACGGGATACCTGACAGCATGCTTTGCCTTGATGGTTGGACCCCAAGGCC
EST: gi|298198196|gb|HO039735.1|HO039735
EST:     GCTTGAGAAGAATTTGCAACCTGGAATGCGTGTTCTTGACGTTGGCTCCG                         GAACGGGATACCTGACAGCATGCTTTGCCTTGATGGTTGGACCCCAAGGCC
genomic: GCTTGAGAAGAATTTGCAACCTGGAATGCGTGTTCTTGACGTTGGCTCCGgtatagttca ... ccctttgcagGAACGGGATACCTGACAGCATGCTTTGCCTTGATGGTTGGACCCCAAGGCC
EST: gi|151406582|gb|EV276397.1|EV276397
EST:     GCTTGAGAAGAATTTGCAACCTGGAATGCGTGTTCTTGACGTTGGCTCCG                         GAACGGGATACCTGACAGCATGCTTTGCCTTGATGGTTGGACCCCAAGGCC
genomic: GCTTGAGAAGAATTTGCAACCTGGAATGCGTGTTCTTGACGTTGGCTCCGgtatagttca ... ccctttgcagGAACGGGATACCTGACAGCATGCTTTGCCTTGATGGTTGGACCCCAAGGCC
EST: gi|192304333|gb|FG996459.1|FG996459
EST:     GCTTGAGAAGAATTTGCAACCTGGAATGCGTGTTCTTGACGTTGGCTCCG                         GAACGGGATACCTGACAGCATGCTTTGCCTTGATGGTTGGACCCCAAGGCC
genomic: GCTTGAGAAGAATTTGCAACCTGGAATGCGTGTTCTTGACGTTGGCTCCGgtatagttca ... ccctttgcagGAACGGGATACCTGACAGCATGCTTTGCCTTGATGGTTGGACCCCAAGGCC
EST: gi|151405371|gb|EV275185.1|EV275185
EST:     GCTTGAGAAGAATTTGCAACCTGGAATGCGTGTTCTTGACGTTGGCTCCG                         GAACGGGATACCTGACAGCATGCTTTGCCCTGATGGTTGGACCCCAAGGCC
genomic: GCTTGAGAAGAATTTGCAACCTGGAATGCGTGTTCTTGACGTTGGCTCCGgtatagttca ... ccctttgcagGAACGGGATACCTGACAGCATGCTTTGCCTTGATGGTTGGACCCCAAGGCC
EST: gi|151401850|gb|EV271663.1|EV271663
EST:     GCTTGAGAAGAATTTGCAACCTGGAATGCGTGTTCTTGACGTTGGCTCCG                         GAACGGGATACCTGACAGCATGCTTTGCCTTGATGGTTGGACCCCAAGGCC
genomic: GCTTGAGAAGAATTTGCAACCTGGAATGCGTGTTCTTGACGTTGGCTCCGgtatagttca ... ccctttgcagGAACGGGATACCTGACAGCATGCTTTGCCTTGATGGTTGGACCCCAAGGCC
EST: gi|15813132|gb|BI785407.1|BI785407
EST:     GCTTGAGAAGAATTTGCAACCTGGAATGCGTGTTCTTGACGTTGGCTCCG                         GAACGGGATACCTGACAGCATGCTTTGCCTTGATGGTTGGACCCCAAGGCC
genomic: GCTTGAGAAGAATTTGCAACCTGGAATGCGTGTTCTTGACGTTGGCTCCGgtatagttca ... ccctttgcagGAACGGGATACCTGACAGCATGCTTTGCCTTGATGGTTGGACCCCAAGGCC
EST: gi|9440177|gb|BE440687.1|BE440687
EST:     GCTTGAGAAGAATTTGCAACCTGGAATGCGTGTTCTTGACGTTGGCTCCG                         GAACGGGATACCTGACAGCATGCTTTGCCTTGATGGTTGGACCCCAAGGCC
genomic: GCTTGAGAAGAATTTGCAACCTGGAATGCGTGTTCTTGACGTTGGCTCCGgtatagttca ... ccctttgcagGAACGGGATACCTGACAGCATGCTTTGCCTTGATGGTTGGACCCCAAGGCC
EST: gi|151395357|gb|EV265228.1|EV265228
EST:     GCTTGAGAAGAATTTGCAACCTGGAATGCGTGTTCTTGACGTTGGCTCCG                         GAACGGGATACCTGACAGCATGCTTTGCCTTGATGGTTGGACCCCAAGGCC
genomic: GCTTGAGAAGAATTTGCAACCTGGAATGCGTGTTCTTGACGTTGGCTCCGgtatagttca ... ccctttgcagGAACGGGATACCTGACAGCATGCTTTGCCTTGATGGTTGGACCCCAAGGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctgaattctctgcatttgatgcacaatgttcatactttggacccctttgcagGAACGGGATACCTGACAGCATGCTTTGCCTTGATGGTTGGACCCCAAGGCCGTGCTATTGGCGTGGAACATATTCCTGAGTTGGTTTCTTTTTCAATCGA
                atttgat  putative branch site (score: 5)
                                            cccctttgc  putative PPT
                atttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctactatatagatttaactggagtggaatttcaatgcattttttctctgaattctctgcatttgatgcacaatgttcatactttggacccctttgcagGAACGGGATACCTGACAGCATGCTTTGCCTTGATGGTTGGACCCCAAGGCCGTGCTATTGGCGTGGAACATATTCCTGAGTTGGTTTCTTTTTCAATCGA

tgctact
- - - - - - - - - - -ggagtgg
- - - - - - - - - - - - - - - - -caatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgcac