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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtctcattttgtttattataaagtttggttaacgttttttttttataaacattaggttaacaatttgataacgttgtatttgttgtgtatttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGTGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG

Basic information

species Glycine max
transcript GLYMA11G08380.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G08380.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 1
-----------------gtctcattttgtttattataaagtttggttaac---gttttttttttataaacattaggtta---acaatttgataacgttgtatttgttgtgtatttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGTGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG
                   |    ||| |||  |||    ||   || |    | || |    ||||   ||| || |    |||   | | || |||||||   || |  |||    ||||||||||||| ||||||||||| || || || ||||||||||||||||| |||||   ||  |||||||| || |||||||||||||| |
gtattcatcaatcattctccctcctttttttgatatctgattcatttgattctgattgtgccatatatgaattgggatccatacatactaaaaatgttgtatacatt-tccatt--ggaacagGATTATGTTCCGACTGTTTTCGATAACTTTAGTGCAAATGTGGTTGTTAATGGAGCCACGGTGAATCTTGGATTGTGGGATACTGCAG

upper sequence: GLYMA11G08380.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G17800.2 (Arabidopsis thaliana), 3'ss of exon 2
--------------------------------------------------------------------------------------gtctcattttgtt-tattataaagtttggttaacgttttttttttataaacattaggtta---acaatttgataacgttgtatttgttgtgtattta---aaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGTGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG
                                                                                        |  |  ||||   | || |    | | |  |   |||||||||      || ||| |      |  ||  || |    |   | ||||  ||| |     ||||||||||||| ||||||||||| || || || || |||||||||||||| |||||   || ||||||||| ||  | |||||||| || |
gtataatgttccttccttagattgaatcatattctgtgttctgtgaattacaagcttcaaaattgtcttctctattgattgatgagaccaaagcttgtggcaatacatgaatcgatccataatttttttttggtgttatgaggatttgtggagctttgtatctcattgaatcttgtaaattcatgtggaacagGATTATGTACCGACTGTTTTCGATAACTTTAGCGCAAATGTGGTTGTTAATGGAGCCACTGTGAATCTTGGGCTATGGGATACCGCAG

upper sequence: GLYMA11G08380.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G51300.1 (Arabidopsis thaliana), 3'ss of exon 1
gtctcattttgtt-tattataaagtttggttaacgtttttt-ttttataaacattaggttaacaatttgataacgttgtatttgttgtgtatttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGTGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG
          ||| | |   ||   ||  || | |||| || ||| || | ||  |    ||||  |   | | |||   | | |  | | |  | | ||||||||||||||| || ||||| || ||||||||||| ||||| || || ||||| |||| ||||||||| || |||||||| ||||| |
----------gttatgtcccaattattctttcatgtttcttgtttcattaccacaacaacaacatatc--tcatgtttcttgtttcttttgtggatatacagGATTATGTGCCTACCGTTTTCGATAATTTCAGTGCCAATGTTGTGGTTAATGGAAGCACTGTGAATCTTGGATTGTGGGACACTGCAG

upper sequence: GLYMA11G08380.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 2
-----gtctcattttgttta-ttataaagtttggttaacgttttttttttataaacattaggttaacaatttgataacgttgtatttgttgtgtatttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGTGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG
     |  || |       | |||   | || || | |   ||||||||  |  |   ||||  ||  | ||   |  ||| ||||| |    ||||   ||||||||||||||||| |||||||| |||||||||||||||||||||||||||||||||  || ||| || || || ||||||||||||||||
gaaaagaatcttccaaaaaaattaaggacttcggatcattcttttttttctttga---taggcaaaggactt---attgttttatttttgaattattgggaaacagGATTATGTGCCAACTGTTTTCGACAATTTCAGTGCAAATGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTG

upper sequence: GLYMA11G08380.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ09765 (Selaginella moellendorffii), 3'ss of exon 1
gtctcattttgtttattataaagtttggttaacgttttttttttataaacattaggttaacaatttgataacgttgtatttgttgtgtatttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGTGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG
                  | |  ||| |||   ||| |||  || |          |    || |   |   | ||   | |||        |  |||||||||| || || ||||||||||| || ||||| || |||||||||||| |||| | || ||| || || ||  | ||||| |||||||
-----------------gtgagatttcgttt-tgttctttcctttt----------tctctaactctcttgggctgggatcgtt-------catcaacagGATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTG

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|5606072|gb|AI900170.1|AI900170
EST:     TGGGCAAAACCTGCTTGCTTATTTCCTACACCAGCAACACTTTCCCCACC                         GATTATGTGCCGACTGTTTTTGACAATTTCAGTGCAAATGTGGTTGTCAAT
genomic: TGGGCAAAACCTGCTTGCTTATTTCCTACACCAGCAACACTTTCCCCACCgttagttctt ... ttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGTGCAAATGTGGTTGTCAAT
EST: gi|58017044|gb|CX703786.1|CX703786
EST:     TACACCAGCAACACTTTCCCCACC                         GATTATGTGCCGACTGTTTTTGACAATTTCAGTGCAAATGTGGTTGTCAAT
genomic: TACACCAGCAACACTTTCCCCACCgttagttctt ... ttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGTGCAAATGTGGTTGTCAAT
EST: gi|19054119|gb|BM732786.1|BM732786
EST:     TGGGCAAAACCTGTTTGCTTATTTCCTACACCAGCAACACTTTTCCCACC                         GATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAAT
genomic: TGGGCAAAACCTGCTTGCTTATTTCCTACACCAGCAACACTTTCCCCACCgttagttctt ... ttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGTGCAAATGTGGTTGTCAAT
EST: gi|58016803|gb|CX703545.1|CX703545
EST:     GGCAAAACCTGCTTGCTTATTTCTTACACCAGCAACACTTTCCCCACC                         GATTATGTGCCGACTGTTTTTGACAATTTCAGTGCAAATGTGGTTGTCAAT
genomic: GGCAAAACCTGCTTGCTTATTTCCTACACCAGCAACACTTTCCCCACCgttagttctt ... ttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGTGCAAATGTGGTTGTCAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaacattaggttaacaatttgataacgttgtatttgttgtgtatttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGTGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG
                    tgataac  putative branch site (score: 2)
                               tatttgttgtgtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctcattttgtttattataaagtttggttaacgttttttttttataaacattaggttaacaatttgataacgttgtatttgttgtgtatttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGTGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA