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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactcctcctccgttaaaccctaacctctctcttccttctattccacgcatccacgatcacactaatttttcagattcgccttccaaattcctaattgattcggatccaatttcgattcgtcgcagGACTCGAACAATCTCAGGGATGCTTTGAAGTATTCGGCTCAGATGCTCTCCGAGCTCAGGACTTCCAAGCTTTCTCCTCACAAGTACTACGAACTAT

Basic information

species Glycine max
transcript GLYMA11G08390.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G08390.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g58700.1 (Oryza sativa), 3'ss of exon 1
gtaactcctcctccgttaaaccctaacctctctcttccttctattccacgcatccacgatcacactaatttttcagattcgccttccaaattcctaattgattcggatccaatttcgattcgt-cgcagGACTCGAACAATCTCAGGGATGCTTTGAAGTATTCGGCTCAGATGCTCTCCGAGCTCAGGACTTCCAAGCTTTCTCCTCACAAGTACTACGAACTAT
                                       |     || |  | ||       |     | | |  || |  ||   |    |  | ||     | ||||      | |||||| ||||||| |||||||| |||| ||||||  | ||||| ||||| |||||||||||||||||  |||| ||   ||| || || |||||||| || || ||||
--------------------------------------gtaaggcccgccaaaccctagctccctcggtctgt--gactgccccctctcgcttatcatctgccccgatcgg----caattcgtgcgcagGATTCGAACAACCTCAAGGATGCGCTCAAGTACTCGGCGCAGATGCTCTCCGAGCTGCGGACCTCGCGGCTCTCGCCGCACAAGTATTATGATCTAT

upper sequence: GLYMA11G08390.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G17790.1 (Arabidopsis thaliana), 3'ss of exon 1
gtaactcctcctccgttaaaccctaacctctctcttccttctattccacgcatccacgatcacactaatttttcagattcg--ccttcca-----------aatt--------cctaatt---gattcggatccaatttcgattcgtcgc---------agGACTCGAACAATCTCAGGGATGCTTTGAAGTATTCGGCTCAGATGCTCTCCGAGCTCAGGACTTCCAAGCTTTCTCCTCACAAGTACTACGAACTAT
|||| | || ||        | ||     || || |   ||| |  |     ||   ||       || ||| || ||| |  | || ||           ||||        |||||||   | || ||    ||  | |  | ||            |||||||||| ||||| |  |||||| | ||||||||||||||||||||   |||| |  ||||||| ||||| || |||||||||||||| || ||||
gtaaattctgcttttcccttcacttcttcctttcgtttctctgtgactattttcgttgaaattgagaaatttccaaatttgtacttttcattgatgtgtagaattgaaggaaccctaattttggttttgggaaaaaacttgtcttgtttttggttaattagGACTCGAATAATCTGAAAGATGCTCTCAAGTATTCGGCTCAGATGCTAAGCGAGTTACGGACTTCGAAGCTATCACCTCACAAGTACTATGATCTAT

upper sequence: GLYMA11G08390.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G51310.1 (Arabidopsis thaliana), 3'ss of exon 1
gtaactcctcctccgttaaaccctaacctctctcttccttctattccacgcatccacgatcacactaatttttcagattc--gccttccaaattcctaattgattcggatccaatttcgatt----cgtcgcagGACTCGAACAATCTCAGGGATGCTTTGAAGTATTCGGCTCAGATGCTCTCCGAGCTCAGGACTTCCAAGCTTTCTCCTCACAAGTACTACGAACTAT
                         ||| |||  | || |||  ||    | ||  | ||||   |    ||   |||    |    | |||| |   |||| ||   | | ||| || | |    | ||||||||||| ||||||||||  || ||| | |||| ||| ||||| ||||||  ||||||  | |||||||||||||||||||| || ||||| ||||| |
-----------------------gtaccactccttcccctctcctctcttcttcatcaatcaattttccattcgggatcttagaaccctaaatcctgcattgttttctaacgaatctccaatttatcctcgcagGACTCCAACAATCTCAAAGACGCTCTAAAGTTTTCTGCTCAAATGCTCAGCGAGCTTCGTACTTCCAAGCTTTCTCCTCATAAATACTATGAACTCT

upper sequence: GLYMA11G08390.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0023g03870.t01 (Vitis vinifera), 3'ss of exon 1
gtaactcctcctccgttaaaccctaacctctctcttccttctattccacgca-------tccacgatcacactaatttttcagattcgccttcc----aaattc---ctaattgattcggatccaatttcgatt-cgtcgcagGACTCGAACAATCTCAGGGATGCTTTGAAGTATTCGGCTCAGATGCTCTCCGAGCTCAGGACTTCCAAGCTTTCTCCTCACAAGTACTACGAACTAT
||||| |   |||| |     ||||   |   | |  |      |  | | |        |||   ||   |   |||| |   ||  |||| |    |||  |   ||||||  |||   |    |||   || | || ||||||||||||||||| ||||| ||  | || || |||||||||||||| ||||||||  | ||||| | ||| || ||||| || |||||||||||||
gtaacacgctctccttctctacctatgtttggtttgacggaagatagaggaaaatgttccccagattcgttccttttttccttttttccctttctgagaaacgcagcctaattttttcccttttttttttttttacttctcagGACTCGAACAATCTGAGGGACGCCCTCAAATACTCGGCTCAGATGCTTTCCGAGCTTCGTACTTCGAGGCTCTCCCCTCATAAATACTACGAACTAT

upper sequence: GLYMA11G08390.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S456_14V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaactcctcctccgttaaaccctaacctctctcttccttctattccacgcatccacgatcacactaatttttcagattcgccttccaaattcctaattgattcggatccaatttcgattcgtcgcagGACTCGAACAATCTCAGGGATGCTTTGAAGTATTCGGCTCAGATGCTCTCCGAGCTCAGGACTTCCAAGCTTTCTCCTCACAAGTACTACGAACTAT
                  || |  ||  |    |    | | || |   |  ||   | |||  ||     | ||||          |     ||||   |||    |   |||  | ||    ||||||    || ||| |  | || ||| | |||||||||||||||||| | || ||||| ||||| |||||||| || || || |||||||| || || |
----------------ggaatctcaaaatgctaccagatgcaatact-tgtgtcacaggtcatgct---cctgcagaaaa----caaaggagactaagcaatt----ttttattatgtttgactgcagGATAGCAATAATTTGCGAGAAGCTCTTAAGTATTCGGCTCAGATGTTGTCTGAGCTGAGGACGTCCAAGCTGTCACCACAAAAGTACTATGAGCTCT

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|193594995|gb|FK546812.1|FK546812
EST:     CCGGAATCGCCGGCCTTCAGCAGAATTCCTTCTACATGCACCGTGCATTG                         GACTCGAACAATCTCAGGGATGCTTTGAAGTATTCGGCTCAGATGCTCTCC
genomic: CCGGAATCGCCGGCCTTCAGCAGAATTCCTTCTACATGCACCGTGCATTGgtaactcctc ... ttcgtcgcagGACTCGAACAATCTCAGGGATGCTTTGAAGTATTCGGCTCAGATGCTCTCC
EST: gi|254342605|gb|GR858767.1|GR858767
EST:     CCGGAATCGCCGGCCTTCAGCAGAATTCCTTCTACATGCACCGTGCATTG                         GACTCGAACAATCTCAGGGATGCTTTGAAGTATTCGGCTCAGATGCTCTCC
genomic: CCGGAATCGCCGGCCTTCAGCAGAATTCCTTCTACATGCACCGTGCATTGgtaactcctc ... ttcgtcgcagGACTCGAACAATCTCAGGGATGCTTTGAAGTATTCGGCTCAGATGCTCTCC
EST: gi|15285344|gb|BI469235.1|BI469235
EST:     CCGGAATCGCCGGCCTTCAGCAGAATTCCTTCTACATGCACCGTGCATTG                         GACTCGAACAATCTCAGGGATGCTTTGAAGTATTCGGCTCAGATGCTCTCC
genomic: CCGGAATCGCCGGCCTTCAGCAGAATTCCTTCTACATGCACCGTGCATTGgtaactcctc ... ttcgtcgcagGACTCGAACAATCTCAGGGATGCTTTGAAGTATTCGGCTCAGATGCTCTCC
EST: gi|208286415|gb|GE084317.1|GE084317
EST:     CCGGAATCGCCGGCCTTCAGCAGAATTCCTTCTACATGCACCGTGCATTG                         GACTCGAACAATCTCAGGGATGCTTTGAAGTATTCGGCTCAGAT
genomic: CCGGAATCGCCGGCCTTCAGCAGAATTCCTTCTACATGCACCGTGCATTGgtaactcctc ... ttcgtcgcagGACTCGAACAATCTCAGGGATGCTTTGAAGTATTCGGCTCAGAT
EST: gi|120531471|gb|EH259604.1|EH259604
EST:     CCGGAATCGCCGGCCTTCAGCAGAATTCCTTCTACATGCACCGTGCATTG                         GACTCGAACAATCTCAGGGATGCTTTGAAGTATTCGGCTCAGATGCTCTCC
genomic: CCGGAATCGCCGGCCTTCAGCAGAATTCCTTCTACATGCACCGTGCATTGgtaactcctc ... ttcgtcgcagGACTCGAACAATCTCAGGGATGCTTTGAAGTATTCGGCTCAGATGCTCTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagattcgccttccaaattcctaattgattcggatccaatttcgattcgtcgcagGACTCGAACAATCTCAGGGATGCTTTGAAGTATTCGGCTCAGATGCTCTCCGAGCTCAGGACTTCCAAGCTTTCTCCTCACAAGTACTACGAACTAT
                     taattgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactcctcctccgttaaaccctaacctctctcttccttctattccacgcatccacgatcacactaatttttcagattcgccttccaaattcctaattgattcggatccaatttcgattcgtcgcagGACTCGAACAATCTCAGGGATGCTTTGAAGTATTCGGCTCAGATGCTCTCCGAGCTCAGGACTTCCAAGCTTTCTCCTCACAAGTACTACGAACTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC