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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttttaaatcacttctcatttattttcaacttgcattttgaatgtctcttgaattttctccctgattcattattgcaatgttactcaaattacgtgcagaatgcatatttaaactttccaattgtatcataatttatattctgcacttgctgtccagTTACTGGAGGAAAATTTGGACTGGGAAGATGTGCAATGGTCGCAAACAGGTGTTTGGATTGCTGGAAAGGAATATACCTTGGCACGAGTGCATTTCTTGT

Basic information

species Glycine max
transcript GLYMA10G31960.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G31960.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os07g29450.1 (Oryza sativa), 3'ss of exon 11
gtatttttaaatcacttctcatttattttcaacttgcattttgaatgtctcttgaattttctccctgattcattattgcaatgttactcaaattacgtgcagaatgcatatttaaactttccaattgtatcataatttatattctgcacttgctgtccagTTACTGGAGGAAAATTTGGACTGGGAAGATGTGCAATGGTCGCAAACAGGTGTTTGGATTGCTGGAAAGGAATATACCTTGGCACGAGTGCATTTCTTGT
|| | || | | | | ||| |||| | || | | | ||||| || | | | || | || | || | || || || ||| | ||| |||| |||||||| ||||| |||||||| |||||||| || ||||||||| ||||||||||||||||| | | || |||||||||||| | |
----------------------------------------------------gtaacgtcctgctt--tctaacattaaaatggtggataattcgcatacagaaaccaca-----attctcacacggtttt----cttgttacctcgac--gcaacgcagGTGCTGCAGGATAATTTGGAATGGGAGGATGTGCAGTGGTCGCAGACTGGTGTTTGGGTTGCTGGAAAGGAATATCCTCTCGCCCGAGTGCATTTCCTAT

upper sequence: GLYMA10G31960.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G08450.2 (Arabidopsis thaliana), 3'ss of exon 11
gtatttttaaatcacttctcatttattttcaacttgcattttgaatgtctcttgaattttctccctgattcattattgcaatgttactcaaattacgtgcagaatgcatatttaaactttccaattgtatcataatttatattctgcacttgctgtccagTTACTGGAGGAAAATTTGGACTGGGAAGATGTGCAATGGTCGCAAACAGGTGTTTGGATTGCTGGAAAGGAATATACCTTGGCACGAGTGCATTTCTTGT
| | || | |||| | |||| || | | ||| | | | |||| | | | | | ||| || | | | || | ||||||| ||| | || ||||||||||| || ||||| ||||| |||||||||||||||||||| || || || | || || || ||||| | |
---------------------------------------------------------------gttaacatttttctccaatttgactcttcttgttttgaaaattctt-tataaaacaaatgctgatgatgtgttgtggattttggaatggag---tagGTGTTGGAGGAGAATCTTGATTGGGAAGATGTACAGTGGTCACAAACTGGTGTTTGGATTGCTGGAAAAGAGTACACTCTTGCTCGTGTTCATTTTCTCT

upper sequence: GLYMA10G31960.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv07s0130g00270.t01 (Vitis vinifera), 3'ss of exon 10
gtatttttaaatcacttctcatttattttcaacttgcattttgaatgtctcttgaattttctccctgattcattattgcaatgttactcaaattacgtgcagaatgcatatttaaactttccaattgtatcataat-ttatattctgcacttgctgtccagTTACTGGAGGAAAATTTGGACTGGGAAGATGTGCAATGGTCGCAAACAGGTGTTTGGATTGCTGGAAAGGAATATACCTTGGCACGAGTGCATTTCTTGT
| | | | | || | || ||| | || | ||| | | | | || |||| || || || | | | || ||| | ||||||| ||| | |||||||| |||||||| ||||| ||||| |||||||| || ||||||||||||||| | | || ||||| |||||| | |
----------------------------------------------------------taccaaatatccaaatggtgatgagctattcacaaaactt---aaatatgtgcctggtaatccattctgaatcagaaccttggatctttttttggttgaacagGTCTTGGAGGAGAATCTCGACTGGGAGGATGTGCAGTGGTCCCAAACTGGTGTTTGTATAGCTGGAAAGGAATATGCGCTTGCTCGAGTTCATTTCCTAT

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|51343542|gb|CO984275.1|CO984275
EST:     AGAAACTGATGCGTACAATTGGCATCCCTTTGCCTATTGAACATATAGAG                         TTACTGGAGGAAAATTTGGACTGGGAAGATGTGCAATGGTCGCAAACAGGT
genomic: AGAAACTGATGCGTACAATTGGCATCCCTTTGCCTATTGAACATATAGAGgtatttttaa ... tgctgtccagTTACTGGAGGAAAATTTGGACTGGGAAGATGTGCAATGGTCGCAAACAGGT
EST: gi|208028852|gb|GD828766.1|GD828766
EST:     AGAAACTGATGCGTACAATTGGCATCCCTTTGCCTATTGAACATATAGAG                         TTACTGGAGGAAAATTTGGACTGGGAAGATGTGCAATGGTCGCAAACA
genomic: AGAAACTGATGCGTACAATTGGCATCCCTTTGCCTATTGAACATATAGAGgtatttttaa ... tgctgtccagTTACTGGAGGAAAATTTGGACTGGGAAGATGTGCAATGGTCGCAAACA
EST: gi|208069252|gb|GD869160.1|GD869160
EST:     AGAAACTGATGCGTACAATTGGCATCCCTTTGCCTATTGAACATATAGAG                         TTACTGGAGGAAAATTTGGACTGGGAAGGTGTGCAATGGTCGCAAACAGGT
genomic: AGAAACTGATGCGTACAATTGGCATCCCTTTGCCTATTGAACATATAGAGgtatttttaa ... tgctgtccagTTACTGGAGGAAAATTTGGACTGGGAAGATGTGCAATGGTCGCAAACAGGT
EST: gi|7235227|gb|AW570556.1|AW570556
EST:     AGAAACTGATGCGTACAATTGGCATCCCTTTGCCTATTGAACATATAGAG                         TTACTGGAGGAAAATTTGGACTGGGAAGATGTGCAATGGTCGCAAACAGGT
genomic: AGAAACTGATGCGTACAATTGGCATCCCTTTGCCTATTGAACATATAGAGgtatttttaa ... tgctgtccagTTACTGGAGGAAAATTTGGACTGGGAAGATGTGCAATGGTCGCAAACAGGT
EST: gi|254344049|gb|GR850959.1|GR850959
EST:     AGAAACTGATGCGTACAATTGGCATCCCTTTGCCTATTGAACATATAGAG                         TTACTGGAGGAAAATTTGGACTGGGAAGATGTGCAATGGTCGCAAACAGGT
genomic: AGAAACTGATGCGTACAATTGGCATCCCTTTGCCTATTGAACATATAGAGgtatttttaa ... tgctgtccagTTACTGGAGGAAAATTTGGACTGGGAAGATGTGCAATGGTCGCAAACAGGT
EST: gi|17963267|gb|BM270018.1|BM270018
EST:     AGAAACTGATGCGTACAATTGGCATCCCTTTGCCTATTGAACATATAGAG                         TTACTGGAGGAAAATTTGGACTGGGAAGATGTGCAATGGTCGCAAACAGGT
genomic: AGAAACTGATGCGTACAATTGGCATCCCTTTGCCTATTGAACATATAGAGgtatttttaa ... tgctgtccagTTACTGGAGGAAAATTTGGACTGGGAAGATGTGCAATGGTCGCAAACAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatatttaaactttccaattgtatcataatttatattctgcacttgctgtccagTTACTGGAGGAAAATTTGGACTGGGAAGATGTGCAATGGTCGCAAACAGGTGTTTGGATTGCTGGAAAGGAATATACCTTGGCACGAGTGCATTTCTTGT
                 aattgtatcataattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttttaaatcacttctcatttattttcaacttgcattttgaatgtctcttgaattttctccctgattcattattgcaatgttactcaaattacgtgcagaatgcatatttaaactttccaattgtatcataatttatattctgcacttgctgtccagTTACTGGAGGAAAATTTGGACTGGGAAGATGTGCAATGGTCGCAAACAGGTGTTTGGATTGCTGGAAAGGAATATACCTTGGCACGAGTGCATTTCTTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
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