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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGGGGATCAGTGAGTGCTCAAGAAGTTTCACCAAATGAATTATACAGCCAGTCTGCAATATACATTGCTGCTGCTCATGCATTGAAACCAAATTATTCAgtaagaagccacagtctatttgtcttgccttgtacatatttattggctttatgcattttttggattagaaatatttttaatctagttaatttcttcctccaattttaatcatgcaatcagctcattattattattaatttggtgtaacag

Basic information

species Glycine max
transcript GLYMA20G35990.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G35990.2 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os03g02270.1 (Oryza sativa), 5'ss of exon 10
---TGGGGGATCAGTGAGTGCTCAAGAAGTTTCACCAAATGAATTATACAGCCAGTCTGCAATATACATTGCTGCTGCTCATGCATTGAAACCAAATTATTCAgtaagaagccacagtctatttgtcttgccttgtacatatttattggctttatgcattttttggattagaaatatttttaatctagttaatttcttcctccaattttaatcatgcaatcagctcattattattattaatttggtgtaacag
      | | || |   || |   ||| || || |||||||| || ||||| ||||| || || ||  | || ||||||||||||||||| ||||||||||||||| |         ||| |||| ||  |  ||    ||  | |     ||  | ||    ||||    | | || |  || | |   ||        ||  |                                                
TACAATGAGGTCTGCAGGTCC---AGATGTCTCTCCAAATGACTTGTACAGTCAGTCCGCCATTTATGTCGCAGCTGCTCATGCATTGAAGCCAAATTATTCAgtatgtgtttttcctctctttgact-actctgcctttaaatttccttattggg-atgccctggaaggtagagatgtgaaaacaaagcaagaagagtttcata------------------------------------------------

upper sequence: GLYMA20G35990.2 (Glycine max), 5'ss of exon 10
lower sequence: AT5G41950.1 (Arabidopsis thaliana), 5'ss of exon 10
TGGGGGATCAGTGAGTGCTCAAGAAGTTTCACCAAATGAATTATACAGCCAGTCTGCAATATACATTGCTGCTGCTCATGCATTGAAACCAAATTATTCAgtaagaagccacagtctatttgtcttgc-cttgtacatatttattggctttatgcattttttggattagaaatatttttaatctagttaatttcttcctccaattttaatcatgcaatcagctcattattattattaatttggtgtaacag
|||||| ||||  |  |   ||||  |  | ||   ||| ||||||||||||||||| || ||||||||||| || ||| ||||||| |||| ||| ||||||||    |  | | | |   | |||  || | |   |  | || |  | || | | | |   || |||   | |   |  |||    |||  |  || |||     ||| |    | ||     |  | ||  |  |   |        
TGGGGGTTCAGGCAACGGCAAAGACATGCCCCCTGGTGAGTTATACAGCCAGTCTGCCATCTACATTGCTGCAGCGCATTCATTGAAGCCAAGTTACTCAgtaag----cttattatctccattttgtactggaatcaagatgtttgaatcatacttgtataaaataagattgaatgccagactaa--gattcatcgcttcaac----atctttgggttaggctgatccttttcctggtccag--------

upper sequence: GLYMA20G35990.2 (Glycine max), 5'ss of exon 10
lower sequence: Vv02s0025g02520.t01 (Vitis vinifera), 5'ss of exon 10
TGGGGGATCAGTGAGTGCTCAAGAAGTTTCACCAAATGAATTATACAGCCAGTCTGCAATATACATTGCTGCTGCTCATGCATTGAAACCAAATTATTCAgtaagaagccacagtctatttgtct-tgccttgtacatatttattggctttatgcattttttggattagaaatatttttaatctagttaatttcttcctccaattttaatcatgcaatcagctcattattattattaatttggtgtaacag
 |  ||  |  |    | | |||||||||| || ||||| || || ||||| ||||| || |||||||| |||||||||||||||||||||||||| |||||||||| || |  ||| | ||| | ||  ||| |       | |     | || |     || |   |||| | |  ||||    || | || | | |    ||                                              
GGCTGGGGCGATAGTAGATAAAGAAGTTTCCCCTAATGAGTTGTATAGCCAATCTGCTATCTACATTGCAGCTGCTCATGCATTGAAACCAAATTACTCAgtaagaaacctct-tctctgtgtgtgtgtgttgaaagatcaaactaaggatgtgaaa---atgaacgggaaagaat--taatagtctttagttttccatgtgctta---------------------------------------------

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|14205428|gb|BG839106.1|BG839106
EST:     AGTCTGCAATATACATTGCTGCTGCTCATGCATTGAAACCAAATTATTCA                         GTTTATAGCAGTGCCTTGCGGTTGGTGCGTTCTATG
genomic: AGTCTGCAATATACATTGCTGCTGCTCATGCATTGAAACCAAATTATTCAgtaagaagcc ... ggtgtaacagGTTTATAGCAGTGCCTTGCGGTTGGTGCGTTCTATG
EST: gi|12773285|gb|BG238212.1|BG238212
EST:     AGTCTGCAATATACATTGCTGCTGCTCATGCATTGAAACCAAATTATTCA                         GTTTATAGCAGTGCCTTGCGGTTGGTGCGTTCTATG
genomic: AGTCTGCAATATACATTGCTGCTGCTCATGCATTGAAACCAAATTATTCAgtaagaagcc ... ggtgtaacagGTTTATAGCAGTGCCTTGCGGTTGGTGCGTTCTATG
EST: gi|22932072|gb|BU549211.1|BU549211
EST:     GTCTGCAATATACA-TGCNNNCTGCTCATGCATTGAAACCAAATTATTCA                         GTTTATAGCAGTGCCTTGCGGTTGGTGCGTTCTATG
genomic: GTCTGCAATATACATTGC-TGCTGCTCATGCATTGAAACCAAATTATTCAgtaagaagcc ... ggtgtaacagGTTTATAGCAGTGCCTTGCGGTTGGTGCGTTCTATG
EST: gi|298173874|gb|HO017210.1|HO017210
EST:     AGTCTGCAATATACATTGCTGCTGCTCATGCATTGAAACCAAATTATTCA                         GTTTATAGCAGTGCCTTGCGGTTGGTGCGTTCTATG
genomic: AGTCTGCAATATACATTGCTGCTGCTCATGCATTGAAACCAAATTATTCAgtaagaagcc ... ggtgtaacagGTTTATAGCAGTGCCTTGCGGTTGGTGCGTTCTATG
EST: gi|254324005|gb|GR836237.1|GR836237
EST:     AGTCTGCAATATACATTGCTGCTGCTCATGCATTGAAACCAAATTATTCA                         GTTTATAGCAGTGCCTTGCGGTTGGTGCGTTCTATG
genomic: AGTCTGCAATATACATTGCTGCTGCTCATGCATTGAAACCAAATTATTCAgtaagaagcc ... ggtgtaacagGTTTATAGCAGTGCCTTGCGGTTGGTGCGTTCTATG
EST: gi|16347758|gb|BI973353.1|BI973353
EST:     AGTCTGCAATATACATTGCTGCTGCTCATGCATTGAAACCAAATTATTCA                         GTTTATAGCAGTGCCTTGCGGTTGGTGCGTTCTATG
genomic: AGTCTGCAATATACATTGCTGCTGCTCATGCATTGAAACCAAATTATTCAgtaagaagcc ... ggtgtaacagGTTTATAGCAGTGCCTTGCGGTTGGTGCGTTCTATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGGGGATCAGTGAGTGCTCAAGAAGTTTCACCAAATGAATTATACAGCCAGTCTGCAATATACATTGCTGCTGCTCATGCATTGAAACCAAATTATTCAgtaagaagccacagtctatttgtcttgccttgtacatatttattggctttatgcattttttggattagaaatatttttaatctagttaatttcttcctccaattttaatcatgcaatcagctcattattattattaatttggtgtaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT