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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAAGCTGATGTTTTCCACATTCTGTCAGGAATGTGGAAGACTCCAGCTGAGAGGTGTTTCATGTGGATTGGAGGCTTTCGGTCATCCGAACTCCTCAAGgtgagaagtttctcttatctatgttttgtaaatgttttttctggtttgaaaattgcttcactaatatctggttgaacattgattgcattccatgcttccc...

Basic information

species Glycine max
transcript GLYMA03G28320.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G28320.1 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os01g17260.1 (Oryza sativa), 5'ss of exon 8
AAAAGCTGATGTTTTCCACATTCTGTCAGGAATGTGGAAGACTCCAGCTGAGAGGTGTTTCATGTGGATTGGAGGCTTTCGGTCATCCGAACTCCTCAAGg--tgagaagtttctct-tatctatgttttgtaaatg--ttttttctggtttgaaaattgcttcactaatatctggttgaacattgattgcattccatgcttccc
 ||||| ||||| || ||  |  | ||||| ||||||||||| |||||||||||||||||| ||||| | ||||| || ||  ||||||| ||  | ||||  ||  |||| |  |  | |   |||| | ||  ||     |   |   ||| |||   | || ||| || |      ||  ||  |  |||   ||  |    
CAAAGCAGATGTCTTTCATGTGTTATCAGGCATGTGGAAGACACCAGCTGAGAGGTGTTTCTTGTGGCTAGGAGGATTCCGACCATCCGAGCTTTTAAAGgtctgtaaagtcttacgatgttcttgttgtttatttgagccatccttctattgcaaagcccctc-ctattaccaaaaccaatgtttctaccataatattat----

upper sequence: GLYMA03G28320.1 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os01g59350.1 (Oryza sativa), 5'ss of exon 9
AAAAGCTGATGTTTTCCACATTCTGTCAGGAATGTGGAAGACTCCAGCTGAGAGGTGTTTCATGTGGATTGGAGGCTTTCGGTCATCCGAACTCCTCAAGgtgagaagtttctcttatctatgttttgtaaatgttttttctggtttgaaaattgcttcactaatatctggttgaacattgattgcattccatgcttccc---
 ||||| || ||||| ||  | ||||| ||||||||||| || || ||||||||||| ||||||||| | || ||||| || ||||| || || || ||||| ||||  | || ||||   | | |||    |  || || ||       |   |       |||       |||| ||  |||   ||   || | |     
CAAAGCAGACGTTTTTCATGTGCTGTCGGGAATGTGGAAAACCCCTGCTGAGAGGTGCTTCATGTGGCTAGGTGGCTTCCGATCATCTGAGCTTCTTAAGgtaagaatatactattat---tatattgcgcctacttattttgaagcctcacccggaggcaaaatgctgacctgaatatatattattttaattgatccaatat

upper sequence: GLYMA03G28320.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G125243_T02 (Zea mays), 5'ss of exon 11
AAAAGCTGATGTTTTCCACATTCTGTCAGGAATGTGGAAGACTCCAGCTGAGAGGTGTTTCATGTGGATTGGAGGCTTTCGGTCATCCGAACTCCTCAAGgtgagaagtttctcttatctatgttttgtaaatgttttttctggtttgaaaattgcttcactaatatctggttgaacattgattgcattccatg---cttccc----
 ||||| |||||||| ||  | ||||| || ||||||||||| || |||||||| |||||||||||| | || ||||| || ||||| || || || |||||   ||   |||  |   | |||||||  ||||     |    |||    |   |||  ||  |  |    |||||    |   |     |||    ||  |    
TAAAGCAGATGTTTTTCATGTGCTGTCTGGGATGTGGAAGACCCCTGCTGAGAGATGTTTCATGTGGTTAGGTGGCTTCCGATCATCTGAGCTTCTTAAGgtagtaa---tctaatggttttgttttg--aatgcacaattaaatttcttgacctcttggctcttgccc--ctgaactccaaggtccccttatgggagttttcattc

upper sequence: GLYMA03G28320.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G019907_T01 (Zea mays), 5'ss of exon 5
AAAAGCTGATGTTTTCCACATTCTGTCAGGAATGTGGAAGACTCCAGCTGAGAGGTGTTTCATGTGGATTGGAGGCTTTCGGTCATCCGAACTCCTCAAGgtgagaagtttctcttatctatgttttgtaaatgttttttctggtttgaaaattgcttcactaatatctggttgaacattgattgcattccatg---cttccc----
 | | | |||||||| ||  | ||||| || ||||||||||| || |||||||| |||||||||||| | || ||||| || ||||| ||  | || |||||   ||   |||  |   | |||||||  ||||     |    ||||   |   |||  ||  |  |   | || |    |   |     |||    ||  |    
TAGATCAGATGTTTTTCATGTGCTGTCTGGGATGTGGAAGACCCCTGCTGAGAGATGTTTCATGTGGTTAGGTGGCTTCCGATCATCTGAGGTTCTTAAGgtagtaa---tctaatggttttgttttg--aatgcacaattaaatttgttgacctcttggctcttgccc--tcgatctccaaggtccccttatgggagttttcgttc

upper sequence: GLYMA03G28320.1 (Glycine max), 5'ss of exon 10
lower sequence: Vv08s0007g05170.t01 (Vitis vinifera), 5'ss of exon 9
AAAAGCTGATGTTTTCCACATTCTGTCAGGAATGTGGAAGACTCCAGCTGAGAGGTGTTTCATGTGGATTGGAGGCTTTCGGTCATCCGAACTCCTCAAGgtgagaagtttctcttatctatgttttgtaaatgttttttctggtttgaaaattgcttcactaatatctggttgaacattgattgcattccatgcttccc-
 || |||||||| |||||||| |||||||||||||||||||| || || ||  ||||||| ||||||||||| || || || ||||| ||| ||||||||||||||| | | || |    ||    | ||  | |  | | |   || ||||   | ||    |||| |         |  ||||   |    | |     
CAAGGCTGATGTCTTCCACATCCTGTCAGGAATGTGGAAGACACCTGCAGAACGGTGTTTTATGTGGATTGGCGGTTTCCGTTCATCTGAAGTCCTCAAGgtgagaattgtttcctgatgattccatctat-tttactgtttaccttaaaaacaacatctactatatgttccctggattaaattgggattttggttgaatg

upper sequence: GLYMA03G28320.1 (Glycine max), 5'ss of exon 10
lower sequence: EFJ18699 (Selaginella moellendorffii), 5'ss of exon 1
AAAAGCTGATGTTTTCCACATTCTGTCAGGAATGTGGAAGACTCCAGCTGAGAGGTGTTTCATGTGGATTGGAGGCTTTCGGTCATCCGAACTCCTCAAGgtgagaagtttctcttatctatgttttgtaaatgttttttctggtttgaaaattgcttcactaatatctggttgaacattgattgcattccatgcttccc
 ||||| ||||| |||||| |  | || || |||||||| ||||| || ||||||||||| |||||||| || |||||  || |||| ||||| ||||||||     || | ||   | | |  || |     || ||   |    |     |   |  ||| ||   |||||     ||| |||  | |          
GAAAGCCGATGTCTTCCACCTCGTCTCTGGGATGTGGAAAACTCCCGCCGAGAGGTGTTTTATGTGGATGGGTGGCTTCAGGCCATCAGAACTTCTCAAGgtacttggtctttcagtttttttcttagcttgagtcttcgtttccatcgttttccatatactgatcgatggtt-----ttgtttgtctccag--------

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|24135626|gb|BU926136.1|BU926136
EST:     AGAGGTGTTTCATGTGGATTGGAGGCTTTCGGTCATCCGAACTCCTCAAG                         CTTCTTCTAAGTCAGTTGGAGCCTTTAGCCGAGCAACAATTGATGGGCATC
genomic: AGAGGTGTTTCATGTGGATTGGAGGCTTTCGGTCATCCGAACTCCTCAAGgtgagaagtt ... actgttgcagCTTCTTCTAAGTCAGTTGGAGCCTTTAGCCGAGCAACAATTGATGGGCATC
EST: gi|13562955|gb|BG551175.1|BG551175
EST:     AGAGGTGTTTCATGTGGATTGGAGGCTTTCGGTCATCCGAACTCCTCAAG                         CTTCTTCTAAGTCAGTTGGAGCCTTTAGCCGAGCAACAATTGATGGGCATC
genomic: AGAGGTGTTTCATGTGGATTGGAGGCTTTCGGTCATCCGAACTCCTCAAGgtgagaagtt ... actgttgcagCTTCTTCTAAGTCAGTTGGAGCCTTTAGCCGAGCAACAATTGATGGGCATC
EST: gi|254316490|gb|GR828027.1|GR828027
EST:     AGAGGTGTTTCATGTGGATTGGAGGCTTTCGGTCATCCGAACTCCTCAAG                         CTTCTTCTAAGTCAGTTGGAGCCTTTAGCCGAGCAACAATTGATGGGCATC
genomic: AGAGGTGTTTCATGTGGATTGGAGGCTTTCGGTCATCCGAACTCCTCAAGgtgagaagtt ... actgttgcagCTTCTTCTAAGTCAGTTGGAGCCTTTAGCCGAGCAACAATTGATGGGCATC
EST: gi|19269047|gb|BM885303.1|BM885303
EST:     AGAGGTGTTTCATGTGGATTGGAGGCTTTCGGTCATCCGAACTCCTCAAG                         CTTCTTCTAAGTCAGTTGGAGCCTTTAGCCGAGCAACAATTGATGGGCATC
genomic: AGAGGTGTTTCATGTGGATTGGAGGCTTTCGGTCATCCGAACTCCTCAAGgtgagaagtt ... actgttgcagCTTCTTCTAAGTCAGTTGGAGCCTTTAGCCGAGCAACAATTGATGGGCATC
EST: gi|9903361|gb|BE612329.1|BE612329
EST:     GGCTTTCGGTCATCCGAACTCCTCAAG                         CTTCTTCTAAGTCAGTTGGAGCCTTTAGCCGAGCAACAATTGATGGGCATC
genomic: GGCTTTCGGTCATCCGAACTCCTCAAGgtgagaagtt ... actgttgcagCTTCTTCTAAGTCAGTTGGAGCCTTTAGCCGAGCAACAATTGATGGGCATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAAGCTGATGTTTTCCACATTCTGTCAGGAATGTGGAAGACTCCAGCTGAGAGGTGTTTCATGTGGATTGGAGGCTTTCGGTCATCCGAACTCCTCAAGgtgagaagtttctcttatctatgttttgtaaatgttttttctggtttgaaaattgcttcactaatatctggttgaacattgattgcattccatgcttccc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC