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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAAGAAGGTGTTCCCGCACTTCTATATACTGGGGTGGTATTCGACTGGGAGTGATGCAGAGGAATCAGACATGCATATTCACAAAGCTgtaagtttgcgttattgcaatttgtcttaatgtaagcatgcctgtgaatagaattggtaggttgctttaggttcatgagggaattttagtaaattgttta...

Basic information

species Glycine max
transcript GLYMA04G12890.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G12890.1 (Glycine max), 5'ss of exon 2
lower sequence: AT5G56280.1 (Arabidopsis thaliana), 5'ss of exon 2
ATAAGAAGGTGTTCCCGCACTTCTATATACTGGGGTGGTATTCGACTGGGAGTGATGCAGAGGAATCAGACATGCATATTCACAAAGCTgtaagtttg-cgttattgcaatttgtcttaatgtaagcatgcct--gtgaatagaattggtaggttgctttaggttcatgagggaattttagtaaattgttta
||||||||||||||||  | |||||||| ||||| ||||| || || || |||||||| |||||||| || |||||||| || |||||||| |||     | | |  | | |  | ||  | |||    |  |  ||   || || ||     ||  | |  | || ||  |  |                 
ATAAGAAGGTGTTCCCTGATTTCTATATTCTGGGATGGTACTCTACGGGAAGTGATGCTGAGGAATCTGATATGCATATCCATAAAGCTgtgagtccaatgctctctctagt-atttttgtataattgagatttggtctctaaaagtgtggtttttgtgtctgctcttggtgacag----------------

upper sequence: GLYMA04G12890.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv19s0015g01950.t01 (Vitis vinifera), 5'ss of exon 2
ATAAGAAGGTGTTCCCGCACTTCTATATACTGGGGTGGTATTCGACTGGGAGTGATGCAGAGGAATCAGACATGCATATTCACAAAGCTgtaagtttgcgttattgcaatttgtcttaatgt-aagcatgcctgtgaatagaattggtaggttgctttaggttcatgagggaattttagtaaattgttta
|||||||||| || ||| |||| |||||||| || ||||| || || || ||||||||  | |||||||| ||||||||||| |||||||||||||  | | || |    | || ||||  | || || |      | |    ||  |   ||| ||||| ||  | | |  | |  |  | ||  |   
ATAAGAAGGTCTTTCCGAACTTTTATATACTTGGATGGTACTCCACCGGAAGTGATGCCCAAGAATCAGATATGCATATTCATAAAGCTgtaagttcacatcatcgttcatagttttaagattaaacacgttc-caagtttttttctttttttggtttagattattaatgataataaatgagatgatact
















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|298179134|gb|HO027605.1|HO027605
EST:     ATTCGACTGG-AGTGATGCAGAGGAATCAGACATGCATATTCACAAAGCT                         TTGATGGATATCAATGAAAGTCCAGTTTATGTTCTTCTCAATCCTTCTATC
genomic: ATTCGACTGGGAGTGATGCAGAGGAATCAGACATGCATATTCACAAAGCTgtaagtttgc ... gctgtaacagTTGATGGATATCAATGAAAGTCCAGTTTATGTTCTTCTCAATCCTTCTATC
EST: gi|298185593|gb|HO030806.1|HO030806
EST:     ATTCGACTGGGAGTGATGCAGAGGAATCAGACATGCATATTCACAAAGCT                         TTGATGGATATCAATGAAAG
genomic: ATTCGACTGGGAGTGATGCAGAGGAATCAGACATGCATATTCACAAAGCTgtaagtttgc ... gctgtaacagTTGATGGATATCAATGAAAG
EST: gi|298165455|gb|HO011504.1|HO011504
EST:     ATTCGACTGGGAGTGATGCAGAGGAATCAGACATGCATATTCACAAAGCT                         TTGATGGATATC
genomic: ATTCGACTGGGAGTGATGCAGAGGAATCAGACATGCATATTCACAAAGCTgtaagtttgc ... gctgtaacagTTGATGGATATC
EST: gi|9986533|gb|BE660641.1|BE660641
EST:     ATTCGACTGGGAGTGATGCAGAGGAATCAGACATGCATATTCACAAAGCT                         TTGATGGATATCAATGAAAGTCCAGTTTATGTTCTTCTCAATCCTTCTATC
genomic: ATTCGACTGGGAGTGATGCAGAGGAATCAGACATGCATATTCACAAAGCTgtaagtttgc ... gctgtaacagTTGATGGATATCAATGAAAGTCCAGTTTATGTTCTTCTCAATCCTTCTATC
EST: gi|18041126|gb|BM309420.1|BM309420
EST:     ATTCGACTGGGAGTGATGCAGAGGGATCAGACATGCATATTCACAAAGCT                         TTGATGGATATCAATGAAAGT
genomic: ATTCGACTGGGAGTGATGCAGAGGAATCAGACATGCATATTCACAAAGCTgtaagtttgc ... gctgtaacagTTGATGGATATCAATGAAAGT
EST: gi|298192702|gb|HO033136.1|HO033136
EST:     ATTCGACTGGGAGTGATGCAGAGGAATCAGACATGCATATTCACAAAGCT                         TTGATGGATATCAATGAAAGTCCAGTTTATGTTCTTCTCAATCCTTCTATC
genomic: ATTCGACTGGGAGTGATGCAGAGGAATCAGACATGCATATTCACAAAGCTgtaagtttgc ... gctgtaacagTTGATGGATATCAATGAAAGTCCAGTTTATGTTCTTCTCAATCCTTCTATC
EST: gi|298199097|gb|HO042460.1|HO042460
EST:     ATTCAACTGGGAGTGATGCAGAGGAATCAGACATGCATATTCACAAAGCT                         TTGATGGATATCAATGAAAGTCCAGTTTATGTTCTTCT
genomic: ATTCGACTGGGAGTGATGCAGAGGAATCAGACATGCATATTCACAAAGCTgtaagtttgc ... gctgtaacagTTGATGGATATCAATGAAAGTCCAGTTTATGTTCTTCT
EST: gi|15203210|gb|BI425978.1|BI425978
EST:     ATTCGACTGGGAGTGATGCAGAGGAATCAGACATGCATATTCACAAAGCT                         TTGATGGATATCAATGAAAGTCCAGTTTATGTTCTTCTCAATCCTTCTATC
genomic: ATTCGACTGGGAGTGATGCAGAGGAATCAGACATGCATATTCACAAAGCTgtaagtttgc ... gctgtaacagTTGATGGATATCAATGAAAGTCCAGTTTATGTTCTTCTCAATCCTTCTATC
EST: gi|15662488|gb|BI699859.1|BI699859
EST:     ATTCGACTGGGAGTGATGCAGAGGAATCAGACATGCATATTCACAAAGCT                         TTGATGGATATCAATGAAAGTCCAGTTTATGTTCTTCTCAATCCTTCTATC
genomic: ATTCGACTGGGAGTGATGCAGAGGAATCAGACATGCATATTCACAAAGCTgtaagtttgc ... gctgtaacagTTGATGGATATCAATGAAAGTCCAGTTTATGTTCTTCTCAATCCTTCTATC
EST: gi|298172080|gb|HO021672.1|HO021672
EST:     ATTCGACTGGGAGTGATGCAGAGGAATCAGACATGCATATTCACAAAGCT                         TTGATGGATATCAATGAAAGTCCAGTTTATGTTCTTCTCAATCCTTC
genomic: ATTCGACTGGGAGTGATGCAGAGGAATCAGACATGCATATTCACAAAGCTgtaagtttgc ... gctgtaacagTTGATGGATATCAATGAAAGTCCAGTTTATGTTCTTCTCAATCCTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATAAGAAGGTGTTCCCGCACTTCTATATACTGGGGTGGTATTCGACTGGGAGTGATGCAGAGGAATCAGACATGCATATTCACAAAGCTgtaagtttgcgttattgcaatttgtcttaatgtaagcatgcctgtgaatagaattggtaggttgctttaggttcatgagggaattttagtaaattgttta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA