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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatggatttggatgagggtaattattcggttacagtatcatgctcaatggataattaagatgtattatattaaagtttcttatgacactttccaaaatattttctccagGTTATTTTCTTGTGGGACAAGTAAAGATGGAGAGTCTTTTCTTGTTGAATGGAATGAAAGTGAAGGCGCCATCAAGAGAACATACAATGGATTCAGAAAA

Basic information

species Glycine max
transcript GLYMA20G38230.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38230.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 14
gtaagatggatttggatgagggtaattattcggttacagtatcatgctca-atggataattaagatgtattatattaaagtttcttatgacactttccaaaatattt-tctccagGTTATTTTCTTGTGGGACAAGTAAAGATGGAGAGTCTTTTCTTGTTGAATGGAATGAAAGTGAAGGCGCCATCAAGAGAACATACAATGGATTCAGAAAA
                             |  |     |||| |   ||  |  ||     ||| ||| ||   |||  |||  || |   | ||| |    | ||  | |  ||||| || || ||||| ||||||||||||||||| || | | | ||||| |||||||||||||||||  | |||||||| |||||   ||| ||  | |||
----------------------------gtaagcagaggtattactttcgtaccga-----aagttgtctttagttattgttg-ttgtactaatttacttgtttttcatatgaagGTTGTTCTCATGTGGAACAAGTAAAGATGGAGATTCATATTTAGTTGAGTGGAATGAAAGTGAAGGATCTATCAAGAGGACATATTCTGGGTTTCGTAAA

upper sequence: GLYMA20G38230.1 (Glycine max), 3'ss of exon 15
lower sequence: AT5G27030.2 (Arabidopsis thaliana), 3'ss of exon 13
-------------------------------------------------------------gtaagatggatttggatgagggtaattattc----ggttacagtatcatgctc---aatggataattaagatgtattatattaaagtttcttat--gacactttccaaaatattttctcc----agGTTATTTTCTTGTGGGACAAGTAAAGATGGAGAGTCTTTTCTTGTTGAATGGAATGAAAGTGAAGGCGCCATCAAGAGAACATACAATGGATTCAGAAAA
                                                              |   |    ||  |||     |  ||| ||    || ||| |  |  ||  |   | |   ||||       |  | | ||||  || | | |      |||||  |  | ||||| ||    || || || |||||||| || |||||||||||||| ||||| || ||||| |||||||||||||||||  | || || || || || || |  ||    |||
gtaagatcttaaactcataaacatttccctcttctataccgcttgttcttcactcctcagtttccaaaatcttcagattcttttgtttactccggaggatactgagttgtgtccttgagtttctaatcttatctttctgttttaagtttaccttttcagtgctttctgatgttttttcccccttcagATTGTTCTCTTGTGGAACGAGTAAAGATGGAGATTCTTTCCTAGTTGAGTGGAATGAAAGTGAAGGATCAATTAAAAGGACGTATAAAGAGTTTCAGAAA

upper sequence: GLYMA20G38230.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 14
--------------------------------------------------------------------------------------gtaagatggatttggatgagggtaattattcggttacagtatcatgctcaat-ggataattaagatgtattatattaaagtttcttatgacactttc---caaaatattttctccagGTTATTTTCTTGTGGGACAAGTAAAGATGGAGAGTCTTTTCTTGTTGAATGGAATGAAAGTGAAGGCGCCATCAAGAGAACATACAATGGATTCAGAAAA
                                                                                      ||||  | | | | | ||    |  | || |  | || ||   |   |  ||   |||  |  ||   |  || |  || |   || ||||  |||    |    | || | | ||| || || |||||||| |||||||||||||| || |||||| | ||||||||||||||||||||||| || || ||||| || || ||||| || ||||| 
gtaagattggtgaaattcacaattccagacctaataaaattttattttatttttctttttgctcaatttaaaatttcaacttttctgtaatgttgttatagttgtc--ttttcataccat-actgtgctacttttgatcaaatatatctgacagaacatttgtaactaatttgtgactttttttttcctcttcttcttttcagATTGTTCTCTTGTGGAACAAGTAAAGATGGGGACTCTTTTTTGGTTGAATGGAATGAAAGTGAAGGAGCAATAAAGAGGACGTATAATGGGTTTAGAAAG

upper sequence: GLYMA20G38230.1 (Glycine max), 3'ss of exon 15
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 14
gtaagatggatttggatgagggtaattattcggttacagtatcatgctcaatggataattaagatgtat---tatattaaagttt--cttatgacactttccaaaatattttctccagGTTATTTTCTTGTGGGACAAGTAAAGATGGAGAGTCTTTTCTTGTTGAATGGAATGAAAGTGAAGGCGCCATCAAGAGAACATACAATGGATTCAGAAAA
                  | | | ||| | | || | | | | || ||| ||   |   | | |||||    |||  | ||  ||   ||||  | | ||      | ||      ||| | || ||||| || |||||||||||||||||||||| ||| || ||||||||||| ||||| || || |||||| | ||||||   || ||| | || 
-----------------aatgatgatt-tactgtcagaatttgatcctccatctttttcttacatgtagaggtatcgtgaatattgatttatctccccttttctctttttgatgttagGCTCTTCTCTTGCGGAACAAGTAAAGATGGAGAGTCTTATCTGGTGGAATGGAATGAGAGTGAGGGTGCAATCAAGCGGACATACTCAGGTTTCCGGAAG

upper sequence: GLYMA20G38230.1 (Glycine max), 3'ss of exon 15
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 14
gtaagatggatttggatgagggtaattattcggttacagtatcatgctcaatggataattaagatgtattatattaaagtttcttatgacactttccaaaatattttctccagGTTATTTTCTTGTGGGACAAGTAAAGATGGAGAGTCTTTTCTTGTTGAATGGAATGAAAGTGAAGGCGCCATCAAGAGAACATACAATGGATTCAGAAAA
       |  || | || | | | | |           ||    ||  ||     || ||  ||   || || ||  |     ||||||   ||| |    | |   | ||||  | ||||||||||| || || ||||||||||| |||| ||| || ||||||||||| || |||||||| || ||| | ||||||   || ||| | || 
-----tcgctttcgaattaagttgagtgaatttaggacgtgatgtgtccatcttgtatttgcgaca-atgatttttga-----ttatgaattttttctt--tgtggacgccagACTCTTTTCTTGTGGAACTAGCAAAGATGGAGAATCTTATCTGGTGGAATGGAATGAGAGCGAAGGCGCAATTAAGCGGACATACTCAGGTTTCCGCAAG

upper sequence: GLYMA20G38230.1 (Glycine max), 3'ss of exon 15
lower sequence: EFJ30926 (Selaginella moellendorffii), 3'ss of exon 14
gtaagatggatttggatgagggtaattattcggttacagtatcatgctcaatggataattaagatgtattatattaaagtttcttatgacactttccaaaatattttctccagGTTATTTTCTTGTGGGACAAGTAAAGATGGAGAGTCTTTTCTTGTTGAATGGAATGAAAGTGAAGGCGCCATCAAGAGAACATACAATGGATTCAGAAAA
                                                                 || ||   | ||  |||  |||  |  |  |     |  ||| ||||| || ||||||||||| ||||| || ||||| |||||||||||||| || ||||||||||||||||| || || || |  || |||||||| ||  | |||
-----------------------------------------------------------------gt-ttgcttcaacctttggtatttccatcacatcctttgtttttccagATTGTTTTCTTGTGGAACAAGCAAGGATGGTGAGTCTTTTCTTGTGGAGTGGAATGAAAGTGAAGGTGCAATTAAAAACACCTACAATGGTTTTCGGAAA

upper sequence: GLYMA20G38230.1 (Glycine max), 3'ss of exon 15
lower sequence: EFJ17248 (Selaginella moellendorffii), 3'ss of exon 14
gtaagatggatttggatgagggtaattattcggttacagtatcatgctcaatggataattaagatgtattatattaaagtttcttatgacactttccaaaatattttctccagGTTATTTTCTTGTGGGACAAGTAAAGATGGAGAGTCTTTTCTTGTTGAATGGAATGAAAGTGAAGGCGCCATCAAGAGAACATACAATGGATTCAGAAAA
                                                                 || ||   | ||  |||  |||  | | |  ||   | | || ||||| || ||||||||||| ||||| || ||||| |||||||||||||| || ||||||||||||||||| || || || |  || |||||||| ||  | |||
-----------------------------------------------------------------gt-ttgcttcaacctttggtatttc-catcacatcctttgttttccagATTGTTTTCTTGTGGAACAAGCAAGGATGGTGAGTCTTTTCTTGTGGAGTGGAATGAAAGTGAAGGTGCAATAAAAAACACCTACAATGGTTTTCGGAAA

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|15200825|gb|BI424551.1|BI424551
EST:     GCCCCTGGTCACTGGTGCACTACAATGCTTTACAGTGCAGATGGAACTAG                         GTTATTTTCTTGTGGGACAAGTAAAGATGGAGAGTCTTTTCTTGTTGAATG
genomic: GCCCCTGGTCACTGGTGCACTACAATGCTTTACAGTGCAGATGGAACTAGgtaagatgga ... ttttctccagGTTATTTTCTTGTGGGACAAGTAAAGATGGAGAGTCTTTTCTTGTTGAATG
EST: gi|298170900|gb|HO015876.1|HO015876
EST:     GCCCCTGGTCACTGGTGCACTACAATGCTTTACAGTGCTGATGGAACTAG                         GTTATTTTCTTGTGGGACAAGTAAAGATGGAGAGTCTTTTCTTGTTGAATG
genomic: GCCCCTGGTCACTGGTGCACTACAATGCTTTACAGTGCAGATGGAACTAGgtaagatgga ... ttttctccagGTTATTTTCTTGTGGGACAAGTAAAGATGGAGAGTCTTTTCTTGTTGAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaagatgtattatattaaagtttcttatgacactttccaaaatattttctccagGTTATTTTCTTGTGGGACAAGTAAAGATGGAGAGTCTTTTCTTGTTGAATGGAATGAAAGTGAAGGCGCCATCAAGAGAACATACAATGGATTCAGAAAA
                                           tattttctcc  CT-rich tract
     atgtattatattaaag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatggatttggatgagggtaattattcggttacagtatcatgctcaatggataattaagatgtattatattaaagtttcttatgacactttccaaaatattttctccagGTTATTTTCTTGTGGGACAAGTAAAGATGGAGAGTCTTTTCTTGTTGAATGGAATGAAAGTGAAGGCGCCATCAAGAGAACATACAATGGATTCAGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA