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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAAAACGGTCAAACTTACGGCACAGACCAATTGGTATAGGAGTACAGGGTCTTGCTGATACTTTCATACTACTTGGCATGGCATTTGATTCACCAGAGgtaaatctacttctgaggctgctgttatattcgttgtatttgtgcttcagtctaatagttcacttggatattaatgcag

Basic information

species Glycine max
transcript GLYMA04G39500.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G39500.1 (Glycine max), 5'ss of exon 11
lower sequence: LOC_Os06g07210.1 (Oryza sativa), 5'ss of exon 11
TGCAAAACGGTCAAACTTACGGCACAGACCAATTGGTATAGGAGTACAGGGTCTTGCTGATACTTTCATACTACTTGGCATGGCATTTGATTCACCAGAGgtaaatctacttctgaggctgctgttatattcgttgtatttgtgcttcagtctaatagttcacttggatattaa-tgcag--------------
 |||||| | |||||  | |||||||| |||||||| || || || || ||  | || |||||||||||| ||||||||||| ||||||||||||||||||||| | | | |   ||     |  |||| | ||  || ||     ||  ||  | | || |||    ||  || ||                 
CGCAAAAAGATCAAATATGCGGCACAGGCCAATTGGCATTGGTGTTCAAGGGTTGGCAGATACTTTCATATTACTTGGCATGCCATTTGATTCACCAGAGgtaacttttcct---agttcagtaatatagtagtactagttagtagtccttcctacacttaactgatgtaaaaaatgtgatcccctcttttcag

upper sequence: GLYMA04G39500.1 (Glycine max), 5'ss of exon 11
lower sequence: LOC_Os02g56100.1 (Oryza sativa), 5'ss of exon 11
TGCAAAACGGTCAAACTTACGGCACAGACCAATTGGTATAGGAGTACAGGGTCTTGCTGATACTTTCATACTACTTGGCATGGCATTTGATTCACCAGAGgtaaatctactt---ctgaggctgctgttatattcgttgtatttgtgcttcagtctaatagttcacttggatattaatgcag
||||||  | |||||  |  ||||||| ||||| || || || || |||||  | || || || |||||  ||||||||||| ||||||||||| ||||||||||| |       || |   ||  ||||| | |  | ||| | | ||||  |  |||      |   ||| ||  | |||
TGCAAAGAGATCAAATATGAGGCACAGGCCAATCGGAATCGGTGTTCAGGGCTTGGCAGACACCTTCATTTTACTTGGCATGCCATTTGATTCAACAGAGgtaaatttttccaacctaaaaatgtggttat-tccaatctatatatacttcgctgaaatgcgatgcaatgatctt--ttcag

upper sequence: GLYMA04G39500.1 (Glycine max), 5'ss of exon 11
lower sequence: GRMZM2G304362_T01 (Zea mays), 5'ss of exon 11
TGCAAAACGGTCAAACTTACGGCACAGACCAATTGGTATAGGAGTACAGGGTCTTGCTGATACTTTCATACTACTTGGCATGGCATTTGATTCACCAGAGgtaaatctacttctgaggctgctgttatattcgttgtatttgtgcttcagtctaa-tagttcacttggatattaatgcag------------
 |||||  |||||||| | || ||||| |||||||| ||||| || || || || || |||||||||||| |||| |||||| | ||||||||||||||||||  | | | | |     |        |||      |  ||| |||   | ||| ||||| |  || | |  ||||               
AGCAAAGAGGTCAAACATGCGTCACAGGCCAATTGGCATAGGTGTTCAAGGCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAGgtaccttttcatttctccgtagctcagcattaacc--acctgttcttttctgtaactagttgatatgta-acaaatggttttatcttttcag

upper sequence: GLYMA04G39500.1 (Glycine max), 5'ss of exon 11
lower sequence: GRMZM2G340527_T01 (Zea mays), 5'ss of exon 11
TGCAAAACGGTCAAACTTACGGCACAGACCAATTGGTATAGGAGTACAGGGTCTTGCTGATACTTTCATACTACTTGGCATGGCATTTGATTCACCAGAGgtaaatctac-ttctgaggctgctgttatattcgttgtatttgtgcttcagtctaatagttcacttggatattaatgcag------------
 |||||  | |||||  | || ||||| |||||||| ||||| || || || || || |||||||||||| || | |||||| |||||||||||| |||||||  | | | ||   | |  |||  |  |||     ||| |    ||| ||  | ||||| |  || | |  ||||               
AGCAAAGAGATCAAATATGCGTCACAGGCCAATTGGCATAGGTGTTCAAGGCCTGGCCGATACTTTCATATTATTGGGCATGCCATTTGATTCACTAGAGgtacctttccatttctatgtagctcat-cattaaccatatgttcctttctgta-attagttgatatgta-acaaatggttttatattttcag

upper sequence: GLYMA04G39500.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv07s0031g01990.t01 (Vitis vinifera), 5'ss of exon 11
TGCAAAACGGTCAAACTTACGGCACAGACCAATTGGTATAGGAGTACAGGGTCTTGCTGATACTTTCATACTACTTGGCATGGCATTTGATTCACCAGAGgtaaatctacttctg--aggc---tgct--gttatattc------gttgtatttgtgcttcagtctaatagttcacttggatattaa-tgcag
||||||| |||||||||| || || ||||| |||||| | ||||| ||||||||||| ||||| |||||  | |||||||||||||||||||||||||||||||| ||| || ||   |||   | ||   || |  ||       ||  | |  | |||   | | ||| || | |||  |||| | |||||
TGCAAAAAGGTCAAACTTGCGTCATAGACCCATTGGTCTTGGAGTTCAGGGTCTTGCAGATACCTTCATTTTGCTTGGCATGGCATTTGATTCACCAGAGgtaaagctaattttgcagggcaaatacttcattgtgctcctgtggattccaatgatacttagctgtgataattaatttgactattgactgcag

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|193697875|gb|FK641130.1|FK641130
EST:     TGGCATGGCATTTGATTCACCAGAG                         GCTCAGCAGTTAAACCAGGAGATATTTGAGACTATATACTATCATGCTCTA
genomic: TGGCATGGCATTTGATTCACCAGAGgtaaatctac ... attaatgcagGCTCAGCAGTTAAACCAGGAGATATTTGAGACTATATACTATCATGCTCTA
EST: gi|193409064|gb|FK373208.1|FK373208
EST:     TGGCATTTGATTCACCAGAG                         GCTCAGCAGTTAAACCAGGAGATATTTGAGACTATATACTATCATGCTCTA
genomic: TGGCATTTGATTCACCAGAGgtaaatctac ... attaatgcagGCTCAGCAGTTAAACCAGGAGATATTTGAGACTATATACTATCATGCTCTA
EST: gi|15199949|gb|BI424092.1|BI424092
EST:     ATTTGATTCACCAGAG                         GCTCAGCAGTTAAACCAGGAGATATTTGAGACTATATACTATCATGCTCTA
genomic: ATTTGATTCACCAGAGgtaaatctac ... attaatgcagGCTCAGCAGTTAAACCAGGAGATATTTGAGACTATATACTATCATGCTCTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCAAAACGGTCAAACTTACGGCACAGACCAATTGGTATAGGAGTACAGGGTCTTGCTGATACTTTCATACTACTTGGCATGGCATTTGATTCACCAGAGgtaaatctacttctgaggctgctgttatattcgttgtatttgtgcttcagtctaatagttcacttggatattaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT