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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggatggggagttagagatatctgtgtttcctcttagtctgctgagattttcatgatcttgaatgtaactttctttacttttccctagGCATTGGAGTCGCCATACCCCTGAGGGTGCTAAACTTGAAGCTGAGTGGAATGCCAAGTTTGCAGAATATGAGAAGAAATACAGTGAGGAAGCTGCAGAG

Basic information

species Glycine max
transcript GLYMA20G38720.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38720.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G010494_T01 (Zea mays), 3'ss of exon 5
----------gtatggatg--gggagttagagatatctgtgtttcctcttagtctgctgagattttcatgatcttgaatgtaactttctttacttttc---cctagGCATTGGAGTCGCCATACCCCTGAGGGTGCTAAACTTGAAGCTGAGTGGAATGCCAAGTTTGCAGAATATGAGAAGAAATACAGTGAGGAAGCTGCAGAG
           |||  |||    |||| |    ||  | |  |   | | |      |  | | | ||        | ||||| || | | |||| ||   |  ||||| ||||||||||||| |  ||||||||||  |||||||||||| |||||||||| ||||| ||||||||| ||||||||||   |||| ||||| |||
tttgttaaaaatatttatgctcagagtaaagagtaaat-taatgtatttaaactcaatacgttctgcaca----caagtgtaa-ttacataacttatcaatcgcagGCACTGGAGTCGCCATATCGATGAGGGTGCTTCACTTGAAGCTGAATGGAATGCCAGGTTTGTAGAATATGAAAAGAAATACAACCAGGAGGCTGCTGAG

upper sequence: GLYMA20G38720.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G45290.1 (Arabidopsis thaliana), 3'ss of exon 5
gtatggatgggg-agttagagatatctgtgtttcctcttagtc-tgctgagattttcatgatcttgaatgtaacttt--ctttacttttccctagGCATTGGAGTCGCCATACCCCTGAGGGTGCTAAACTTGAAGCTGAGTGGAATGCCAAGTTTGCAGAATATGAGAAGAAATACAGTGAGGAAGCTGCAGAG
||| | |      |  ||   |  ||| | | |  |  | ||  || |  ||    | || | | | |  | ||| |   | |  | ||  |||| |||||||| || || || || || || |||   ||||||||||| ||||||||||| |||||||  ||||||||||||||    |||||||||||||||
gtaagtagaacttaactatgcacttctatttatggttatggttgtggtatgagaacc-tgctttggtaatttactataattcttatgttttctagCCATTGGAGCCGTCACACGCCCGAAGGGGCTGCTCTTGAAGCTGATTGGAATGCCAAATTTGCAGCTTATGAGAAGAAATATCCGGAGGAAGCTGCAGAG

upper sequence: GLYMA20G38720.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv16s0022g01440.t01 (Vitis vinifera), 3'ss of exon 5
gtatggatggggagttagagatatctgtgtttcctcttagtctgctgagattttcatgatcttgaatgtaactttctttacttttccctagGCATTGGAGTCGCCATACCCCTGAGGGTGCTAAACTTGAAGCTGAGTGGAATGCCAAGTTTGCAGAATATGAGAAGAAATACAGTGAGGAAGCTGCAGAG
|||| ||    |||  |  | |   | || ||| | ||  ||   | |  |||  ||   ||| | || | |||  | |  ||  |   ||||| ||||| ||||| | |||||| || |||   ||||||||||| |||||||||||||||||||| ||||||||||||||||  || ||||| ||||| 
gtattgaaattgag--aaggttgcttttgcttcatgtt--tcaaattaagtttgaat--cctttagtg-agcttcttgtgtttcac---agGCACTGGAGCCGCCACATCCCTGATGGAGCTGCCCTTGAAGCTGAATGGAATGCCAAGTTTGCAGAGTATGAGAAGAAATACAAAGAAGAAGCAGCAGAA

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|7283818|gb|AW596420.1|AW596420
EST:     AATCTTGGATGGCCATACGAGCCTTTCCATGTGCCAGAAGATGTTAAAAA                         GCATTGGAGTCGCCATACCCCTGAGGGTGCTAAACTTGAAGCTGAGTGGAA
genomic: AATCTTGGATGGCCATACGAGCCTTTCCATGTGCCAGAAGATGTTAAAAAgtatggatgg ... ttttccctagGCATTGGAGTCGCCATACCCCTGAGGGTGCTAAACTTGAAGCTGAGTGGAA
EST: gi|27808938|gb|CB063360.1|CB063360
EST:     AATCTTGGATGGCCATACGAGCCTTTCCATGTGCCAGAAGATGTTAAAAA                         GCATTGGAGTCGCCATACCCCTGAGGGTGCTAAACTTGAAGCTGAGTGGAA
genomic: AATCTTGGATGGCCATACGAGCCTTTCCATGTGCCAGAAGATGTTAAAAAgtatggatgg ... ttttccctagGCATTGGAGTCGCCATACCCCTGAGGGTGCTAAACTTGAAGCTGAGTGGAA
EST: gi|16279267|gb|BI943346.1|BI943346
EST:     GCCATACGAGCCTTTCCATGTGCCAGAAGATGTTAAAAA                         GCATTGGAGTCGCCATACCCCTGAGGGTGCTAAACTTGAAGCTGAGTGGAA
genomic: GCCATACGAGCCTTTCCATGTGCCAGAAGATGTTAAAAAgtatggatgg ... ttttccctagGCATTGGAGTCGCCATACCCCTGAGGGTGCTAAACTTGAAGCTGAGTGGAA
EST: gi|7692105|gb|AW760220.1|AW760220
EST:     AATCTTGGATGGCCATACGAGCCTTTCCATGTGCCAGAAGATGTTAAAAA                         GCATTGGAGTCGCCATACCCCTGAGGGTGCTAAACTTGAAGCTGAGTGGAA
genomic: AATCTTGGATGGCCATACGAGCCTTTCCATGTGCCAGAAGATGTTAAAAAgtatggatgg ... ttttccctagGCATTGGAGTCGCCATACCCCTGAGGGTGCTAAACTTGAAGCTGAGTGGAA
EST: gi|120532309|gb|EH260442.1|EH260442
EST:     AATCTTGGATGGCCATACGAGCCTTTCCATGTGCCAGAAGATGTTAAAAA                         GCATTGGAGTCGCCATACCCCTGAGGGTGCTAAACTTGAAGCTGAGTGGAA
genomic: AATCTTGGATGGCCATACGAGCCTTTCCATGTGCCAGAAGATGTTAAAAAgtatggatgg ... ttttccctagGCATTGGAGTCGCCATACCCCTGAGGGTGCTAAACTTGAAGCTGAGTGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagtctgctgagattttcatgatcttgaatgtaactttctttacttttccctagGCATTGGAGTCGCCATACCCCTGAGGGTGCTAAACTTGAAGCTGAGTGGAATGCCAAGTTTGCAGAATATGAGAAGAAATACAGTGAGGAAGCTGCAGAG
                             atgtaac  putative branch site (score: 3)
                                taactttctttacttt  CT-rich tract
                                        tttactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggatggggagttagagatatctgtgtttcctcttagtctgctgagattttcatgatcttgaatgtaactttctttacttttccctagGCATTGGAGTCGCCATACCCCTGAGGGTGCTAAACTTGAAGCTGAGTGGAATGCCAAGTTTGCAGAATATGAGAAGAAATACAGTGAGGAAGCTGCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG