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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGTCTATAGTTTTGGTGTTGTTCTTCTTGAGCTTCTTACAGGAAGAAAACCTGTTGACCATACCATGCCTAGAGGACAGCAGAGTCTTGTCACATGGgtcagtgtgtctgcttaaactcatacctcatccgtgctgctgcttttcaatcatttaacactggttgtcggccataggtattttgttgacattgatatttttttgtag

Basic information

species Glycine max
transcript GLYMA20G38980.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38980.1 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os09g33860.1 (Oryza sativa), 5'ss of exon 6
TGATGTCTATAGTTTTGGTGTTGTTCTTCTTGAGCTTCTTACAGGAAGAAAACCTGTTGACCATACCATGCCTAGAGGACAGCAGAGTCTTGTCACATGGgtcagtgtgtc-tgcttaaactca-tacctcatccgtgctgctgcttttcaatcatttaacactggttgtcggccataggtattttgttgacattgatatttttttgtag
|||||| ||||||||||| ||||||||||| |||||||| |||||||| ||||| || || || || |||||||| || ||||||||||| || |||||||| ||  | |  |   |||| | | |||   ||      ||     | |    | |     | ||||    ||  | |  || |||||||| |     | | |       
TGATGTATATAGTTTTGGAGTTGTTCTTCTAGAGCTTCTAACAGGAAGGAAACCAGTAGATCACACAATGCCTAGGGGTCAGCAGAGTCTGGTTACATGGgtaagcattttatttgtaaatttactacaatatttaacatgagagctgtttgcc-tcagctattggtaaaagg--agaattactttgttgataagatcactct-------

upper sequence: GLYMA20G38980.1 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os01g67340.1 (Oryza sativa), 5'ss of exon 6
TGATGTCTATAGTTTTGGTGTTGTTCTTCTTGAGCTTCTTACAGGAAGAAAACCTGTTGACCATACCATGCCTAGAGGACAGCAGAGTCTTGTCACATGGgtcagtgtgtctgcttaaactcatacctcatccgtgctgctgcttttcaatcattt---aaca-ctggtt--gtcggccatag-gtattttgttgaca--ttgat-atttttttgtag-------------------------------------------------------------------------
|||||| ||||| || || ||||||||  | || ||||| |||||||||||||| || || ||||| ||||||||||| ||||||||  | || |||||||| | |||      |  |  | |  | |    | ||  | |   ||   ||||  |   || | ||| ||  |  |   |||| || |   ||| |||  ||||| | |    |||||                                                                         
TGATGTGTATAGCTTCGGAGTTGTTCTCTTGGAACTTCTGACAGGAAGAAAACCAGTAGATCATACAATGCCTAGAGGGCAGCAGAGCTTGGTTACATGGgt-aatgttcaccatatagtttactcatttatcttgtcgttaagttcagatcacatctgaatatctgatttagcagcttatagtgtctacagttaacaccttgattagtacaatgtagcaatacgcagcccaatcctttagtggctactttttacctagttctctgagcatgtctcagttctgttttgcag

upper sequence: GLYMA20G38980.1 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os03g62700.1 (Oryza sativa), 5'ss of exon 6
TGATGTCTATAGTTTTGGTGTTGTTCTTCTTGAGCTTCTTACAGGAAGAAAACCTGTTGACCATACCATGCCTAGAGGACAGCAGAGTCTTGTCACATGGgtcagtgtgtctgcttaaactcatacctcatccgtgc-tgctgcttttcaatcatttaacactggttgtcggccataggtattttgt-tgacattgatatttttttgtag
|||||| || ||||||||||| |||||| | || || || || ||||| ||||| || ||||| || |||||| | |||||||| ||||| ||||| ||||| ||| |||||     | || | | |  |  ||| | | |     |||   |   | |||  |       ||  |   |  |  |  ||| | | | |           
TGATGTGTACAGTTTTGGTGTAGTTCTTTTGGAACTCCTGACTGGAAGGAAACCAGTGGACCACACAATGCCTCGGGGACAGCAAAGTCTAGTCACTTGGgtaagt-tgtctctaccacctaaaagcggagtcgtccatacgctccttcccacgcgtcacaaagcacacaagcactgccttctaggcctgaaaataacaga---------

upper sequence: GLYMA20G38980.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G029530_T01 (Zea mays), 5'ss of exon 6
TGATGTCTATAGTTTTGGTGTTGTTCTTCTTGAGCTTCTTACAGGAAGAAAACCTGTTGACCATACCATGCCTAGAGGACAGCAGAGTCTTGTCACATGGgtcagtgtgtctgcttaaactcatacctcatccgtgctgctgcttttcaatcatttaacactggttgtcggc-cataggtattttgttgacat-tgatatttttttgtag
|||||| ||||| ||||| ||||||||| | |||||||| |||||||| ||||| || || ||||| ||||||||||| ||||||||||| || |||||||| ||  | |        | ||  | |    |  |  | |  |||   ||  |||| |  ||||||| | |  | | | |||  | || | || | ||||   |      
TGATGTATATAGCTTTGGGGTTGTTCTTTTAGAGCTTCTAACAGGAAGGAAACCAGTAGATCATACAATGCCTAGAGGTCAGCAGAGTCTGGTTACATGGgtaagcattttgttcctgagtcccaacaagcctattattcaactt---aagaatttca-gctggttgcccgtgctttgctatgatttttatatatcatataaat------

upper sequence: GLYMA20G38980.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G153945_T03 (Zea mays), 5'ss of exon 6
TGATGTCTATAGTTTTGGTGTTGTTCTTCTTGAGCTTCTTACAGGAAGAAAACCTGTTGACCATACCATGCCTAGAGGACAGCAGAGTCTTGTCACATGGgtcagtgtgtctgcttaaactcatacc-tcatccgtgctgctgcttttcaatcatttaacactggttgtcggccataggtattttgttgacattgatatttttttgtag
|||||| ||||||||||| ||||| ||| | ||||||||||| ||||| |||||||| || ||||| ||||| || || |||||||||||||| || |||||  |  |      ||    ||||||   ||| |    || || |||  ||||| ||    |   || ||    | |  ||       |  ||| |||  |  |     
TGATGTATATAGTTTTGGGGTTGTCCTTTTAGAGCTTCTTACTGGAAGGAAACCTGTAGATCATACAATGCCAAGGGGCCAGCAGAGTCTTGTTACTTGGgtatgaattaaaattt----tcatactaccattctcaatgatgttttaaaatcagtttttgccatttctcccgaacaattaccgacaagctatttatacatgct-----

upper sequence: GLYMA20G38980.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G346132_T01 (Zea mays), 5'ss of exon 6
TGATGTCTATAGTTTTGGTGTTGTTCTTCTTGAGCTTCTTACAGGAAGAAAACCTGTTGACCATACCATGCCTAGAGGACAGCAGAGTCTTGTCACATGGgtcagtgtgtctgcttaaactcatacctcatccgtgctgctgcttttcaatcatttaacactggttgtcggccataggtattttgttgacattgatatttttttgtag
|||||| ||||| || || || |||||| | |||||| | ||||| ||||| || || |||||||| ||||||||||| |||||||| || || || |||||  ||     |||| ||  |  | |||     || ||  |||  ||  ||    | |   ||  | |  |   |   |    | ||||       | || | |    
TGATGTATATAGCTTCGGAGTAGTTCTTTTGGAGCTTTTGACAGGTAGAAAGCCAGTAGACCATACAATGCCTAGAGGGCAGCAGAGCCTAGTAACTTGGgtatgttcacttgct-aactttttccctttgttgtccttttgcggttagatg---tgaacttgtatataagtagtttctgcaatattgaagcaacaaattgtgt----

upper sequence: GLYMA20G38980.1 (Glycine max), 5'ss of exon 7
lower sequence: AT2G43230.1 (Arabidopsis thaliana), 5'ss of exon 5
TGATGTCTATAGTTTTGGTGTTGTTCTTCTTGAGCTTCTTACAGGAAGAAAACCTGTTGACCATACCATGCCTAGAGGACAGCAGAGTCTTGTCACATGGgtcagtgtgtctgcttaaactcatacctcatccgtgctgctgcttttcaatcatttaacactggttgtcggccataggtattttgttgacattgatatttttttgtag
|||||| || |||||||| ||||| ||| | || |||||||| || |||||||| ||||| ||||| |||||| | || || |||||||||||||| ||||| | |     | |||||  | |   ||| | | | |||   ||    |||| |||           | ||  |||  | | |   | |   | ||||          
TGATGTTTACAGTTTTGGAGTTGTGCTTTTGGAACTTCTTACCGGGAGAAAACCGGTTGATCATACTATGCCTCGTGGTCAACAGAGTCTTGTCACTTGGgt-acttaacttacttaatttga---ctctttctttctgagactaccaaatcttttc----------ttggttataactttctctgtaaatctaatatccag------

upper sequence: GLYMA20G38980.1 (Glycine max), 5'ss of exon 7
lower sequence: Vv05s0124g00360.t01 (Vitis vinifera), 5'ss of exon 6
TGATGTCTATAGTTTTGGTGTTGTTCTTCTTGAGCTTCTTACAGGAAGAAAACCTGTTGACCATACCATGCCTAGAGGACAGCAGAGTCTTGTCACATGGgtcagtgtgtctgcttaaactcatacctcatccgtgctgctgcttttcaatcatttaacactggttg---tcggccataggtattttgttgacattgatatttttttgtag--------------------------
|||||| ||||||||||| ||||||||  | |||||||| || || |||||||||||||| |||||||||||| | ||||| || ||||| ||||| |||||  | || | | |||    |  | ||| ||  |       || |||   |||   |   |   |     |   | |     | ||  ||  | ||||||| | | | ||                           
TGATGTGTATAGTTTTGGAGTTGTTCTGTTAGAGCTTCTAACTGGGAGAAAACCTGTTGATCATACCATGCCTCGTGGACAACAAAGTCTGGTCACCTGGgt--gggttttttcttctttttctgcct-atttgcttaaaagccttttgttcacccagtgcctttcaagtttctctactccaaattgcttttctttgatatatatctataatctaaagtgaacatttctcatcttag

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|19053775|gb|BM732442.1|BM732442
EST:     AACCTGTTGACCATACCATGCCTAGAGGACAGCAGAGTCTTGTCACATGG                         GCTACTCCAAGATTAAGTGAAGATAAAGTGAAACAGTGCGTTGACCCAAAA
genomic: AACCTGTTGACCATACCATGCCTAGAGGACAGCAGAGTCTTGTCACATGGgtcagtgtgt ... ttttttgtagGCTACTCCAAGATTAAGTGAAGATAAAGTGAAACAGTGCGTTGACCCAAAA
EST: gi|15663739|gb|BI701110.1|BI701110
EST:     AACCTGTTGACCATACCATGCCTAGAGGACAGCAGAGTCTTGTCACATGG                         GCTACTCCAAGATTAAGTGAAGATAAAGTGAAACAGTGCGTTGAC
genomic: AACCTGTTGACCATACCATGCCTAGAGGACAGCAGAGTCTTGTCACATGGgtcagtgtgt ... ttttttgtagGCTACTCCAAGATTAAGTGAAGATAAAGTGAAACAGTGCGTTGAC
EST: gi|15663685|gb|BI701056.1|BI701056
EST:     AACCTGTTGACCATACCATGCCTAGAGGACAGCAGAGTCTTGTCACATGG                         GCTACTCCAAGATTAAGTGAAGATAAAGTGAAACAGTGCGTT
genomic: AACCTGTTGACCATACCATGCCTAGAGGACAGCAGAGTCTTGTCACATGGgtcagtgtgt ... ttttttgtagGCTACTCCAAGATTAAGTGAAGATAAAGTGAAACAGTGCGTT
EST: gi|8669663|gb|BE190770.1|BE190770
EST:     AACCTGTTGACCATACCATGCCTAGAGGACAGCAGAGTCTTGTCACATGG                         GCTACTCCAAGATTAAGTGAAGATAAAGTGAAACAGTGCGTTGACCCAAAA
genomic: AACCTGTTGACCATACCATGCCTAGAGGACAGCAGAGTCTTGTCACATGGgtcagtgtgt ... ttttttgtagGCTACTCCAAGATTAAGTGAAGATAAAGTGAAACAGTGCGTTGACCCAAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATGTCTATAGTTTTGGTGTTGTTCTTCTTGAGCTTCTTACAGGAAGAAAACCTGTTGACCATACCATGCCTAGAGGACAGCAGAGTCTTGTCACATGGgtcagtgtgtctgcttaaactcatacctcatccgtgctgctgcttttcaatcatttaacactggttgtcggccataggtattttgttgacattgatatttttttgtag

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