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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttttgtatgtagtggagctagttttcaagccttgacaattacttgtttgaaactttgtagtttagtgagtgctaacacattgattgtaaaatatgtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG

Basic information

species Glycine max
transcript GLYMA07G01440.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 5
--------------------------------------------------------------------------------------------atttttgtatgtag---tggagctagttttcaagccttgacaattacttgtttgaaactttgtagtttagtgagtgctaacacattgattgtaaaatatgtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG
|||| | ||| | | || ||| ||| | | | | || | || | | || ||||| | | | || | |||| |||| || |||| || | | || | |||| || | |||||| | |||||||||||||| ||||||||||| ||||||||||| ||
gttgtacttaacccactttattcattatctcatctgtaatcgtgttgttctgtacagcaccaaatctggtgttcacatgtaaaataagtctccttttggcatgaatacttatagatagattttcttctt--atggcaaactgcacatatgattacaatata-tgagtatttattt-tcatttactatgtatgcagGTCACTGGCCAAGATTTGAACCTTGTACCAAGATGCCGGCGTGTATATTCACATGCTCATGATTACCATATTAATTCCATTTCAAATAATAG

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 5
--------------------------------------------atttttgtatgtagtggagctagt-tttcaagcc--ttgacaattacttgtttgaaactttgtagtttagtg-agtgctaac-acattgattgtaaaatatgtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG
|| ||| | | | |||| || ||| | || ||||| | | | | | ||| | | || |||| || | ||| |||| | || || || | | || ||| ||||||| | |||||||| |||||||||||||| |||||||| ||||| |||| || ||
gtagttgtacttaacctctatatatcttaatcaacagaagatgacttgatgtcttgatcagctctagcacatctagctggcatatgataacttgcacggcaacctatgatcaagtccaaaattgactgcatttcttat----catgcagGTTGCAAGTCAAGATGTGAACCTTGTTGCTAGATGTCGACGTGTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAG

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 5
-----------------------------------------atttttgtatgtagtggagctagt-tttcaagcc--ttgacaattacttgtttgaaactttgtagtttagtg-agtgctaac-acattgattgtaaaatatgtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG
|| ||| | | | |||| || ||| | || ||||| | | | | | ||| | | || |||| || | ||| |||| | || || || | | || ||| ||||||| | |||||||| |||||||||||||| |||||||| ||||| |||| || ||
gttgtacttaacctctatatatcttaatcaacagaagatgacttgatgtcttgatcagctctagcacatctagctggcatatgataacttgcacggcaacctatgatcaagtccaaaattgactgcatttcttat----catgcagGTTGCAAGTCAAGATGTGAACCTTGTTGCTAGATGTCGACGTGTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAG

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 5
-------------------------------------------------------------atttttgtatgtagtggagctagttttcaagccttgacaa--------ttacttgtttgaaactttgtagttta-gtgagtgctaacaca--------ttgattgtaaaatatgtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG
|| | | | || ||||| ||||| | | | | | | | ||| | | | |||| ||| | | || | |||| |||| || |||| || | | || || || | | | |||||||||||||| ||||| || ||||||||||| ||||||||||| ||
gtagtacttaaacccacttcatctatcatctctaggttgtacaacatgaggaattagcattgcttgcatgtacaacacagtagtttttccccttgtgacagagaactagacattcttctaacagactatagataatatcagtgataattctgaatactttcctttactatttatgcagGTTACAGGCCAAGAATTTACTCATGTTGCGAGAAGCAGACGTGTATATGCCCATGCCCATGACTACCATATTAATTCCATTTCAAATAATAG

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G142334_T01 (Zea mays), 3'ss of exon 5
---------------------------------------------------------------------------------atttttgtatgtagtggagctagttt--tcaagccttgacaattact---tgtttga--aactttgtagtttagtgagtgcta-acacattgattgtaaaatat--gtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG
|||| || | | | | ||| || | | | || || | | | | |||||| | || | || || || | | | |||| | | |||| || | ||| || || || | | || | || || ||||||||||| ||||| ||||| |||||||| ||||| || |||||||||||
gctgtacttaactcagtttcatttattcacctggcaaaaagcatattctaattatttagaaccattatgccattacctggaatttatgcagcgggaaaatgcattttagtcgattcatcgtccttcctgtctatgtaaccaactttttttttcacaatttgttacactgacccagtctaaactgtaaacagGTTACAACCCAAGAAACAAGCCTTGCTGCGAGTTGCCGAAGAGTATATGCTCATGCACATGACTATCATATAAATTCAATATCAAATAACAG

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 5
------------------------------------------------------------------------------------atttttgtatgtagtggagctagttt--tcaagccttgacaattact---tgtttga--aactttgtagtttagtgagtgcta-acacattgattgtaaa--atatgtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG
|||| || | | | | ||| || | | | || || | | | | |||||| | || | || || || | | | |||| || |||| || | ||| || || || | | || | || || ||||||||||| ||||| ||||| |||||||| ||||| || |||||||||||
gtagctgtacttaactcagtttcatttattcacctggcaaaaagcatattctaattatttagaaccattatgccattacctggaatttatgcagcgggaaaatgcattttagtcgattcatcgtccttcctgtctatgtaaccaactttttttttcacaatttgttacactgacccagtctaaactgtaaacagGTTACAACCCAAGAAACAAGCCTTGCTGCGAGTTGCCGAAGAGTATATGCTCATGCACATGACTATCATATAAATTCAATATCAAATAACAG

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 6
-----------------atttttgtatgtagtggagctagttttcaagccttgaca---attacttgt--ttgaaactttgtagtttagtgagtgct------aacacattgattgt---aaaatatgtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG
| || | ||| || | ||| || | | || || |||| | ||||| | || | | | | ||| |||| | | | ||||| |||| ||||| | || | | || ||| ||||||| | |||| ||| |||||||| ||||| ||||| ||||||||||||||||| ||
gtaagctatactcgacaacttatatat-tattaactttagcatttgaaattgtacttgtataacttttaagtgaaattatgcaaaactgcagctatttagtccaactcatttctctttcgaccatatgcagGTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGCTCATGCTCACGATTACCATATAAATTCTATTTCAAATAATAG

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G164185_T01 (Zea mays), 3'ss of exon 5
-----------------------------------------------------------------------atttttgtatgtagtggagctag--------tttt---caagccttgacaattacttgtttgaa-----actttgtagtttagtgagtgctaacac--attgattgtaaaatat--gtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG
||| || || | ||| |||| |||| | || | ||| | ||| | | ||| | ||| | | | ||| | | | | |||| | | |||| || ||||| || || ||| | | | | || || ||||||||||| ||||| ||||| || ||||| ||||| || |||||||||||
gttgtacttaactcagtttcatttatgcaccttgcaaaaccatattgtagttatttagaactattgagctgattcctggatattgtgtagctgaaaattgtattttagttgattctaaaatatttcctgtctatgtaaccattttttcttttcacaatttgttacattgactcagtataaactgtaaacagGTTACAAGCCAAGAAACAAGTCTTGCCACAAGTTGCCGAAGAGTATATGCTCATGCACATGACTACCATATAAATTCGATATCAAATAACAG

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 5
--------------------------------------------------------------------------atttttgtatgtagtggagctag---------ttt--tcaagccttgacaattacttgtttgaa-----actttgtagtttagtgagtgctaacac--attgattgtaaa--atatgtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG
||| || || | ||| |||| ||| | | || | ||| | ||| | | ||| | ||| | | | ||| | | | | |||| || |||| || ||||| || || ||| | | | | || || ||||||||||| ||||| ||||| || ||||| ||||| || |||||||||||
gtagttgtacttaactcagtttcatttatgcaccttgcaaaaccatattgtagttatttagaactattgagctgattcctggatattgtgtagctgaaaattgtattttagttgattctaaaatatttcctgtctatgtaaccattttttcttttcacaatttgttacattgactcagtataaactgtaaacagGTTACAAGCCAAGAAACAAGTCTTGCCACAAGTTGCCGAAGAGTATATGCTCATGCACATGACTACCATATAAATTCGATATCAAATAACAG

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 7
-------atttttgtatgtagt--ggagctagttttcaagccttgacaattacttgtttgaaactttgtagtttagtgagtgctaacacattgattgtaaaatatgtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG
| | | | ||| | || | ||| | || |||| || || | | || | ||| || | || |||| | | |||| ||||||| ||||||||| | || |||||| ||||||| ||||||||||| |||||||||||||||||||||||||| || |||||||||||
catggccttcactaccactgattaggaattgattcttaagtcatg-caata--ttacttaata-ttgctcatttgtagactaatagttcatt-----tgacatatacagGTAACTAGCCATGAGTCGAGCCCTGTGGCTAGATGTCGAAGAGTATATGCTCATGCTCATGATTATCATATTAATTCAATCTCAAATAACAG

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 5
atttttgtatgtagtggagctagttttcaagccttgacaatt---acttgtttgaaactttgtagtttagtgagtgctaacacattgattgtaaaatatgtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG
| ||| | | | | ||| ||| | | | | | | | | ||||| | || | | || | | || |||| ||||| |||||||| ||||| | | |||||| |||| || ||||| |||||||||||||||||||| ||||||||||| || || |||| |||
ttgtttccttttgtcgtaactaaagctcagtaccaaattagtctaatgcactagtcaatttgtgttctactt-gaacttatgggt--gtttctgcatatatagGTTACCAGCCAGGAGACTAACCTTGTGGCTAGATGCCGAAGAGTGTATGCCCATGCTCATGATTACCATATTAATTCAATCTCCAATAGCAG

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 5
atttttgtatgtagtggagctagttttcaagcctt--gacaattacttgtttgaaactttgtagt---ttagtgagtgctaacacattgattgtaaaatatgtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG
| || | ||||| | | | | | || ||| | || | || | | | || | ||||||| | | | || |||||||||||| | |||| ||||||||| |||||||| ||||||||||||| ||||| |||||||| || |||||||| ||||||||||||||||| ||
-----gttccaaggtatacttagttattacgtcattggatgtttaataagtttagtgttcatgataactgcctgtgatctaacacttccagtatacaatatgtagGTATCAAGCCCTGAGACCAGCCTGGTGGCTAGATGTCGTAGAGTTTATGCTCATGCTCACGACTATCATATCAATTCTATTTCAAATAATAG

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|208080786|gb|GD875084.1|GD875084
EST:     ACGATTTCTCATTTCCACCAGAAGGCGTACCTTCTCTAAGATTACCATTG                         GTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCC
genomic: ACGATTTCTCATTTCCACCAGAAGGCGTACCTTCTCTAAGATTACCATTGgtagttgtgt ... aaatatgtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCC
EST: gi|22525826|gb|BU084637.1|BU084637
EST:     ACGATTTCTCATTTCCACCAGAAGGCGTACCTTCTCTAAGATTACCATTG                         GTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCC
genomic: ACGATTTCTCATTTCCACCAGAAGGCGTACCTTCTCTAAGATTACCATTGgtagttgtgt ... aaatatgtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttgaaactttgtagtttagtgagtgctaacacattgattgtaaaatatgtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG
                                   attgattgtaaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttttgtatgtagtggagctagttttcaagccttgacaattacttgtttgaaactttgtagtttagtgagtgctaacacattgattgtaaaatatgtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG

- - - - - gtagtgg
- - - - - - - - - - - - -ttcaagc
- - - - - - - - - - - - - - - - cttgaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgagtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacacat