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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGGGATGCTCTCAACTCCGCACTCGATGAGGAAATGTCAGCTGATCCTAAAGTCTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAGgttggttagttagttagtttagttgtcttgccaacctctccttttaagaacttcattgacttaactttcttccttctttcattttag

Basic information

species Glycine max
transcript GLYMA14G36540.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G36540.2 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os09g33500.1 (Oryza sativa), 5'ss of exon 3
--------CAGGGATGCTCTCAACTCCGCACTCGATGAGGAAATGTCAGCTGATCCTAAAGTCTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAGgttggttagttagttagtttagttgtcttgccaacctctccttttaagaacttcattgacttaactttcttccttctttcattttag
        | | || || || ||||| ||||||||||| |||||||| |||||||||   || ||  ||||||||||||||||     |   |  |    ||  ||   ||   |   |  || || | ||| |  |     | |||| ||    | |                                     
ATGACTGTCCGTGAAGCGCTGAACTCTGCACTCGATGAAGAAATGTCTGCTGATCCTTCTGTTTTTCTGATGGGTGAAGAGgt-----acacttggaactcactcact-ttctctccctgatttgtgt-gtttttctaaggccttctctttcgtggcag------------------------------------

upper sequence: GLYMA14G36540.2 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os08g42410.2 (Oryza sativa), 5'ss of exon 2
CAGGGATGCTCTCAACTCCGCACTCGATGAGGAAATGTCAGCTGATCCTAAAGTCTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAGgttggttagtta-gttag------------tttag----ttgtcttgccaacctctccttttaagaacttcattgacttaactttcttccttctttcattttag--
  | || ||  | || || || || |||||||| ||||| ||||| |||   || ||||||||||| ||||||||||| ||||| || || ||||| |||||  || | ||   ||||            ||| |    || || || ||   |    || | |  |||  || |       | |||| | |    ||||||    
GCGTGAAGCATTGAATTCTGCCCTTGATGAGGAGATGTCTGCTGACCCTTCTGTTTTCTTGATGGGAGAAGAGGTTGGAGAATACCAAGGGGCATATAAGgtgagtaatttttattagaccaatgctgtctttggcccattatcatgacataattaatttctgaatactaaatagtaaagcttctctttcctgcaacattttgcag

upper sequence: GLYMA14G36540.2 (Glycine max), 5'ss of exon 4
lower sequence: AT5G50850.1 (Arabidopsis thaliana), 5'ss of exon 4
--------CAGGGATGCTCTCAACTCCGCACTCGATGAGGAAATGTCAGCTGATCCTAAAGTCTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAGgttggttagttagttagtttagttgtcttgccaacctctccttttaagaacttcattgacttaactttcttccttctttcattttag
        ||| |||||||| || || ||| | |||||||||||||| |||||||||||||| ||  | ||||||||||||||| |        |   ||  |   |  ||  |     | ||  | || |    |   |||  |||| | ||    |  |  ||    ||                        
ATGACAGTCAGAGATGCTCTAAATTCTGCAATTGATGAGGAAATGTCTGCTGATCCTAAAGTATTTGTCATGGGTGAAGAGgttagttgcagctaacatgtttgataaattcatcttgcaatt--tctaatcagat-atcaatatctcatcttt--tatcttgttattgtag-----------------------

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|209713861|gb|BW684054.1|BW684054
EST:     AAGTCTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAG                         ATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGCTTCTCGATACT
genomic: AAGTCTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAGgttggttagt ... ttcattttagATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
EST: gi|7588536|gb|AW704259.1|AW704259
EST:     AAGTCTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAG                         ATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
genomic: AAGTCTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAGgttggttagt ... ttcattttagATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
EST: gi|120533350|gb|EH261483.1|EH261483
EST:     AAGTCTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAG                         ATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
genomic: AAGTCTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAGgttggttagt ... ttcattttagATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
EST: gi|298196446|gb|HO041189.1|HO041189
EST:     AAGTCTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAG                         ATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
genomic: AAGTCTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAGgttggttagt ... ttcattttagATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
EST: gi|192323797|gb|FK015608.1|FK015608
EST:     AAGTCTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAG                         ATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
genomic: AAGTCTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAGgttggttagt ... ttcattttagATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
EST: gi|37994649|gb|CF806308.1|CF806308
EST:     GAATATCAGGGTGCATACAAG                         ATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
genomic: GAATATCAGGGTGCATACAAGgttggttagt ... ttcattttagATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
EST: gi|17400857|gb|BM177639.1|BM177639
EST:     AAGTCTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAG                         ATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
genomic: AAGTCTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAGgttggttagt ... ttcattttagATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
EST: gi|21638580|gb|BM139626.1|BM139626
EST:     AAGTCTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAN                         ATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
genomic: AAGTCTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAGgttggttagt ... ttcattttagATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
EST: gi|151396530|gb|EV266407.1|EV266407
EST:     AAGTCTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAG                         ATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
genomic: AAGTCTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAGgttggttagt ... ttcattttagATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
EST: gi|254335254|gb|GR846751.1|GR846751
EST:     AAGTCTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAG                         ATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
genomic: AAGTCTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAGgttggttagt ... ttcattttagATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
EST: gi|254340298|gb|GR858423.1|GR858423
EST:     AAGTCTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAG                         ATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
genomic: AAGTCTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAGgttggttagt ... ttcattttagATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
EST: gi|254319588|gb|GR829100.1|GR829100
EST:     AAGTCTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAG                         ATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
genomic: AAGTCTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAGgttggttagt ... ttcattttagATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
EST: gi|16996929|gb|BM086301.1|BM086301
EST:     AAGTCTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAG                         ATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
genomic: AAGTCTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAGgttggttagt ... ttcattttagATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGGGATGCTCTCAACTCCGCACTCGATGAGGAAATGTCAGCTGATCCTAAAGTCTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAGgttggttagttagttagtttagttgtcttgccaacctctccttttaagaacttcattgacttaactttcttccttctttcattttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG