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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctctcttttttaaactgtatatttttattaaagaacaaaaaattgataccgataaaaaaaattgtctcgcagATCCTACTTACATGATCCGTGCTATCCCAAGTAATGCATCTGATAATGTATACTGCACCCTCCTTGCCCAAAGTGCTGTTCATGGTGCAATGGCAGGATA

Basic information

species Glycine max
transcript GLYMA15G02400.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G02400.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os05g44922.1 (Oryza sativa), 3'ss of exon 12
gtgagc-tctcttttttaaactgtatatttttattaaagaacaaaaaattgataccgat-aaaaaaaattgt-----------------ctcgcagATCCTACTTACATGATCCGTGCTATCCCAAGTAATGCATCTGATAATGTATACTGCACCCTCCTTGCCCAAAGTGCTGTTCATGGTGCAATGGCAGGATA
|| |   | | |  || | || | |||   || ||| | | |  |  | || |  | ||   |  || ||||                  | ||||||||||| ||||||||||| ||||| ||||| |||||||| || ||||| |||||||| || || ||||| |||||| |||||||||||||||| || ||
gtaactatgtttgcttcacacaggataaggttgttacacatcttattactggtctctattgtactaagttgtgaagttccctattattatttgcagATCCTACCTACATGATCCGAGCTATTCCAAGCAATGCATCAGACAATGTCTACTGCACGCTGCTGGCCCACAGTGCTATTCATGGTGCAATGGCCGGCTA

upper sequence: GLYMA15G02400.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 12
----------------------------------------------------gtgagctctcttttttaaactgtatatttttattaaagaacaaaaaattg--ataccgataaaaaaaattgtctcgcagATCCTACTTACATGATCCGTGCTATCCCAAGTAATGCATCTGATAATGTATACTGCACCCTCCTTGCCCAAAGTGCTGTTCATGGTGCAATGGCAGGATA
                                                     |||  |     |||| |  ||||| |   |||      |   ||  |||  ||| |        |  |    | |||||||| || |||||||||||||| || ||||| |||||||| || ||||| |||||||| || || || || |||||  ||||||| |||||||| |||||
gtaaagatcttgtttttatgttcaattctcgatgcacatgcggagtgctagtttgaagtactactttttatatgtatctgagtatctccctatggaatgttgcaataacagcctgttatttctaatggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA

upper sequence: GLYMA15G02400.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os06g05860.1 (Oryza sativa), 3'ss of exon 12
------------gtgagctctcttttttaaactgtatatttttattaaaga-acaaaaaattgataccgataaaaaaaattgtctcgcagATCCTACTTACATGATCCGTGCTATCCCAAGTAATGCATCTGATAATGTATACTGCACCCTCCTTGCCCAAAGTGCTGTTCATGGTGCAATGGCAGGATA
             |    |||  ||||   |    |   |||  || |    ||   ||    ||  |       |   || | | ||||||||||| |||||||| ||||| || || || ||||||||||| ||||| || ||||| ||  | || || ||||  |||||||| || ||||| |||||
gtcagtcgcctcttttattctacttttagcatcccaagctttgcttgatttcactgtaacaaaatctcagatcttatgcttctattgcagATCCTACATACATGATACGTGCCATTCCTAGCAATGCATCTGACAATGTGTATTGCACACTGTTGGCACACAGTGTGGTTCATGGAGCCATGGCTGGATA

upper sequence: GLYMA15G02400.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 12
gtga--gctctctttttta-------aac----tgtatatttttattaaagaacaaaaaattgataccgataaaaa-------aaattgtctcgcagATCCTACTTACATGATCCGTGCTATCCCAAGTAATGCATCTGATAATGTATACTGCACCCTCCTTGCCCAAAGTGCTGTTCATGGTGCAATGGCAGGATA
|| |  |   |||||||||       |||    |||   ||| || |  | | ||    |  ||  | ||| ||         |  || |   | |||||| |||||||||||||||||||| ||||| |||||||| || ||||| || |||||||| || || || |||||  |||||||||||||||| |||||
gtaatcgtcttcttttttacttggtgaacgcagtgttagtttgtaatttatagcatgtcaaggaatctgatgaagtgcctgccatttttttatgtagATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCTATTGCACCCTGCTCGCACATAGTGCCATTCATGGTGCAATGGCGGGATA

upper sequence: GLYMA15G02400.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G004932_T01 (Zea mays), 3'ss of exon 12
----------gtgagctctcttttttaaactgtatatttttattaaagaacaaaaaattgataccgataaaaaaaattgtc-----tcgcagATCCTACTTACATGATCCGTGCTATCCCAAGTAATGCATCTGATAATGTATACTGCACCCTCCTTGCCCAAAGTGCTGTTCATGGTGCAATGGCAGGATA
          || |    | |||||   | || ||||  || | | | |     | |||| | | |  | || |     ||     | ||||||||||| |||||| |||||||||| ||||| |||||||| || ||||| ||||| || || || ||||| |||||| | |||||||||||||| || ||
gtagccatttgtaactcttatttttgctattg-atatagttgtaacacatttctagattggt-ctgtgacaatattccatcggaattggcagATCCTACATACATGGTCCGTGCTATTCCAAGCAATGCATCAGACAATGTCTACTGTACACTTCTAGCCCACAGTGCTATCCATGGTGCAATGGCGGGGTA

upper sequence: GLYMA15G02400.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S69_13V6.1 (Physcomitrella patens), 3'ss of exon 12
-----------------------gtgagctctcttttttaaactgtatatttttattaaagaacaaaaaattgataccgataa--aaaaaattgtctcgcagATCCTACTTACATGATCCGTGCTATCCCAAGTAATGCATCTGATAATGTATACTGCACCCTCCTTGCCCAAAGTGCTGTTCATGGTGCAATGGCAGGATA
                       ||| ||| |  || ||      | || |    | ||||| |    ||   | ||  | |       |   || | |||||||| ||||||||||| || ||| | || |||| ||||||||||||||| ||||||||| |  | || || |||||  | |||||||| ||||| || | 
gtatacaagaccctacttttaatgtgggctatggttattgtgggctgtagtacgctgaaagagcgctcaac--acactaacagttgtggatccgtttggcagATCCAACTTACATGATTCGAGCTGTACCGAGTATTGCATCTGATAATGTTTACTGCACCTTGTTGGCGCATAGTGCCATCCATGGTGCTATGGCTGGTTT

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|26047392|gb|CA784199.1|CA784199
EST:     GATCACTTTGAAAAACGTCAAAAAATGGCTATAAATCTGAAGTACATAG                         ATCCTACTTACATGATCCGTGCTATCCCAAGTAATGCATCTGATAATGTAT
genomic: GATCACTTTGAAAAACGTCAAAAAATGGCTATAAATCTGAAGTACATAGgtgagctctc ... tgtctcgcagATCCTACTTACATGATCCGTGCTATCCCAAGTAATGCATCTGATAATGTAT
EST: gi|151400140|gb|EV269954.1|EV269954
EST:     GATCACTTTGAAAAACGTCAAAAAATGGCTATAAATCTGAAGTACATAG                         ATCCTACCTACATGATCCGTGCTATCCCAAGTAATGCATCTGATAATGTAT
genomic: GATCACTTTGAAAAACGTCAAAAAATGGCTATAAATCTGAAGTACATAGgtgagctctc ... tgtctcgcagATCCTACTTACATGATCCGTGCTATCCCAAGTAATGCATCTGATAATGTAT
EST: gi|151406712|gb|EV276527.1|EV276527
EST:     GATCACTTTGAAAAACGTCAAAAAATGGCTATAAATCTGAAGTACATAG                         ATCCTACTTACATGATCCGTGCTATCCCAAGTAATGCATCTGATAATGTAT
genomic: GATCACTTTGAAAAACGTCAAAAAATGGCTATAAATCTGAAGTACATAGgtgagctctc ... tgtctcgcagATCCTACTTACATGATCCGTGCTATCCCAAGTAATGCATCTGATAATGTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatttttattaaagaacaaaaaattgataccgataaaaaaaattgtctcgcagATCCTACTTACATGATCCGTGCTATCCCAAGTAATGCATCTGATAATGTATACTGCACCCTCCTTGCCCAAAGTGCTGTTCATGGTGCAATGGCAGGATA
                       aattgat  putative branch site (score: 4)
                                            ttgtctc  putative PPT
     ttttattaaagaacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagctctcttttttaaactgtatatttttattaaagaacaaaaaattgataccgataaaaaaaattgtctcgcagATCCTACTTACATGATCCGTGCTATCCCAAGTAATGCATCTGATAATGTATACTGCACCCTCCTTGCCCAAAGTGCTGTTCATGGTGCAATGGCAGGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT