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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactaactaactcatcaaatcaaagagttttttttgtctcatttcccgaaaccgtcgtcgttttatcttaaaccgtgtgtcgtttttgttttttcagGTATGGGCGCGGCGTACGGCACCGCGAAGAGCGGCGTCGGGGTTGCGTCGATGGGCGTGATGAGGCCGGAGCTGGTGATGAAATCGATCGTGCCGGTTGT

Basic information

species Glycine max
transcript GLYMA02G05630.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G05630.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os11g06890.2 (Oryza sativa), 3'ss of exon 1
----gtaactaactaactcatcaaatcaaagagttt----tttttgtctcatttcccgaaaccgtcgtcgttttatcttaaaccgtgtgtcgtttttgttttttcagGTATGGGCGCGGCGTACGGCACCGCGAAGAGCGGCGTCGGGGTTGCGTCGATGGGCGTGATGAGGCCGGAGCTGGTGATGAAATCGATCGTGCCGGTTGT
     |    | |  | |  |      ||| ||||      ||| |  ||  |||  ||    |   |    |||| |         | || ||     | || |||| ||||| ||||||||||| || ||||||||||||||||| || ||||| |||||||||||| | |||||||| |||||||| || |||||||| || ||
ccgattggagatcggatttgtggggaaaaaaagttgggagctttggattctgttcttgatggggggatttgcttatttgc-------tttcattcgatctgttgcagGCATGGGTGCGGCGTACGGGACGGCGAAGAGCGGCGTCGGCGTGGCGTCCATGGGCGTGATGCGCCCGGAGCTCGTGATGAAGTCCATCGTGCCCGTGGT

upper sequence: GLYMA02G05630.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g73130.1 (Oryza sativa), 3'ss of exon 1
gtaactaactaactcatcaaatcaaagagttttttttgtct-catttcccgaaaccgtcgtcgttttatcttaaaccgtgtgtcgtttttgttttttcagGTATGGGCGCGGCGTACGGCACCGCGAAGAGCGGCGTCGGGGTTGCGTCGATGGGCGTGATGAGGCCGGAGCTGGTGATGAAATCGATCGTGCCGGTTGT
  ||  ||  | |  |  ||     |        |   ||| ||  |  |   |             ||        |    | | || |  |||| |||| ||||| ||||||||||| || ||   ||||||||||||||| |||   ||||| |||||| ||||||||||||||||||| |||||||||||||| ||
agaaaaaaagatcgtaaaaagctcgatcaaacgatcgatctgcaagtttctgcattacgaattacgaattgatggatgaaatttggttataattttgcagGCATGGGGGCGGCGTACGGGACGGCTCGGAGCGGCGTCGGGGTGGCGCACATGGGGGTGATGCGGCCGGAGCTGGTGATGAAGTCGATCGTGCCGGTGGT

upper sequence: GLYMA02G05630.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os05g01560.1 (Oryza sativa), 3'ss of exon 1
gtaactaactaactcatcaaatcaaagagttttttttgtctcatttcccgaaaccgtcgtcgttttatcttaaaccgtgt-gtcgtttttgttttttcagGTATGGGCGCGGCGTACGGCACCGCGAAGAGCGGCGTCGGGGTTGCGTCGATGGGCGTGATGAGGCCGGAGCTGGTGATGAAATCGATCGTGCCGGTTGT
                   || |    | | ||     || | |||| ||   ||       | | |||| | |    || | |          |   ||| |||||||| || ||||||||||| ||||||||||| || || ||||| ||||| |||||| | ||||| ||||||||||| || ||||| || || ||
-----------------gtaagctcccaatcttccccttcac-tttctcggggccag----atctgatctgagatgaggttgacacacgacgcatgcaagGCATGGGCGCCGCCTACGGCACCGCCAAGAGCGGCGTGGGCGTGGCGTCCATGGGGGTGATGCGCCCGGAACTGGTGATGAAGTCCATCGTCCCCGTCGT

upper sequence: GLYMA02G05630.2 (Glycine max), 3'ss of exon 1
lower sequence: AC216067.3_FGT002 (Zea mays), 3'ss of exon 1
---gtaactaactaactcatcaaatcaaagagttttttttgtctcatttcccgaaaccgtcgtcgttttatcttaaaccgtgtgtcgtttttgttttttcagGTATGGGCGCGGCGTACGGCACCGCGAAGAGCGGCGTCGGGGTTGCGTCGATGGGCGTGATGAGGCCGGAGCTGGTGATGAAATCGATCGTGCCGGTTGT
    |       |      |   ||   |||  |      | ||  |  |   | || | |   ||  |  ||       | | | | ||       | |||| |||||||| |||||||| |||||||||||||||||||| || ||||||||||| |||||| |||||||||| || ||||| || |||||||| || ||
gatttggtccgatcgggtgtgggatttcagaaatcgaca-gccttttcccgtcagacaggcag-gtcctgactacgctgttcttttgcttgatccgatgcagGCATGGGCGCAGCGTACGGGACCGCGAAGAGCGGCGTCGGCGTGGCGTCGATGGGTGTGATGCGGCCGGAGCTCGTCATGAAGTCCATCGTGCCCGTGGT

upper sequence: GLYMA02G05630.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G177005_T01 (Zea mays), 3'ss of exon 1
-------gtaactaactaactcatcaaatcaaagagttttttttgtctcatttcccgaaaccgtcgtcgttttatcttaaaccgtgtgtcgtttttgttttttcagGTATGGGCGCGGCGTACGGCACCGCGAAGAGCGGCGTCGGGGTTGCGTCGATGGGCGTGATGAGGCCGGAGCTGGTGATGAAATCGATCGTGCCGGTTGT
        |        |     ||  ||   |||      |  |  |  |    ||   | || |  |  |   ||       | | | | ||         |||| |||||||| |||||||| |||||||||||||||||||| || ||||||||||| |||||| |||||||||| || ||||| || |||||||| || ||
tggtccgatcgggtgtcagtctgtcggattccagaaagcggtgggctttttcggtcggg-cagttgctgactaggctgt-----tattttgcttgatccggcgcagGCATGGGCGCCGCGTACGGGACCGCGAAGAGCGGCGTCGGCGTGGCGTCGATGGGTGTGATGCGGCCGGAGCTCGTCATGAAGTCCATCGTGCCCGTGGT

upper sequence: GLYMA02G05630.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G101020_T01 (Zea mays), 3'ss of exon 1
---gtaact--aactaactcatcaaatcaaagagttttttttgtctcatttcccgaaaccgtcgtcgttttatcttaaaccgtgtgtcgtttttgttttttcagGTATGGGCGCGGCGTACGGCACCGCGAAGAGCGGCGTCGGGGTTGCGTCGATGGGCGTGATGAGGCCGGAGCTGGTGATGAAATCGATCGTGCCGGTTGT
     || |     |   ||       |   ||  | |    |    ||||   |        | | |   ||||    | |||| | || | ||  |   |||| ||||| ||||||||||| || || ||||| |||||||| || ||||| ||||| || ||| | || ||||| || ||||| || |||||||| || ||
gagagaatttgggttggatccatgtggctgggacgtgtgagggcgaaatttttggtggtgaatgacatg--atctccctctgtgtat-gtgtgtggctcg-cagGCATGGGGGCGGCGTACGGGACAGCCAAGAGTGGCGTCGGCGTGGCGTCCATGGGTGTCATGCGCCCAGAGCTCGTCATGAAGTCCATCGTGCCCGTGGT

upper sequence: GLYMA02G05630.2 (Glycine max), 3'ss of exon 1
lower sequence: AT1G19910.1 (Arabidopsis thaliana), 3'ss of exon 1
gtaactaactaactcatcaaatcaaagagttttttttgtctcattt-cccgaaaccgtcgtcgttttatcttaaaccgtgtgtcgtt---tttgttt---tttcagGTATGGGCGCGGCGTACGGCACCGCGAAGAGCGGCGTCGGGGTTGCGTCGATGGGCGTGATGAGGCCGGAGCTGGTGATGAAATCGATCGTGCCGGTTGT
||| | | || | |  || | ||      | | || | |||  ||| |||  ||  |   | | |  |  |   | |   |    ||   |  | ||   ||||||||||||| || |||||||| || ||||||||||| || || || ||||||||||| |||||||| || ||||| |||||||||||||| || || |||||
gta-ccatctgatttctccattcccccgatctcttatctctttttttcccagaattgattttgatccaaatctgatctgatccgattcgatcggattatgtttcagGTATGGGAGCAGCGTACGGGACAGCGAAGAGCGGGGTTGGTGTAGCGTCGATGGGTGTGATGAGACCAGAGCTTGTGATGAAATCGATTGTTCCTGTTGT

upper sequence: GLYMA02G05630.2 (Glycine max), 3'ss of exon 1
lower sequence: AT1G75630.2 (Arabidopsis thaliana), 3'ss of exon 1
gtaactaactaactcatcaaatcaaagagttttttttgtctcatttcccgaaaccg------tcgtcgttttatcttaaaccgtgtgtcgtttttgttttttcagGTATGGGCGCGGCGTACGGCACCGCGAAGAGCGGCGTCGGGGTTGCGTCGATGGGCGTGATGAGGCCGGAGCTGGTGATGAAATCGATCGTGCCGGTTGT
                | | ||   |||    | | |     |||||||  ||  |       |   |||||   ||  |        || |||  | |||||||||||||| || |||||||| || |||||||| || || || |||||||||||||| |||||||| || || || || ||||||||||| || || |||||
---------------gtaagatttcagatccctctcttgtcaatttccccgaattgaatcacccaatgtttttgattcgattcgaatccgatttgatgttttcagGTATGGGAGCAGCGTACGGGACGGCGAAGAGTGGAGTTGGAGTTGCGTCGATGGGAGTGATGAGACCTGAACTTGTTATGAAATCGATTGTTCCTGTTGT

upper sequence: GLYMA02G05630.2 (Glycine max), 3'ss of exon 1
lower sequence: PP1S45_100V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------gtaactaactaactcatcaaatcaaagagttttttttgtctcatttcccgaaaccgtcgtcgttttatcttaaaccgtgtgtcgtttttgttttttcagGTATGGGCGCGGCGTACGGCACCGCGAAGAGCGGCGTCGGGGTTGCGTCGATGGGCGTGATGAGGCCGGAGCTGGTGATGAAATCGATCGTGCCGGTTGT
            | |    ||| ||  |    |  |||   |||  |   ||   |  |      | |   || |  || |||| ||| | |  |||||||      |||| |||||||| || || || || || ||||| || || || || || || ||||| |||||| |||| |||||||||||||| ||||||||||| || ||
aagcagtgacgttgagggcctatcttgttgttttgaaggactttgatcagcttgctcgct-----ctttaccgat--atgttaacccgag-gaggtttttgagc--gcagGCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTGCCAGTGGT

upper sequence: GLYMA02G05630.2 (Glycine max), 3'ss of exon 1
lower sequence: PP1S45_97V6.1 (Physcomitrella patens), 3'ss of exon 1
---gtaactaact--aactcatcaaatcaaagagttttttttgtctcatttcccgaaaccgtcgtcgttttatcttaaaccgtgtgtcgtttttgttttttcagGTATGGGCGCGGCGTACGGCACCGCGAAGAGCGGCGTCGGGGTTGCGTCGATGGGCGTGATGAGGCCGGAGCTGGTGATGAAATCGATCGTGCCGGTTGT
     | | |  |    | |  ||  |   || |  |  | |     ||  ||   ||   || | | | |   | |||  |||    |||||||      |||| |||||||| || || || || || ||||| || || || || || || ||||| |||||| |||| |||||||||||||| |||||||| || || ||
ataacagcgatgttgggcaccccactttcgagtgcctcatctaggatatggcctcgaaat-tcctagatatgaataaaatggtg-aaggtttttgcgc--gcagGCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTACCAGTGGT

upper sequence: GLYMA02G05630.2 (Glycine max), 3'ss of exon 1
lower sequence: PP1S200_79V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaactaactaact-catcaaatcaaagagttttttttgtctcatttcccgaa-accgtcgtcgtttt--atcttaaaccgtgtgtcgttt-ttgttttttcagGTATGGGCGCGGCGTACGGCACCGCGAAGAGCGGCGTCGGGGTTGCGTCGATGGGCGTGATGAGGCCGGAGCTGGTGATGAAATCGATCGTGCCGGTTGT
    |     |||    |          || ||   ||  ||||  |   |     | |||    |      | | |||    ||| |  | || ||   ||||| |||||||| || || || || || ||||| || || || || || || ||||| |||||| |||| |||||||||||||| ||||||||||| || ||
----cccgtgaacggtgttgggcacttaagcttcaatttcctcagctagggtgcgacttcgaaactcctggacatgaactaaatgttgaatgttattgcgtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTGCCTGTGGT

upper sequence: GLYMA02G05630.2 (Glycine max), 3'ss of exon 1
lower sequence: EFJ33972 (Selaginella moellendorffii), 3'ss of exon 1
gtaactaactaactcatcaaatcaaagagttttttttgtctcatttcccgaaaccgtcgtcgttttatcttaaaccg---tgtgtcgtttttgtttttt-cagGTATGGGCGCGGCGTACGGCACCGCGAAGAGCGGCGTCGGGGTTGCGTCGATGGGCGTGATGAGGCCGGAGCTGGTGATGAAATCGATCGTGCCGGTTGT
                                           |   ||  |  | |  || | ||   |  || ||   || |  |  |   |   || |||| ||||| || || || ||||| || ||||||||||| || || ||||| |||||||| ||||| |||||||| ||||||||||||||||| ||||| ||
------------------------------------------gtaagccagattctttttcctctttgatctaatcgcaatgcgatggatcaatcgattacagGCATGGGAGCTGCCTATGGCACTGCCAAGAGCGGCGTGGGCGTGGCGTCCATGGGCGTCATGAGACCGGAGCTCGTGATGAAATCGATCGTCCCGGTGGT

upper sequence: GLYMA02G05630.2 (Glycine max), 3'ss of exon 1
lower sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 1
---------------------------------------------------------------------------------------gtaactaactaactcatcaaatcaaagagttttttttgtctcatttcccgaaaccgtcgtcgttttatcttaaaccgtgtgtcgtttttgttttttcagGTATGGGCGCGGCGTACGGCACCGCGAAGAGCGGCGTCGGGGTTGCGTCGATGGGCGTGATGAGGCCGGAGCTGGTGATGAAATCGATCGTGCCGGTTGT
                                                                                        |     |   | ||  |    |   | | |||  ||| | || | ||||| |      ||     ||     |   | |   |   || | ||| |||| ||||| || || || || ||||| ||||| || || || || || || |||||||||||| |||||||||| |||||||||||||||||||| || ||
gtaagttcttgcctctcaccgccatggctggactggatctagggttgtggtgcgtgtctcggctgcgcggcattgcaatgcctgagcttgggccatggattcgcctt-cctgcgcgatttccttgccacaat-cccgagatttcgatcccaaaattccccattttcttatggaattttctttgcagGCATGGGAGCTGCCTATGGAACCGCAAAGAGTGGTGTTGGAGTGGCATCCATGGGCGTGATGCGGCCGGAGCTCGTGATGAAATCGATCGTGCCAGTGGT

upper sequence: GLYMA02G05630.2 (Glycine max), 3'ss of exon 1
lower sequence: EFJ26016 (Selaginella moellendorffii), 3'ss of exon 1
---------------------------------------------------------------------------------------gtaactaactaactcatcaaatcaaagagttttttttgtctcatttcccgaaaccgtcgtcgttttatcttaaaccgtgtgtcgtttttgttttttcagGTATGGGCGCGGCGTACGGCACCGCGAAGAGCGGCGTCGGGGTTGCGTCGATGGGCGTGATGAGGCCGGAGCTGGTGATGAAATCGATCGTGCCGGTTGT
                                                                                        |     |   | ||  |    |   | | |||  ||| | || | ||||| |      ||     ||     |   | |   |   || | ||| |||| ||||| || || || || ||||| ||||| || || || || ||||| |||||||||||| |||||||||| |||||||||||||||||||| || ||
gtaagttcttgcctctcaccgccatggctggactggatctagggttgtggtgcgtgtctcggctgcgcggcattgcaatgcctgagcttgggccatggattcgcctt-cctgcgcgatttccttgccacaat-cccgatatttcgatcccaaaattccccattttctcatggaattttctttgcagGCATGGGAGCTGCCTATGGAACCGCAAAGAGTGGTGTTGGAGTGGCGTCCATGGGCGTGATGCGGCCGGAGCTCGTGATGAAATCGATCGTGCCAGTGGT

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|13181537|gb|BG352877.1|BG352877
EST:     CGCTCCTTTCTTTGGCTTCCTCGGAGCCGCCGCTGCCCTCGTTTTTTCCT                         GTATGGGCGCGGCGTACGGCACCGCGAAGAGCGGCGTCGGGGTTGCGTCGA
genomic: CGCTCCTTTCTTTGGCTTCCTCGGAGCCGCCGCTGCCCTCGTTTTTTCCTgtaactaact ... gttttttcagGTATGGGCGCGGCGTACGGCACCGCGAAGAGCGGCGTCGGGGTTGCGTCGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcccgaaaccgtcgtcgttttatcttaaaccgtgtgtcgtttttgttttttcagGTATGGGCGCGGCGTACGGCACCGCGAAGAGCGGCGTCGGGGTTGCGTCGATGGGCGTGATGAGGCCGGAGCTGGTGATGAAATCGATCGTGCCGGTTGT
                                     tcgtttttgttttttc  CT-rich tract
                                        tttttgttttttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactaactaactcatcaaatcaaagagttttttttgtctcatttcccgaaaccgtcgtcgttttatcttaaaccgtgtgtcgtttttgttttttcagGTATGGGCGCGGCGTACGGCACCGCGAAGAGCGGCGTCGGGGTTGCGTCGATGGGCGTGATGAGGCCGGAGCTGGTGATGAAATCGATCGTGCCGGTTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT