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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggaattcaatgaataacttttcttgtttctttgctgaaagttgtgtggattgtctaatatggttccattggcttttatgtgcagCGGTAAATAAAGATGAATTGCTTCAAATGGTTAGATTTGGGGCTGAAATGGTTTTCAGTTCCAAGGATAGTACAATTACAGATGAAGATATTGATAGAAT

Basic information

species Glycine max
transcript GLYMA15G10370.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 13
-gtaggaattcaatgaataacttttcttgtttctttgctgaaagttgtgtggattgtctaatatggttccattggcttttatgtgcagCGGTAAATAAAGATGAATTGCTTCAAATGGTTAGATTTGGGGCTGAAATGGTTTTCAGTTCCAAGGATAGTACAATTACAGATGAAGATATTGATAGAAT
  |||   ||   |  ||||  | |  || ||      ||||| ||      ||    |||| |  |||  | |   | | |   |||| || ||||| |||||  |  | || ||||| |||||||| ||||||||||| ||||| ||||||||||| ||||| |||||||||||||||||  | ||
gttagttttttgcttcataaaatgt--tgcttgacaaatgaaaatt-caaacatcaattaatgttcttctgtcgtggtgttt---cagCTGTCAATAAGGATGAGCTATTGCAGATGGTCAGATTTGGTGCTGAAATGGTATTCAGCTCCAAGGATAGCACAATAACAGATGAAGATATTGACCGCAT

upper sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 13
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 13
gtaggaattcaatgaataacttttcttgtttctttgctgaaagttgtgtggattgtctaatatggttccattggcttttatgtgcagCGGTAAATAAAGATGAATTGCTTCAAATGGTTAGATTTGGGGCTGAAATGGTTTTCAGTTCCAAGGATAGTACAATTACAGATGAAGATATTGATAGAAT
||| |  ||   ||  |    | | || | | |  |  |  | |  ||  | | ||   |||||| |  |||   || |   | |||| || ||||| |||||  || | |||||||| |||||||| || |||||||| |||||||||||||| || |||||||||||||| ||||||||  | ||
gtatgtttttgctgcttg---tattttatgtttaagaaggcattcatgcag-tagtaagatatggatttattttgttcttctttcagCTGTCAATAAGGATGATCTGTTGCAAATGGTAAGATTTGGTGCGGAAATGGTATTCAGTTCCAAGGACAGCACAATTACAGATGAGGATATTGACCGTAT

upper sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 10
gtaggaattcaatgaataacttttcttgtttctttgctgaaagttgtgtggattgtctaatatggttccattggcttt----tatgtgcagCGGTAAATAAAGATGAATTGCTTCAAATGGTTAGATTTGGGGCTGAAATGGTTTTCAGTTCCAAGGATAGTACAATTACAGATGAAGATATTGATAGAAT
||| |  ||  ||   |  | |||||  ||  |||    |   ||   | | |||      || ||||      | ||    | | |  ||| || ||||| |||||  | || ||||||||  | ||||| |||||||||||||||||||| ||||| || ||||| || ||||| || |||||  | ||
gtatggttttgatatttgccatttctatttgttttaagcattttttactagtttgatctggattgttctgacaacattctcatttattaagCTGTCAATAAGGATGATCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT

upper sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 13
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 13
gtaggaattcaatgaataacttttcttgtttctttgctgaaagttgtgtggattgtctaatatggttccattgg--------cttttatgtgcagCGGTAAATAAAGATGAATTGCTTCAAATGGTTAGATTTGGGGCTGAAATGGTTTTCAGTTCCAAGGATAGTACAATTACAGATGAAGATATTGATAGAAT
||| |  |   || | |  | |||  | ||| |||   | |  ||   |   | ||   |||||| |   |  |        ||||| |||  ||| || ||||| |||||  | || ||||||||  | ||||| |||||||||||||||||||| ||||| || ||||| || ||||| || |||||  | ||
gtatggttatgat-atttgcctttgctatttgtttcaagcatttttctttactagttggatatggattattctgacaacattcttttttgttaagCTGTCAATAAGGATGACCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT

upper sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 13
lower sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 13
gtaggaattcaatgaataacttttcttgtttctttgctgaaagttgtgtggattgtctaatatggttccattggcttttatgtgcagCGGTAAATAAAGATGAATTGCTTCAAATGGTTAGATTTGGGGCTGAAATGGTTTTCAGTTCCAAGGATAGTACAATTACAGATGAAGATATTGATAGAAT
||| |      ||  |    ||   || |   || | | |    ||   | ||||     |||       ||  |||   | |||||| || ||||| ||||| |||||||||||||| |||| ||| ||||| ||||| |||||||| || ||||| ||||| ||||| || ||||||||||||||
gtaagtgcgttatacagtgattgctttatgcattggttcatctctgacagaattg----gtat-------ttatcttaactatgcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGGTGTTCAGTTCTAAAGATAGCACAATCACAGACGAGGATATTGATAGAAT

upper sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 13
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 13
gtaggaattcaatgaataacttttcttgtttctttgctgaaagttgtgtggattgtctaatatggttccattggcttttatgtgcagCGGTAAATAAAGATGAATTGCTTCAAATGGTTAGATTTGGGGCTGAAATGGTTTTCAGTTCCAAGGATAGTACAATTACAGATGAAGATATTGATAGAAT
||| |   |     | | |   |  | | |    |  || |  || | |    | | ||   || || | ||  ||||  | | |||| || ||||| ||||| |||||||||||||| |||| ||| ||||||||||| || ||||| || ||||| |||||||| ||||| |||||||| |||||
gtaagtgcttgtgtactgaggctgttagatg---tattggattttctcttacatatatatactgatttctttt-ctttgctttccagCTGTTAATAAGGATGAGTTGCTTCAAATGGTGAGATATGGTGCTGAAATGGTGTTTAGTTCTAAAGATAGCACAATTACGGATGAGGATATTGACAGAAT

upper sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 13
gtaggaattcaatgaat----aacttttcttgtttctttgc-tgaaagttgtgtggattgt--ctaatatggttccattggcttt-----tatgtgcagCGGTAAATAAAGATGAATTGCTTCAAATGGTTAGATTTGGGGCTGAAATGGTTTTCAGTTCCAAGGATAGTACAATTACAGATGAAGATATTGATAGAAT
||  |   |   || ||    | |||   |||     |  | ||  | ||    | | |    | | ||   ||   |||  |||       | |||||| || || ||||||||  | || |||||||| || ||||| ||||||||||||||||| ||||||||||| |||||||| |||||||| || || || ||
gtgagccatttctgcattacaagcttgctttgcactatgacatgctaattcatagaactagaaccactaacattttgttgtttttgtgggcttttgcagCTGTGAACAAAGATGAGCTACTGCAAATGGTCAGGTTTGGTGCTGAAATGGTTTTCAGCTCCAAGGATAGCACAATTACGGATGAAGACATAGACAGGAT

upper sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 13
lower sequence: EFJ32950 (Selaginella moellendorffii), 3'ss of exon 12
gtaggaattcaatgaataacttttcttgtttctttgctgaaagttgtgtggattgtctaatatggttccattggcttttatgtgcagCGGTAAATAAAGATGAATTGCTTCAAATGGTTAGATTTGGGGCTGAAATGGTTTTCAGTTCCAAGGATAGTACAATTACAGATGAAGATATTGATAGAAT
                                | ||  |  |  ||| |  |   |   |  |  |  || | ||||    |  |||| || || || |||||  | |||||||||||| |||  || || || |||||||||||||| || |||||||| || || ||||||||||| ||| | ||
-------------------------------gtatgtggttaaatgtttcaacgttgccactttttgacacttgcttg---gcacagCTGTTAACAAGGATGAGCTTCTTCAAATGGTTCGATACGGCGCGGAGATGGTTTTCAGTTCTAAAGATAGTACCATAACCGATGAAGATATAGATCGTAT

upper sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 13
lower sequence: EFJ15818 (Selaginella moellendorffii), 3'ss of exon 12
gtaggaattcaatgaataacttttcttgtttctttgctgaaagttgtgtggattgtctaatatggttccattggcttttatgtgcagCGGTAAATAAAGATGAATTGCTTCAAATGGTTAGATTTGGGGCTGAAATGGTTTTCAGTTCCAAGGATAGTACAATTACAGATGAAGATATTGATAGAAT
                                             || |  |   |   |  |  |  || | ||||    |  |||| || || || |||||  | |||||||||||| |||  || || || |||||||||||||| || |||||||| || || ||||||||||| ||| | ||
---------------------------------------------gtttcaacgttgccactttttgacacttgcttg---gcacagCTGTTAACAAGGATGAGCTTCTTCAAATGGTTCGATACGGCGCGGAGATGGTTTTCAGTTCTAAAGATAGTACCATAACCGATGAAGATATAGATCGTAT

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|193688000|gb|FK628315.1|FK628315
EST:     TGCACTTGATGCTCTGGTGATTCAGCAAGGACAATTGGCTGAGCAGAAGA                         CGGTAAATAAAGATGAATTGCTTCAAATGGTTAGATTTGGGGCTGAAATGG
genomic: TGCACTTGATGCTCTGGTGATTCAGCAAGGGCGATTGGCTGAGCAGAAGAgtaggaattc ... ttatgtgcagCGGTAAATAAAGATGAATTGCTTCAAATGGTTAGATTTGGGGCTGAAATGG
EST: gi|193487791|gb|FK452772.1|FK452772
EST:     TGCACTTGATGCTCTGGTGATTCAGCAAGGGCGATTGGCTGAGCAGAAGA                         CGGTAAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGGGCTGAAATGG
genomic: TGCACTTGATGCTCTGGTGATTCAGCAAGGGCGATTGGCTGAGCAGAAGAgtaggaattc ... ttatgtgcagCGGTAAATAAAGATGAATTGCTTCAAATGGTTAGATTTGGGGCTGAAATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgctgaaagttgtgtggattgtctaatatggttccattggcttttatgtgcagCGGTAAATAAAGATGAATTGCTTCAAATGGTTAGATTTGGGGCTGAAATGGTTTTCAGTTCCAAGGATAGTACAATTACAGATGAAGATATTGATAGAAT
                      gtctaat  putative branch site (score: 3)
                                          cttttat  putative PPT
                       tctaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggaattcaatgaataacttttcttgtttctttgctgaaagttgtgtggattgtctaatatggttccattggcttttatgtgcagCGGTAAATAAAGATGAATTGCTTCAAATGGTTAGATTTGGGGCTGAAATGGTTTTCAGTTCCAAGGATAGTACAATTACAGATGAAGATATTGATAGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA