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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattagagtttcatgtccattctttattcatctgtgaataacgacctcttgggctggtttatgaatttttgggtggacttgcattacagGGAGGTACATTTACAGTGACTAACCTGGGAGGGCCATTTGGTGTCAAACAATTCTGTGCAATCATCAATCCTCCTCAGGCAGGCATTCTTGCCGTTGGAT

Basic information

species Glycine max
transcript GLYMA16G00590.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G00590.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os02g01500.1 (Oryza sativa), 3'ss of exon 16
gtaattagagtttcatgtccattctttattcatctgtgaataacgacctcttgggctggtttatgaatttttgggtggacttgcattacagGGAGGTACATTTACAGTGACTAACCTGGGAGGGCCATTTGGTGTCAAACAATTCTGTGCAATCATCAATCCTCCTCAGGCAGGCATTCTTGCCGTTGGAT
|||  | || |  ||||    |   | ||  |    |||   || || || |    |   ||   |||| | |        ||| || |||||||| ||||| ||  |  | ||||| ||||| || || ||  |||||||||||||||| ||||| |||||||||||| |||  ||  | ||| ||||  
gtatatgga-tcgcatg---gtagctaatataagcatgag--acaacatcatt--tttccttgaaaattctgg--------tgcttttcagGGAGGCACATTCACCATATCAAACCTAGGAGGTCCTTTCGGAATCAAACAATTCTGTGCCATCATAAATCCTCCTCAGTCAGCAATCTTGGCCATTGGTA

upper sequence: GLYMA16G00590.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G161969_T01 (Zea mays), 3'ss of exon 11
gtaattagagtttcatgtccattctttattc-atctgtgaataacgacctcttgggctggtttatgaatttttgggtggacttgcattacagGGAGGTACATTTACAGTGACTAACCTGGGAGGGCCATTTGGTGTCAAACAATTCTGTGCAATCATCAATCCTCCTCAGGCAGGCATTCTTGCCGTTGGAT
       |  | || ||   | |   | | | |     |||  | ||  |             ||||  | |||  | |       || ||||| || || || ||  |  | ||| ||||||| || || ||  |||||||||||||||| ||||| |||||||||||| |||  ||| | ||  |||| |
-------gtatatcgtgcatactaggtgtgctaagcaggaaagaagaaatgagaaaaaaaaccatgatatattg--ttgctgcatttttcagGGTGGCACCTTCACGATATCAAACTTGGGAGGTCCCTTCGGAATCAAACAATTCTGTGCCATCATAAATCCTCCTCAGTCAGCAATTTTGGCTATTGGTT

upper sequence: GLYMA16G00590.1 (Glycine max), 3'ss of exon 16
lower sequence: AT1G54220.2 (Arabidopsis thaliana), 3'ss of exon 16
gtaattagagtttcatgtccattctttattcatctgtgaataacgacctcttgggctggtttatgaatttttgggtggacttgcatta-cagGGAGGTACATTTACAGTGACTAACCTGGGAGGGCCATTTGGTGTCAAACAATTCTGTGCAATCATCAATCCTCCTCAGGCAGGCATTCTTGCCGTTGGAT
                |   |||| ||||    ||   | |||  |  ||||       |   | ||  |     |   || |  ||  |||||||| |||||||| ||  ||||| ||||||| || |||||  |||| |||||||||||| || | ||||| ||||| || | |||||| || |||||||
------------gtgagagaattcattatcttactc--actaatcatatctt-------tcagtaaacatgctaataatctcgttttctcagGGAGGAACATTTACTGTCTCTAACTTGGGAGGACCTTTTGGCATCAAGCAATTCTGTGCAGTCGTTAATCCACCTCAAGCCGCCATTCTAGCAGTTGGAT

upper sequence: GLYMA16G00590.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv09s0002g01800.t01 (Vitis vinifera), 3'ss of exon 17
gtaattagagtttcatgtccattctttattcatctgtgaataacgacctcttgggct-ggtttatgaatttttgggtggacttgcattacagGGAGGTACATTTACAGTGACTAACCTGGGAGGGCCATTTGGTGTCAAACAATTCTGTGCAATCATCAATCCTCCTCAGGCAGGCATTCTTGCCGTTGGAT
    | | | ||   | || ||   |||||  |   ||   |  || | || ||| |     ||||||   | |  | | | | | || |||||||| |||||||| ||| |||| |||||||| || |||||| |||| ||||||||||| |||||||||||||||||| |||||||||| ||| |||| |
---gtaaaaattatgtttcaatg--ttattagttgttggcaagtgatcgctagggtttaacatatgaaaactggcttcgtcct-ccttgcagGGAGGGACATTTACTGTGTCTAATCTGGGAGGACCCTTTGGTATCAAGCAATTCTGTGCCATCATCAATCCTCCTCAGTCAGGCATTCTAGCCATTGGGT

upper sequence: GLYMA16G00590.1 (Glycine max), 3'ss of exon 16
lower sequence: PP1S78_56V6.1 (Physcomitrella patens), 3'ss of exon 14
-------------gtaattagagtttcatgtccattctttattcatctgtgaataacgacctcttgggctggtttatgaatttttgggtggacttgcattacagGGAGGTACATTTACAGTGACTAACCTGGGAGGGCCATTTGGTGTCAAACAATTCTGTGCAATCATCAATCCTCCTCAGGCAGGCATTCTTGCCGTTGGAT
             || ||| ||   | |||    || ||| ||  | |     |  |  | | ||   ||   |      |||||   || |       | ||||| || ||||||||| |  | ||  ||||||| || |||||  | |||||||| ||||| ||||||||||||||||| |||| ||||||||| |||||  
attccgtgtttctgtgatttgaagattatgatttttattttttagtttcatttttccttcgttttttactaaat----gttttttaactgcaacaattctgcagGGTGGAACATTTACAATCTCCAATTTGGGAGGACCTTTTGGGATTAAACAATTTTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGA

upper sequence: GLYMA16G00590.1 (Glycine max), 3'ss of exon 16
lower sequence: EFJ28117 (Selaginella moellendorffii), 3'ss of exon 11
gtaattagagtttcatgtccattctttattcatctgtgaataacgacctcttgggctggtttatgaatttttgggtggacttgcattacagGGAGGTACATTTACAGTGACTAACCTGGGAGGGCCATTTGGTGTCAAACAATTCTGTGCAATCATCAATCCTCCTCAGGCAGGCATTCTTGCCGTTGGAT
                                   || |       | |     | |  || |     |  || ||    | |  |  ||||| || || || || ||  | ||| |||| || ||||||||| |||||||||| ||||| ||||||||||| || ||| |  ||||||||||||| ||  
-----------------------------------gtaagcgtttgctttgcatgatacttgaaacgctcatgagtcccttggtgtcgcagGGTGGCACGTTCACGGTCTCGAACTTGGGTGGACCATTTGGTATCAAACAATTTTGTGCTATCATCAATCCGCCACAGTCGTGCATTCTTGCCGTCGGCA

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|192329901|gb|FK021487.1|FK021487
EST:     AATTGGCAAAGAAAGCCAAAGAAAACAGCTTGAAACCCCAAGAATATGAG                         GGAGGTACATTTACAGTGACTAACCTGGGAGGGCCATTTGGTGTCAAACAA
genomic: AATTGGCAAAGAAAGCCAAAGAAAACAGCTTGAAACCCCAAGAATATGAGgtaattagag ... tgcattacagGGAGGTACATTTACAGTGACTAACCTGGGAGGGCCATTTGGTGTCAAACAA
EST: gi|151404893|gb|EV274707.1|EV274707
EST:     AATTGGCAAAGAAAGCCAAAGAAAACAGCTTGAAACCCCAAGAATATGAG                         GGAGGTACATTTACAGTGACTAACCTGGGAGGGCCATTTGGTGTCAAACAA
genomic: AATTGGCAAAGAAAGCCAAAGAAAACAGCTTGAAACCCCAAGAATATGAGgtaattagag ... tgcattacagGGAGGTACATTTACAGTGACTAACCTGGGAGGGCCATTTGGTGTCAAACAA
EST: gi|18732669|gb|BM527176.1|BM527176
EST:     AATTGGCAAAGAAAGCCAAAGAAAACAGCTTGAAACCCCAAGAATATGAG                         GGAGGTACATTTACAGTGACTAACCTGGGAGGGCCATTTGGTGTCAAACAA
genomic: AATTGGCAAAGAAAGCCAAAGAAAACAGCTTGAAACCCCAAGAATATGAGgtaattagag ... tgcattacagGGAGGTACATTTACAGTGACTAACCTGGGAGGGCCATTTGGTGTCAAACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaataacgacctcttgggctggtttatgaatttttgggtggacttgcattacagGGAGGTACATTTACAGTGACTAACCTGGGAGGGCCATTTGGTGTCAAACAATTCTGTGCAATCATCAATCCTCCTCAGGCAGGCATTCTTGCCGTTGGAT
 gaataac  putative branch site (score: 2)
                       tttatgaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattagagtttcatgtccattctttattcatctgtgaataacgacctcttgggctggtttatgaatttttgggtggacttgcattacagGGAGGTACATTTACAGTGACTAACCTGGGAGGGCCATTTGGTGTCAAACAATTCTGTGCAATCATCAATCCTCCTCAGGCAGGCATTCTTGCCGTTGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC