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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattatcctctcttttttttttctgaacctttctggttttttattatttcatgtcatgattatgtttatattataattcaagcgtgaagcttgtttttatatttttcatttagggaatttgtggaaaataacctataatatttttgtagcaaactcatctctagattaactggatcttcttcagGTTGACCCAACCACTGGTGAGGCTGAAGATGATGGTGTCGAAGATGAATACCAGCTGGAGGATCTGGAGATTGTTGCAGCAGATTACGTGTTGAAAGTGG

Basic information

species Glycine max
transcript GLYMA06G01520.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G01520.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G178618_T01 (Zea mays), 3'ss of exon 16
gtattatcctctcttttttttttctgaacctttctggttttttattatttcatgtcatgattatgtttatattataattcaagcgtgaagcttgtttttatatttttcatttagggaatttgtggaaaataacctataatatttttgtagcaaactcatctctagattaactggatcttcttcagGTTGACCCAACCACTGGTGAGGCTGAAGATGATGGTGTCGAAGATGAATACCAGCTGGAGGATCTGGAGATTGTTGCAGCAGATTACGTGTTGAAAGTGG
                                                       ||| ||  |||| | ||   ||||     |||||   || ||| ||   ||||  || |  || | |   |   |||  | |  |  |||||       ||||| | | |            |  |||||||||| ||| |||| ||||| |||||||||||||||||||| ||||| |||||||| || ||||| || || ||| | || |||||  ||||||| ||||
-----------------------------------------------------cacataatc-tgttcagat---aattt----gtgaaa--tgctttcatgcctttccatttg--aagtggcaaacggtaatttgt--tgattttg------gctcatttattg------------tgtttcagGTTGATCCATCCACGGGTGAAGCTGAAGATGATGGTGTCGAGGATGAGTACCAGCTTGAAGATCTTGAAATCGTTTCTGCTGATTATATGTTGAAGGTGG

upper sequence: GLYMA06G01520.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G036034_T01 (Zea mays), 3'ss of exon 16
gtattatcctctcttttttttttctgaacctttctggttttttattatttcatgtcatgattatgtttatattataattcaagcgtgaagcttgtttttatatttttcatttagggaatttgtggaaaataacctataatatttttgtagcaaactcatctctagattaactggatcttcttcagGTTGACCCAACCACTGGTGAGGCTGAAGATGATGGTGTCGAAGATGAATACCAGCTGGAGGATCTGGAGATTGTTGCAGCAGATTACGTGTTGAAAGTGG
                                                         |  ||    |  |   ||||||     |||||   || ||| ||   ||||  || |  || | |   | ||||| || |   |||||       ||||||| | |            | |  |||||||||| ||| |||| |||||  |||||||||||||||| || ||||| |||||||| || ||||| || || ||| | || |||||  ||||||| ||||
---------------------------------------------------------tacttgatctgttcagataattt----gtgaaa--tgctttcatgcctttccatttg--aagtggcaaacaataatctgttg-atttt-------aactcatttgt------------tttgtttcagGTTGATCCATCCACGGGTGAAACTGAAGATGATGGTGTTGAGGATGAGTACCAGCTTGAAGATCTTGAAATAGTTTCTGCTGATTATATGTTGAAGGTGG

upper sequence: GLYMA06G01520.1 (Glycine max), 3'ss of exon 16
lower sequence: AT4G34450.1 (Arabidopsis thaliana), 3'ss of exon 15
----------------gtattatcctc--tcttttttttttctgaacctttctggttttttattatttcatgtcatgattatgtttatattataattcaagcgtgaagcttgtttttatatttttcatttagggaatttgtggaaaataacctataatatttttgtagcaaactcatctctagattaactggatcttctt---cagGTTGACCCAACCACTGGTGAGGCTGAAGATGATGGTGTCGAAGATGAATACCAGCTGGAGGATCTGGAGATTGTTGCAGCAGATTACGTGTTGAAAGTGG
                 ||||  | ||  ||||||| ||| || |  ||            || ||    |||   ||     | || |  |  | |||    || ||     |   | |      | | |    | |    ||||| ||   | || | | |  || | |  |  | | |   || | || || |  |    ||||||||||||| ||| ||||| || ||||||||||| || |||||||| |||||||| |||||||| ||| |||| || | ||||||| || |||||||||
gtacatgttaaataggctattcacttccatctttttatttacttacactgaaaatgaccccataatactttgtggagaactcttataaacaacgactca--tttggagaggagtaccagaa---cgactcaaattaatcacagaaaacaa---agaaaactctc-taactacattgtttgtgctttta-tgaatgtgttaaaacagGTTGACCCAAGCACAGGTGAAGCAGAAGATGATGGAGTAGAAGATGAGTACCAGCTAGAGGATCTTGAGGTTGTAGCTGGAGATTACATGGTGAAAGTGG

upper sequence: GLYMA06G01520.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv03s0063g02450.t01 (Vitis vinifera), 3'ss of exon 16
gtattatcctctcttttttttttctgaacctttctggttttttattatttcatgtcatgattatgtttatattataattcaagcgtgaagcttgtttttatatttttcatttagggaatttgtggaaaataacctataatatttttgtagcaaactcatctctagattaactggatcttcttcagGTTGACCCAACCACTGGTGAGGCTGAAGATGATGGTGTCGAAGATGAATACCAGCTGGAGGATCTGGAGATTGTTGCAGCAGATTACGTGTTGAAAGTGG
                                                                      | || || | |  | |  ||  || ||  ||| |  | |  ||   |  |     |||| |  ||| |   ||||  |      |   | | | | |||         | | |||||||| ||||| ||||||||| | || || |||||||||||||| ||||||||||||||||| || ||  |||||||||| ||||| |||||||| || |
--------------------------------------------------------------------caaatagaaattacac-tagaggatgcttccatactgatgaacta---atctccaacaaaaaattctacatggttttcat------catgtgttttgttta-------tatttccagGTTGATCCAACTACTGGTGAGACAGAGGAAGATGGTGTCGAAGACGAATACCAGCTGGAGGACCTTGAAGTTGTTGCAGCTGATTATGTGTTGAAGGTTG

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|192308895|gb|FK002119.1|FK002119
EST:     GAAATTTATTGTCAAAGAG                         GTTGACCCAACCACTGGTGAGGCTGAAGATGATGGTGTCGAAGATGAATAC
genomic: GAAATTTATTGTCAAAGAGgtattatcct ... tcttcttcagGTTGACCCAACCACTGGTGAGGCTGAAGATGATGGTGTCGAAGATGAATAC
EST: gi|26268306|gb|CA819369.1|CA819369
EST:     TGCCAACAGTTGGAAAATTTTCTAACATTCTGAAATTTATTGTCAAAGAG                         GTTGACCCAACCACTGGTGAGGCTGAAGATGATGGTGTCGAAGATGAATAC
genomic: TGCCAACAGTTGGAAAATTTTCTAACATTCTGAAATTTATTGTCAAAGAGgtattatcct ... tcttcttcagGTTGACCCAACCACTGGTGAGGCTGAAGATGATGGTGTCGAAGATGAATAC
EST: gi|58024186|gb|CX710927.1|CX710927
EST:     TGCCAACAGTTGGAAAATTTTTTAACATTCTGAAATTTATTGTCAAAGAG                         GTTGACCCAACCACTGGTGAGGCTGAAGATGATGGTGTCGAAGATGAATAC
genomic: TGCCAACAGTTGGAAAATTTTCTAACATTCTGAAATTTATTGTCAAAGAGgtattatcct ... tcttcttcagGTTGACCCAACCACTGGTGAGGCTGAAGATGATGGTGTCGAAGATGAATAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacctataatatttttgtagcaaactcatctctagattaactggatcttcttcagGTTGACCCAACCACTGGTGAGGCTGAAGATGATGGTGTCGAAGATGAATACCAGCTGGAGGATCTGGAGATTGTTGCAGCAGATTACGTGTTGAAAGTGG
                                  gattaac  putative branch site (score: 2)
                                             tcttcttc  putative PPT
     ataatatttttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattatcctctcttttttttttctgaacctttctggttttttattatttcatgtcatgattatgtttatattataattcaagcgtgaagcttgtttttatatttttcatttagggaatttgtggaaaataacctataatatttttgtagcaaactcatctctagattaactggatcttcttcagGTTGACCCAACCACTGGTGAGGCTGAAGATGATGGTGTCGAAGATGAATACCAGCTGGAGGATCTGGAGATTGTTGCAGCAGATTACGTGTTGAAAGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT