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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtacttacaattctcacataactgatcattcatacatgcagctgaggaattgcattttaaatagttctaatttctaacacactaatttttgcagTTACATGGCTCCTGAATACTTCATGTATGGCAAAGTAAATGACAAGATTGATGTCTATGCATTTGGTGTAGTGCTTCTTGAGCTTCTTTCAGGGAGAAAG

Basic information

species Glycine max
transcript GLYMA13G09620.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G09620.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g62340.1 (Oryza sativa), 3'ss of exon 6
gtttgtacttacaattctcacataactgatcattcatacatgcagctgaggaattgcattttaaatagttctaatttctaa-cacactaatttt--tgcagTTACATGGCTCCTGAATACTTCATGTATGGCAAAGTAAATGACAAGATTGATGTCTATGCATTTGGTGTAGTGCTTCTTGAGCTTCTTTCAGGGAGAAAG
            || |  ||  |   || | |||  |||  ||   ||      | | |||   |    |  |||  |||| || |||| |  |    ||| ||| ||||||| || || ||   | | || || || ||||| ||||||||||||||||||||||| || ||  |||| ||| || ||||||| ||||  
----------gtaagtaccatctctatgct-atttttaccagctattg-----ctacttttatcaagtgtgaaatgcctaagcaaactactcctgtgacagATACTTGGCTCCCGAGTATTTTTCGCACGGGAAGGTCAATGAGAAGATTGATGTCTATGCATTTGGAGTTGTAATTCTGGAGATTATTTCAGGAAGAAGA

upper sequence: GLYMA13G09620.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G032337_T02 (Zea mays), 3'ss of exon 7
gtttgtacttacaattctcacataactgatcattcatacatgcagctgaggaattgcattttaaatagttctaatttctaacacactaatttttgcagTTACATGGCTCCTGAATACTTCATGTATGGCAAAGTAAATGACAAGATTGATGTCTATGCATTTGGTGTAGTGCTTCTTGAGCTTCTTTCAGGGAGAAAG
||||||   |  ||   |    | | || |  | | |     | | ||  | |||| |     ||| | | || |  |  | | |   || || |||| ||| |||||||||||||||||||| ||||||| ||     |||| || ||||| ||||| || ||||| || ||||| |||||  | || || || || 
gtttgtttct-taacaattgttttattgtttttccgt-----ctgttgtagcattggagc---aattgctttactgacatagagat--atcttggcagATACTTGGCTCCTGAATACTTCATGCATGGCAAGGTGGGCAACAAAATCGATGTGTATGCTTTCGGTGTTGTACTTCTGGAGCTCATCTCTGGCAGGAAA

upper sequence: GLYMA13G09620.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G77280.1 (Arabidopsis thaliana), 3'ss of exon 8
gtttgtacttacaattctcacataactgatcattcatacatgcagctgaggaattgcattttaaatagttctaatttctaacacactaatttt-tgcagTTACATGGCTCCTGAATACTTCATGTATGGCAAAGTAAATGACAAGATTGATGTCTATGCATTTGGTGTAGTGCTTCTTGAGCTTCTTTCAGGGAGAAAG
               | | |  ||    |   ||     |      | | |||  |   || |||  |||||  |  ||||    ||  |||| ||||| ||| ||||||| || |||||||||||||| || || ||||| ||||| ||||| |||||||| || || || || || ||| | ||||| || ||||| 
--------------gtatgaagtactctaggttttgggta-atgtttcatgaaa-gttcttgaaaatgttcttgtg-ctaatcttctgtttttgtgcagATACTTGGCTCCAGAGTACTTCATGTATGGTAAGGTGAATGATAAGATAGATGTGTATGCATTCGGCGTTGTTCTCCTCGAGTTACTTTCGGGAAGAAAA

upper sequence: GLYMA13G09620.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv18s0001g01680.t01 (Vitis vinifera), 3'ss of exon 7
------------------------------------------------gtttgtacttacaattctcacataactgatcattcatacatgcagctgaggaattgcattttaaatagttctaatttctaac--------------acactaatttt---tgcagTTACATGGCTCCTGAATACTTCATGTATGGCAAAGTAAATGACAAGATTGATGTCTATGCATTTGGTGTAGTGCTTCTTGAGCTTCTTTCAGGGAGAAAG
                                                ||   |  | | ||     | | | |  |  |||   |  |   |||    |||      | ||| |||| | | || | |               ||| | |||||   ||||||||||||||||||||||||||||||||||||||||||||||| ||||| |||||||| ||||||||||| || || |||||||||||||| || ||||| 
gtttgtgcttcttctctagtagctataacttctatgtcccacattcttgtcatttttcagaagatcaataaaccccactattttgaattatggctttaaaatcttgagtaaaaaagttattacttgtcattgagaaagttcagaacatttattttctctgcagTTACATGGCTCCTGAATACTTCATGTATGGCAAAGTAAATGAGAAGATAGATGTCTACGCATTTGGTGTTGTCCTCCTTGAGCTTCTTTCGGGAAGAAAA

upper sequence: GLYMA13G09620.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S249_93V6.1 (Physcomitrella patens), 3'ss of exon 7
gtttgtacttacaattctca--cataactgatcattcatacatgcagctgaggaat-tgcattttaaatagttcta--------atttctaac---acactaatttttgcagTTACATGGCTCCTGAATACTTCATGTATGGCAAAGTAAATGACAAGATTGATGTCTATGCATTTGGTGTAGTGCTTCTTGAGCTTCTTTCAGGGAGAAAG
|| | |||   |  | | ||   ||  ||||  | ||| ||||    |||     | ||  |||| || |   | |        |||||| |    | | | |  | ||||| ||  | || |||||||||||||||||||| | ||| ||  |||||| ||||||||| || ||||| || || || ||||||||  |  | ||  |    
gtatctacagcctttccccaattatcgctgaa-actcagacat-tgtctgtcttttctgtgttttgaacacagcaatatggaaaatttctgatctaagagtgacctctgcagATATCTCGCACCTGAATACTTCATGTATGGGAGAGTGAACAACAAGACTGATGTCTACGCTTTTGGCGTTGTACTGCTTGAGCTCATAACCGGTCGGCCA

upper sequence: GLYMA13G09620.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S242_29V6.1 (Physcomitrella patens), 3'ss of exon 8
--gtttgtacttacaat-tctcacataactg-atcattcatacatgcagctgaggaattgcattttaaatagttctaatttctaacacactaatttttgcagTTACATGGCTCCTGAATACTTCATGTATGGCAAAGTAAATGACAAGATTGATGTCTATGCATTTGGTGTAGTGCTTCTTGAGCTTCTTTCAGGGAGAAAG
  || ||   ||| | | |  | | |  ||| | |     ||    |  |  || | | | ||  |  |||  |  | |  ||  |    ||  | |  ||| ||| |||| || ||||||||||||||||| |  || || |||||||| ||||| || ||||| |||||||||||| | |||||| |  | || || || 
gggtgtgggattaaactgtggcgctttcctgcagccactgtatcatcgacgtagcagtcg-atcgttgatacata-actgactggcgttatatctctaccagGTACTTGGCCCCGGAATACTTCATGTATGGGAGGGTGAACGACAAGATCGATGTGTACGCATTCGGTGTAGTGCTTTTAGAGCTTATCACGGGTAGGAAA

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|58025403|gb|CX712144.1|CX712144
EST:     TCAACTTCATCATCACATATATTTTGCACAGATGTTGCTGGAACCTTTGG                         TTACATGGCTCCTGAATACTTCATGTATGGCAAAGTAAATGACAAGATTGA
genomic: TCAACCTCATCATCACATATAATTTGCACAGATGTTGCTGGAACCTTTGGgtttgtactt ... atttttgcagTTACATGGCTCCTGAATACTTCATGTATGGCAAAGTAAATGACAAGATTGA
EST: gi|20498207|gb|BQ273137.1|BQ273137
EST:     TCAACCTCATCATCACATATAATTTGCACAGATGTTGCTGGAACCTTTGG                         TTACATGGCTCCTGAATACTTCATGTATGGCAAAGTAAATGACAAGATTGA
genomic: TCAACCTCATCATCACATATAATTTGCACAGATGTTGCTGGAACCTTTGGgtttgtactt ... atttttgcagTTACATGGCTCCTGAATACTTCATGTATGGCAAAGTAAATGACAAGATTGA
EST: gi|58015154|gb|CX701896.1|CX701896
EST:     TCAACCTCATCATCACATATAA-TTGCACAGATGTTGCTGGAACC-TTGG                         TTACATGGCTCCTGAATACTTCATGTATGGCAAAGTAAATGACAAGATTGA
genomic: TCAACCTCATCATCACATATAATTTGCACAGATGTTGCTGGAACCTTTGGgtttgtactt ... atttttgcagTTACATGGCTCCTGAATACTTCATGTATGGCAAAGTAAATGACAAGATTGA
EST: gi|151397175|gb|EV267048.1|EV267048
EST:     TCAACCTCATCATCACATATAATTTGCACAGATGTTGCTGGAACCTTTGG                         TTACATGGCTCCTGAATACTTCATGTATGGCAAAGTAAATGACAAGATTGA
genomic: TCAACCTCATCATCACATATAATTTGCACAGATGTTGCTGGAACCTTTGGgtttgtactt ... atttttgcagTTACATGGCTCCTGAATACTTCATGTATGGCAAAGTAAATGACAAGATTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctgaggaattgcattttaaatagttctaatttctaacacactaatttttgcagTTACATGGCTCCTGAATACTTCATGTATGGCAAAGTAAATGACAAGATTGATGTCTATGCATTTGGTGTAGTGCTTCTTGAGCTTCTTTCAGGGAGAAAG
                                              tttttgc  CT-rich tract
              attttaaatagttcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtacttacaattctcacataactgatcattcatacatgcagctgaggaattgcattttaaatagttctaatttctaacacactaatttttgcagTTACATGGCTCCTGAATACTTCATGTATGGCAAAGTAAATGACAAGATTGATGTCTATGCATTTGGTGTAGTGCTTCTTGAGCTTCTTTCAGGGAGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA