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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccatgacttaatttattagttatttgagtttaccatgatagttggcatatgtattctggtgtgctttctcaaaaattaatcatttggattaagattgcagATGGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACAAATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGC

Basic information

species Glycine max
transcript GLYMA08G09050.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G09050.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g48270.1 (Oryza sativa), 3'ss of exon 8
------ccatgacttaatttat-tagttatttgagtttaccatgatagttggcatatgtattctggtgtgctttctcaaaaattaatcatttggattaagattgcagATGGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACAAATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGC
       ||| | || || | | || | ||       |    ||||  ||     |  |  |       ||  ||   ||   | || |||||  ||     ||||||||||||| || || ||||||||||| || ||||||||| |||| || |||||| | || ||||||||||||||||| ||| | || ||| | ||||| |
aacctttcataaattgatatgtataataatcctgaacttgtgtgat--ttcattcacatggtgataaaagcagtcatgaattctgataatttg--ttg---ctgcagATGGATGGGTTAACTAAGACAGATGATCTCGTTTTTGTTCTAGCCGCCACAAATTTGCCATGGGAACTGGATGCAGCAATGTTGCGCCGTTTGGAGAAAC

upper sequence: GLYMA08G09050.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g55260.1 (Oryza sativa), 3'ss of exon 8
------------------------------------------------------ccatgactt--aatttattagttatttgagttt--accatgatagttggcatatgtattctggtgtgctttctcaaaaattaatcatttggattaag----attgcagATGGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACAAATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGC
                                                       || |  ||   | ||  || |  ||    ||   ||  |   |  |  || |   |   |   ||    | |||||  ||    ||||   | ||     | ||||||||||||| |||||||||||  | ||  |||| |||||  | || ||||||||| | || ||||||||||| ||||| ||||| || || |||||||| |
gtttctgcttgtttgaacatatcaaaattaagcttgctagtgtagcactccaagtcacggtttcctacttcataatctttcagcttgaaactgtcccaactccca-acaaacaata-cgtcagatttcaaagtttctatatttctgtcaatgtttactgcagATGGATGGCTTGACAAAGACGAACGACTTGGTATTTGTACTTGCAGCAACAAATTTACCTTGGGAACTGGACGCAGCTATGCTCCGCCGGCTTGAGAAAC

upper sequence: GLYMA08G09050.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G022777_T01 (Zea mays), 3'ss of exon 8
---------------------------------------------ccatgacttaatttattagttatttgagtttaccatgatagttggcatatgtattc---tggtgtgctttctcaaaaattaatcatttggattaag---------attgcagATGGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACAAATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGC
                                                ||   ||  | |||  || ||| |  |   |       |||   | ||   ||   | |||| | |   | |||  |||   ||  | ||| |         |||||||||||||||||||||||||||| | ||  |||| |||||  | || || |||||||||||||||||| |||||||||||||||| || || ||||||||||
gtttctgcttgtttggtgatgtcaagtataaattagttagcccagatttgtaatacctgatttcttgtttcatgtcttctcctggcttgaattgtgccgtcaagtagtgtccctgggctaaatgtaacatttatgtttatgccaatgtctattgcagATGGATGGTTTGACAAAGACAAACGACTTGGTATTTGTACTTGCAGCTACAAATCTTCCCTGGGAATTGGATGCAGCCATGCTCCGCCGGCTTGAGAAGC

upper sequence: GLYMA08G09050.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G115766_T02 (Zea mays), 3'ss of exon 7
ccatgacttaatttattagttatttgagtttaccatgatagttggcatatgtattctggtgtgctttctcaaaaattaatcatttggatt-aagattgcagATGGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACAAATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGC
|||  | |     |  | |  |    | |   |     |  | || |    | |     ||   ||  | |     | |   ||||  || |    ||||||||||||| ||||| ||||||||||| || ||||||||| |||| ||||||||| | || |||||| |||||||||| ||||| || || || |||||||
ccacaagtgtccct-ctggacaaccaactggtcttcagttttggggactgttgtctctatggtattgattatttcatgacattttgattttattgctgcagATGGATGGGTTGACTAAGACAGATGAGCTTGTTTTTGTTCTAGCAGCAACAAATTTACCATGGGAATTGGATGCAGCAATGCTGCGTCGGCTGGAGAAGC

upper sequence: GLYMA08G09050.1 (Glycine max), 3'ss of exon 8
lower sequence: AT2G34560.2 (Arabidopsis thaliana), 3'ss of exon 8
ccatgacttaatttattagttatttgagtttaccatgatagttggcatatgtattctggtgtgctttctcaaaaattaatc-atttggattaagattgcagATGGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACAAATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGC
   | |  |   | |  | | | |||  | |  ||  | ||||  |||     ||| ||         |||  ||| || |  ||   |||    |||||||||||||| ||    || ||  |||| || || ||||||||||| ||||||||||| ||||||||||| |||||||| ||||| || ||||| ||||| |
--gtaaaatg-ctcaaaaatgaattggttct--cacaaaagtt--catcatctttccggacca-----tcagtaataaacctgttcaaatt----ttgcagATGGATGGGTTACAGAAAACGAATGAGCTCGTATTTGTTTTAGCAGCAACAAATCTCCCCTGGGAACTAGATGCAGCTATGCTCCGGCGTCTAGAGAAAC

upper sequence: GLYMA08G09050.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv10s0003g03500.t01 (Vitis vinifera), 3'ss of exon 8
--ccatgacttaatttattagttatttgagtttaccatgatagttggcatatgtattctggtgtgctttctcaaaaattaatcatttggattaagattgcagATGGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACAAATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGC
    || ||| | | |     || ||| | |       |||   |   ||||   |||   | | |||||||| ||||| || | |||||||| |||||||||||||||||||||||||||||||||| || |||||||||||||| ||||||||||| || |||||| |||||||||| ||||| || || ||||| ||| 
acagataactaactctgaatatttttt-attcattggagatgaatcaaatatcacttcaactatactttctcagaaattgatgacttggatta-gattgcagATGGATGGTTTGACAAAGACAGATGAGCTTGTTTTTGTTTTAGCAGCAACAAATCTCCCATGGGAATTGGATGCAGCGATGCTCCGTCGCCTTGAAAAGA

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|58024174|gb|CX710915.1|CX710915
EST:     GCAGTGAACACGAAGCTAGTAGACGGTTGAAAACAGAGCTTCTCATTCAG                         ATGGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACA
genomic: GCAGTGAACACGAAGCTAGTAGACGGTTGAAAACAGAGCTTCTCATTCAGgtgatggttg ... aagattgcagATGGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACA
EST: gi|58023441|gb|CX710182.1|CX710182
EST:     GCAGTGAACACGAAGCTAGTAGACGGTTGAAAACAGAGCTTCTCATTCAG                         ATGGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACA
genomic: GCAGTGAACACGAAGCTAGTAGACGGTTGAAAACAGAGCTTCTCATTCAGgtgatggttg ... aagattgcagATGGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACA
EST: gi|58024561|gb|CX711302.1|CX711302
EST:     GCAGTGAACACGAAGCTAGTAGACGGTTGAAAACAGAGCTTCTCATTCAG                         ATGGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACA
genomic: GCAGTGAACACGAAGCTAGTAGACGGTTGAAAACAGAGCTTCTCATTCAGgtgatggttg ... aagattgcagATGGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACA
EST: gi|298186847|gb|HO033946.1|HO033946
EST:     GCAGTGAACACGAAGCTAGTAGACGGTTGAAAACAGAGCTTCTCATTCAG                         ATGGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACA
genomic: GCAGTGAACACGAAGCTAGTAGACGGTTGAAAACAGAGCTTCTCATTCAGgtgatggttg ... aagattgcagATGGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACA
EST: gi|58023989|gb|CX710730.1|CX710730
EST:     GCAGTGAACACGAAGCTAGTAGACGGTTGAAAACAGAGCTTCTCATTCAG                         ATGGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACA
genomic: GCAGTGAACACGAAGCTAGTAGACGGTTGAAAACAGAGCTTCTCATTCAGgtgatggttg ... aagattgcagATGGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACA
EST: gi|58018662|gb|CX705404.1|CX705404
EST:     GCAGTGAACACGAAGCTAGTAGACGGTTGAAAACAGAGCTTCTCATTCAG                         ATGGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACA
genomic: GCAGTGAACACGAAGCTAGTAGACGGTTGAAAACAGAGCTTCTCATTCAGgtgatggttg ... aagattgcagATGGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACA
EST: gi|10848344|gb|BF071723.1|BF071723
EST:     GCAGTGAACACGAAGCTAGTAGACGGTTGAAAACAGAGCTTCTCATTCAG                         ATGGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACA
genomic: GCAGTGAACACGAAGCTAGTAGACGGTTGAAAACAGAGCTTCTCATTCAGgtgatggttg ... aagattgcagATGGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACA
EST: gi|192331318|gb|FK021015.1|FK021015
EST:     GCAGTGAACACGAAGCTAGTAGACGGTTGAAAACAGAGCTTCTCATTCAG                         ATGGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACA
genomic: GCAGTGAACACGAAGCTAGTAGACGGTTGAAAACAGAGCTTCTCATTCAGgtgatggttg ... aagattgcagATGGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACA
EST: gi|58020971|gb|CX707713.1|CX707713
EST:     GCAGTGAACACGAAGCTAGTAGACGGTTGAAAACAGAGCTTCTCATTCAG                         ATGGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACA
genomic: GCAGTGAACACGAAGCTAGTAGACGGTTGAAAACAGAGCTTCTCATTCAGgtgatggttg ... aagattgcagATGGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACA
EST: gi|58021730|gb|CX708471.1|CX708471
EST:     GCAGTGAACACGAAGCTAGTAGACGGTTGAAAACAGAGCTTCTCATTCAG                         ATGGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACA
genomic: GCAGTGAACACGAAGCTAGTAGACGGTTGAAAACAGAGCTTCTCATTCAGgtgatggttg ... aagattgcagATGGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACA
EST: gi|58021561|gb|CX708302.1|CX708302
EST:     GCAGTGAACACGAAGCTAGTAGACGGTTGAAAACAGAGCTTCTCATTCAG                         ATGGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACA
genomic: GCAGTGAACACGAAGCTAGTAGACGGTTGAAAACAGAGCTTCTCATTCAGgtgatggttg ... aagattgcagATGGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatgtattctggtgtgctttctcaaaaattaatcatttggattaagattgcagATGGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACAAATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGC
                            aattaat  putative branch site (score: 3)
                         aaaaattaatcatttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccatgacttaatttattagttatttgagtttaccatgatagttggcatatgtattctggtgtgctttctcaaaaattaatcatttggattaagattgcagATGGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACAAATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
-catgact
- - - - - - - - - - - - - - - - ccatgat
- - - - - - - - - - - - - - - - - - - - - - gcatatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - tctggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaattaa