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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatgaatgccatttgtatgatgcacacaaatgctgtataaagccatcagaaactagttattacttagtagttgtatcttctactaaatgtttagccagacattttttcagttttaactgaccctactgtgtttttgaacttcagAGTTTGTTAGAAAAAGGCTACGAACTTGTATCTGGTGGAACTGACAACCATTTAGTGTTGGTGAACTTAAGAAACAAG

Basic information

species Glycine max
transcript GLYMA14G36280.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G36280.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 11
gtaaaatgaatgccatttgtatgatgcacacaaatgctgtataaagccatca-gaaactagttattacttagtagttgtatcttctactaaatgtttagccagacattttttcagttttaactgaccctactgtgtttt-tgaacttcagAGTTTGTTAGAAAAAGGCTACGAACTTGTATCTGGTGGAACTGACAACCATTTAGTGTTGGTGAACTTAAGAAACAAG
                                               || || |  || | ||   | ||| | ||| |      |  | ||| | |      ||||||   |   ||   || | |     |   ||| | |  | ||||| |||  || |||||||||||||||||| |||||||| ||||||||||||||||||||||| ||  | |  | ||||
-----------------------------------------------cagcatgttacgaattgcaaattattggtttttcaacatgatgaat-tgtgctttaacatttgaaccacttc--cttatctggtggcaatttatcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCATTTAGTGTTGGTAAATCTCAAGAGCAAG

upper sequence: GLYMA14G36280.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 10
gtaaaatgaatgccatttgtatgatgcacacaaatgctgtataaagccatcagaaactagttattacttagtagttgtatcttctactaaatgtttagccagacattttttcagttttaactgac--cctactgtgtttttgaacttcagAGTTTGTTAGAAAAAGGCTACGAACTTGTATCTGGTGGAACTGACAACCATTTAGTGTTGGTGAACTTAAGAAACAAG
                                                | |   | || |     ||  |   ||  | ||||  |  || | || |    ||   | |  |||||| ||       | |  || || | |     ||||||  || |   |||||| || ||||| || |||||||| |||||||||||||||||  |||||||  | |  || |||
------------------------------------------------aacttcagctggaagaaacacaaatgtgttgtcttgaagcaa-tattaattgtgatgctata-cagtttgaatcacttacttgatgggtatattgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAG

upper sequence: GLYMA14G36280.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 11
---------------------gtaaaatgaatgccatttgtatgatgcacacaaatgctgt--ataaagccatcagaaactag--ttattacttagtagtt-gtatcttctactaaatgtttagccagacattttttcagttttaact----gaccctactgtgtttttgaacttcagAGTTTGTTAGAAAAAGGCTACGAACTTGTATCTGGTGGAACTGACAACCATTTAGTGTTGGTGAACTTAAGAAACAAG
                     || | ||  ||||  ||| | |  |   | ||| |    |   | | || |     |  ||   || ||   ||  |||| |||| ||||  | ||| |||    | |  ||     |||||  |||     |  || || | |||||    | |||||| ||||||| |||||||| |||||||||||||| |||||||| ||||||||||| |||||||| || | |||||||
gtaaaaggctccttgatgctagttacatttatgcagtttttcttgtttgc-caattttcattggttatgctagttacatttaacatttttcactatcagttagtattttcttgttaat-tttgttgatattttggagaagtttacacttttaaagtcttcttttttttttggttgcagAGTCTGTTAGAGAAAGGCTATGAACTTGTATCTGGCGGAACTGATAACCATTTAGTCTTGGTGAATTTGAAAAACAAG

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|19269481|gb|BM885737.1|BM885737
EST:     TCAAGAATTACCAAAAGCAAGTACTTAGCAACTGCTCAGCATTTGCACAG                         AGTTTGTTAGAAAAAGGCTACGAACTTGTATCTGGTGGAACTGACAACCAT
genomic: TCAAGAATTACCAAAAGCAAGTACTTAGCAACTGCTCAGCATTTGCACAGgtaaaatgaa ... tgaacttcagAGTTTGTTAGAAAAAGGCTACGAACTTGTATCTGGTGGAACTGACAACCAT
EST: gi|192312199|gb|FK003920.1|FK003920
EST:     TCAAGAATTACCAAAAGCAAGTACTTAGCA-CTGCTCAGCATTTGCACAG                         AGTT-GTTAGAAAAA
genomic: TCAAGAATTACCAAAAGCAAGTACTTAGCAACTGCTCAGCATTTGCACAGgtaaaatgaa ... tgaacttcagAGTTTGTTAGAAAAA
EST: gi|6915301|gb|AW396831.1|AW396831
EST:     TCAAGAATTACCAAAAGCAAGTACTTAGCAACTGCTCAGCATTTGCACAG                         AGTTTGTTAGAAAAAGGCTACTAACTTGTATCTGGTGGAACTGACAACCAT
genomic: TCAAGAATTACCAAAAGCAAGTACTTAGCAACTGCTCAGCATTTGCACAGgtaaaatgaa ... tgaacttcagAGTTTGTTAGAAAAAGGCTACGAACTTGTATCTGGTGGAACTGACAACCAT
EST: gi|7796703|gb|AW782097.1|AW782097
EST:     TCAAGAATTACCAAAAGCAAGTACTTAGCAACTGCTCAGCATTTGCACAG                         AGTTTGTTAGAAAAAGGCTACGAACTTGTATCTGGTGGAACTGACAACCAT
genomic: TCAAGAATTACCAAAAGCAAGTACTTAGCAACTGCTCAGCATTTGCACAGgtaaaatgaa ... tgaacttcagAGTTTGTTAGAAAAAGGCTACGAACTTGTATCTGGTGGAACTGACAACCAT
EST: gi|19348549|gb|BM893081.1|BM893081
EST:     TCAAGAATTACCAAAAGCAAGTACTTAGCAACTGCTCAGCATTTGCACAG                         AGTTTGTTAGAAAAAGGCTACGAACTTGTATCTGGTGGAACTGACAACCAT
genomic: TCAAGAATTACCAAAAGCAAGTACTTAGCAACTGCTCAGCATTTGCACAGgtaaaatgaa ... tgaacttcagAGTTTGTTAGAAAAAGGCTACGAACTTGTATCTGGTGGAACTGACAACCAT
EST: gi|105631822|gb|DW246196.1|DW246196
EST:     ACTTAGCGACTGCTCAGCATTTGCACAG                         AGTTTGTTAGAAAAAGGCTACGAACTTGTATCTGGTGGAACTGACAACCAT
genomic: ACTTAGCAACTGCTCAGCATTTGCACAGgtaaaatgaa ... tgaacttcagAGTTTGTTAGAAAAAGGCTACGAACTTGTATCTGGTGGAACTGACAACCAT
EST: gi|151409184|gb|EV278992.1|EV278992
EST:     TCAAGAATTACCAAAAGCAAGTACTTAGCAACTGCTCAGCATTTGCACAG                         AGTTTGTTAGAAAAAGGCTACGAACTTGTATCTGGTGGAACTGACAACCAT
genomic: TCAAGAATTACCAAAAGCAAGTACTTAGCAACTGCTCAGCATTTGCACAGgtaaaatgaa ... tgaacttcagAGTTTGTTAGAAAAAGGCTACGAACTTGTATCTGGTGGAACTGACAACCAT
EST: gi|192315079|gb|FK010449.1|FK010449
EST:     TCAAGAATTACCAAAAGCAAGTACTTAGCAACTGCTCAGCATTTGCACAG                         AGTTTGTTAGAAAAAGGCTACGAACTTGTATCTGGTGGAACTGACAACCAT
genomic: TCAAGAATTACCAAAAGCAAGTACTTAGCAACTGCTCAGCATTTGCACAGgtaaaatgaa ... tgaacttcagAGTTTGTTAGAAAAAGGCTACGAACTTGTATCTGGTGGAACTGACAACCAT
EST: gi|13240115|gb|BG359424.1|BG359424
EST:     TCAAGAATTACCAAAAGCAAGTACTTAGCAACTGCTCAGCATTTGCACAG                         AGTTTGTTAGAAAAAGGCTACGAACTTGTATCTGGTGGAACTGACAACCAT
genomic: TCAAGAATTACCAAAAGCAAGTACTTAGCAACTGCTCAGCATTTGCACAGgtaaaatgaa ... tgaacttcagAGTTTGTTAGAAAAAGGCTACGAACTTGTATCTGGTGGAACTGACAACCAT
EST: gi|192312198|gb|FK003919.1|FK003919
EST:     TCAAGAATTACCAAAAGCAAGTACTTAGCA-CTGCTCAGCATTTGCACAG                         AGTTTGTTAGAAAAA
genomic: TCAAGAATTACCAAAAGCAAGTACTTAGCAACTGCTCAGCATTTGCACAGgtaaaatgaa ... tgaacttcagAGTTTGTTAGAAAAA
EST: gi|192298247|gb|FG992067.1|FG992067
EST:     TCAAGAATTACCAAAAGCAAGTACTTAGCAACTGCTCAGCATTTGCACAG                         AGTTTGTTAGAAAAAGGCTACGAACTTGTATCTGGTGGAACTGACAACCAT
genomic: TCAAGAATTACCAAAAGCAAGTACTTAGCAACTGCTCAGCATTTGCACAGgtaaaatgaa ... tgaacttcagAGTTTGTTAGAAAAAGGCTACGAACTTGTATCTGGTGGAACTGACAACCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttagccagacattttttcagttttaactgaccctactgtgtttttgaacttcagAGTTTGTTAGAAAAAGGCTACGAACTTGTATCTGGTGGAACTGACAACCATTTAGTGTTGGTGAACTTAAGAAACAAG
                         aactgac  putative branch site (score: 2)
                                       tgttttt  putative PPT
           attttttcagttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaatgaatgccatttgtatgatgcacacaaatgctgtataaagccatcagaaactagttattacttagtagttgtatcttctactaaatgtttagccagacattttttcagttttaactgaccctactgtgtttttgaacttcagAGTTTGTTAGAAAAAGGCTACGAACTTGTATCTGGTGGAACTGACAACCATTTAGTGTTGGTGAACTTAAGAAACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA