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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgatgtgcatgcacaaaaaactgaacctaaactattccagacatgatggattcactcatcaaaattattaatcttcagctcattctttcgtgttactagGCTGACAATCTGCGGCAGCAGACATTACAACAAATGCTTCGAATATTAACGACCAGGCAATCGGCTCGTGCTCTTCTTGCCATCAGTGATTATTTCTCAC

Basic information

species Glycine max
transcript GLYMA03G28320.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G28320.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os03g20310.4 (Oryza sativa), 3'ss of exon 8
----atgatgtgcatgcacaaaaaactgaacctaaactattccagacatgatggattcactcatcaaaattattaatcttcagctcattctttcgtgttactagGCTGACAATCTGCGGCAGCAGACATTACAACAAATGCTTCGAATATTAACGACCAGGCAATCGGCTCGTGCTCTTCTTGCCATCAGTGATTATTTCTCAC
     |    | | |           ||| ||  | | | | | |  |   |    | || | |     || | ||     || ||     ||| |  | | ||||||||||| ||||||||||||| ||||| |||||||  |||||  | || | | | ||| | || |||||||| ||||| ||   |||||| |||||||
tgtgttccctttcttatttgtgcttttgatcccgagcaagttctgcaagttttagatgaccctttttttttctgaag----agttctaatcttctttctgccagGCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACAATCCGACAAGCTGCCCGTGCTCTACTTGCAATACATGATTACTTCTCAC
















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|10254538|gb|BE822304.1|BE822304
EST:     TGGCTATNNCCATGGGAAAGCTTGGTACACTTGAGGGGTTTCTTCACCAG                         GCTGACAATCTGCGGCAGCAGACATTACAACAAATGCTTCGAATATTAACG
genomic: TGGCTATGGCCATGGGAAAGCTTGGTACACTTGAGGGGTTTCTTCACCAGgtacgctcat ... gtgttactagGCTGACAATCTGCGGCAGCAGACATTACAACAAATGCTTCGAATATTAACG
EST: gi|24135626|gb|BU926136.1|BU926136
EST:     TGGCTATGGCCATGGGAAAGCTTGGTACACTTGAGGGGTTTCTTCACCAG                         GCTGACAATCTGCGGCAGCAGACATTACAACAAATGCTTCCGA-TATTAAC
genomic: TGGCTATGGCCATGGGAAAGCTTGGTACACTTGAGGGGTTTCTTCACCAGgtacgctcat ... gtgttactagGCTGACAATCTGCGGCAGCAGACATTACAACAAATGCTTC-GAATATTAAC
EST: gi|254326605|gb|GR841197.1|GR841197
EST:     TGGCTATGGCCATGGGAAAGCTTGGTACACTTGAGGGGTTTCTTCACCAG                         GCTGACAATCTGCGGCAGCAGACATTACAACAAATGCTTCGAATATTAACG
genomic: TGGCTATGGCCATGGGAAAGCTTGGTACACTTGAGGGGTTTCTTCACCAGgtacgctcat ... gtgttactagGCTGACAATCTGCGGCAGCAGACATTACAACAAATGCTTCGAATATTAACG
EST: gi|254316491|gb|GR828028.1|GR828028
EST:     TGGCTATGGCCATGGGAAAGCTTGGTACACTTGAGGGGTTTCTTCACCAG                         GCTGACAATCTGCGGCAGCAGACATTACAACAAATGCTTCGAATATTAACG
genomic: TGGCTATGGCCATGGGAAAGCTTGGTACACTTGAGGGGTTTCTTCACCAGgtacgctcat ... gtgttactagGCTGACAATCTGCGGCAGCAGACATTACAACAAATGCTTCGAATATTAACG
EST: gi|57575242|gb|CX548217.1|CX548217
EST:     TGGCTATGGCCATGGGAAAGCTTGGTACACTTGAGGGGTTTCTTCACCAG                         GCTGACAATCTGCGGCAGCAGACATTACAACAAATGCTTCGAATATTAACG
genomic: TGGCTATGGCCATGGGAAAGCTTGGTACACTTGAGGGGTTTCTTCACCAGgtacgctcat ... gtgttactagGCTGACAATCTGCGGCAGCAGACATTACAACAAATGCTTCGAATATTAACG
EST: gi|15816144|gb|BI788419.1|BI788419
EST:     TGGCTATGGCCATGGGAAAGCTTGGTACACTTGAGGGGTTTCTTCACCAG                         GCTGACAATCTGCGGCAGCAGACATTACAACAAATGCTTCGAATATTAACG
genomic: TGGCTATGGCCATGGGAAAGCTTGGTACACTTGAGGGGTTTCTTCACCAGgtacgctcat ... gtgttactagGCTGACAATCTGCGGCAGCAGACATTACAACAAATGCTTCGAATATTAACG
EST: gi|6913075|gb|AW394605.1|AW394605
EST:     GGTTTCTTCACCAG                         GCTGACAATCTGCGGCAGCAGACATTACAACAAATGCTTCGAATATTAACG
genomic: GGTTTCTTCACCAGgtacgctcat ... gtgttactagGCTGACAATCTGCGGCAGCAGACATTACAACAAATGCTTCGAATATTAACG
EST: gi|254316490|gb|GR828027.1|GR828027
EST:     TGGCTATGGCCATGGGAAAGCTTGGTACACTTGAGGGGTTTCTTCACCAC                         GCTGACAATCTGCGGCAGCAGACATTACAACAAATGCTTCGAATATTAACG
genomic: TGGCTATGGCCATGGGAAAGCTTGGTACACTTGAGGGGTTTCTTCACCAGgtacgctcat ... gtgttactagGCTGACAATCTGCGGCAGCAGACATTACAACAAATGCTTCGAATATTAACG
EST: gi|19269047|gb|BM885303.1|BM885303
EST:     TGGCTATGGCCATGGGAAAGCTTGGTACACTTGAGGGGTTTCTTCACCAG                         GCTGACAATCTGCGGCAGCAGACATTACAACAAATGCTTCGAATATTAACG
genomic: TGGCTATGGCCATGGGAAAGCTTGGTACACTTGAGGGGTTTCTTCACCAGgtacgctcat ... gtgttactagGCTGACAATCTGCGGCAGCAGACATTACAACAAATGCTTCGAATATTAACG
EST: gi|193484781|gb|FK449933.1|FK449933
EST:     TGGCTATGGCCATGGGAAAGCTTGGTACACTTGAGGGGTTTCTTCACCAG                         GCTGACAATCTGCGGCAGCAGACATTACAACAAATGCTTCGAATATTAACG
genomic: TGGCTATGGCCATGGGAAAGCTTGGTACACTTGAGGGGTTTCTTCACCAGgtacgctcat ... gtgttactagGCTGACAATCTGCGGCAGCAGACATTACAACAAATGCTTCGAATATTAACG
EST: gi|51337854|gb|CO981720.1|CO981720
EST:     TGGCTATGGCCATGGGAAAGCTTGGTACACTTGAGGGGTTTCTTCACCAG                         GCTGACAATCTGCGGCAGCAGACATTACAACAAATGCTTCGAATATTAACG
genomic: TGGCTATGGCCATGGGAAAGCTTGGTACACTTGAGGGGTTTCTTCACCAGgtacgctcat ... gtgttactagGCTGACAATCTGCGGCAGCAGACATTACAACAAATGCTTCGAATATTAACG
EST: gi|57574999|gb|CX547974.1|CX547974
EST:     TGGCTATGGCCATGGGAAAGCTTGGTACACTTGAGGGGTTTCTTCACCAG                         GCTGACAATCTGCGGCAGCAGACATTACAACAAATGCTTCGAATATTAACG
genomic: TGGCTATGGCCATGGGAAAGCTTGGTACACTTGAGGGGTTTCTTCACCAGgtacgctcat ... gtgttactagGCTGACAATCTGCGGCAGCAGACATTACAACAAATGCTTCGAATATTAACG
EST: gi|9903361|gb|BE612329.1|BE612329
EST:     TGGCTATGGCCATGGGAAAGCTTGGTACACTTGAGGGGTTTCTTCACCAG                         GCTGACAATCTGCGGCAGCAGACATTACAACAAATGCTTCGAATATTAACG
genomic: TGGCTATGGCCATGGGAAAGCTTGGTACACTTGAGGGGTTTCTTCACCAGgtacgctcat ... gtgttactagGCTGACAATCTGCGGCAGCAGACATTACAACAAATGCTTCGAATATTAACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatggattcactcatcaaaattattaatcttcagctcattctttcgtgttactagGCTGACAATCTGCGGCAGCAGACATTACAACAAATGCTTCGAATATTAACGACCAGGCAATCGGCTCGTGCTCTTCTTGCCATCAGTGATTATTTCTCAC
                     tattaat  putative branch site (score: 2)
                                      ttctttcgt  putative PPT
             atcaaaattattaatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgatgtgcatgcacaaaaaactgaacctaaactattccagacatgatggattcactcatcaaaattattaatcttcagctcattctttcgtgttactagGCTGACAATCTGCGGCAGCAGACATTACAACAAATGCTTCGAATATTAACGACCAGGCAATCGGCTCGTGCTCTTCTTGCCATCAGTGATTATTTCTCAC

-tgatgtg
- - - - catgcac
- - - - - - - - - - -ctgaacc
- - - - - - - - - - - - - - - - - - -ccagaca
- - - - - - - - - - - - - - - - - - - - - - - - - - tcactca