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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttctcttttctttttaaatttctttttctataaaaaagaatgatttttatctttactttttaatcttattctgtttttctctcgttttcctattttagCCTGTTCAAGAACCAAAAAAGATGACACAAATAATTGTAGATGCTTTGGAGATCACTGGACAGAGGGGCATCATCAATAAAGGATGGGGAGGTCTTGGGA

Basic information

species Glycine max
transcript GLYMA18G28130.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G28130.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv07s0005g05600.t01 (Vitis vinifera), 3'ss of exon 9
tcttctcttttctttttaaatttctttttctataaaaaagaatgatttttatctttactttttaatcttattctgtttttctctcgttttcctattttagCCTGTTCAAGAACCAAAAAAGATGACACAAATAATTGTAGATGCTTTGGAGATCACTGGACAGAGGGGCATCATCAATAAAGGATGGGGAGGTCTTGGGA
|      || |     || |  | | |  || |      || || | | ||  | | ||  ||| | | |||| ||| |   ||  |  |  ||||||||||||||||||||||| | || ||||| ||||||||||| |||||| ||||    |||||||||||||||||||| |||||||| ||||| || |||||||
ttaaaatttgttgccatacagatgtctggcttttgtttggactgctatgtagttattctccttattatgattcagttgtaaccttttcattttattttagCCTGTTCAAGAACCAGAGAAAATGACTCAAATAATTGTGGATGCTCTGGAAGAGACTGGACAGAGGGGCATCATTAATAAAGGCTGGGGTGGCCTTGGGA
















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|15288220|gb|BI472111.1|BI472111
EST:     AATGGCTTGAAGAAGGAGACAAACCTATTTACATTGGATTTGGTAGCCTG                         CCTGTTCAAGAACCAAAAAAGATGACACAAATAATTGTAGATGCTTTGGAG
genomic: AATGGCTTGAAGAAGGAGACAAACCTATTTACATTGGATTTGGTAGCCTGgtgagtcttt ... cctattttagCCTGTTCAAGAACCAAAAAAGATGACACAAATAATTGTAGATGCTTTGGAG
EST: gi|9204101|gb|BE330325.1|BE330325
EST:     AATGGCTTGAAGAAGGAGACAAACCTATTTACATTGGATTTGGTAGCCTG                         CCTGTTCAAGAACCAAAAAAGATGACACAAATAATTGTAGATGCTTTGGAG
genomic: AATGGCTTGAAGAAGGAGACAAACCTATTTACATTGGATTTGGTAGCCTGgtgagtcttt ... cctattttagCCTGTTCAAGAACCAAAAAAGATGACACAAATAATTGTAGATGCTTTGGAG
EST: gi|6566103|gb|AW233863.1|AW233863
EST:     AATGGCTTGAAGAAGGAGACAAACCTATTTACATTGGATTTGGTAGCCTG                         CCTGTTCAAGAACCAAAAAAGATGACACAAATAATTGTAGATGCTTTGGAG
genomic: AATGGCTTGAAGAAGGAGACAAACCTATTTACATTGGATTTGGTAGCCTGgtgagtcttt ... cctattttagCCTGTTCAAGAACCAAAAAAGATGACACAAATAATTGTAGATGCTTTGGAG
EST: gi|22525050|gb|BU083861.1|BU083861
EST:     AATGGCTTGAAGAAGGAGACAAACCTATTTACATTGGATTTGGTAGCCTG                         CCTGTTCAAGAACCAAAAAAGATGACACAA
genomic: AATGGCTTGAAGAAGGAGACAAACCTATTTACATTGGATTTGGTAGCCTGgtgagtcttt ... cctattttagCCTGTTCAAGAACCAAAAAAGATGACACAA
EST: gi|51338437|gb|CO982303.1|CO982303
EST:     ATTGGATTTGGTAGCCTG                         CCTGTTCAAGAACCAAAAAAGATGACACAAATAATTGTAGATGCTTTGGAG
genomic: ATTGGATTTGGTAGCCTGgtgagtcttt ... cctattttagCCTGTTCAAGAACCAAAAAAGATGACACAAATAATTGTAGATGCTTTGGAG
EST: gi|58017155|gb|CX703897.1|CX703897
EST:     AATGGCTTGAAGAAGGAGACAAACCTATTTACATTGGATTTGGTAGCCTG                         CCTGTTCAAGAACCAAAAAAGATGACACAAATAATTGTAGATGCTTTGGAG
genomic: AATGGCTTGAAGAAGGAGACAAACCTATTTACATTGGATTTGGTAGCCTGgtgagtcttt ... cctattttagCCTGTTCAAGAACCAAAAAAGATGACACAAATAATTGTAGATGCTTTGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttatctttactttttaatcttattctgtttttctctcgttttcctattttagCCTGTTCAAGAACCAAAAAAGATGACACAAATAATTGTAGATGCTTTGGAGATCACTGGACAGAGGGGCATCATCAATAAAGGATGGGGAGGTCTTGGGA
              ttttaat  putative branch site (score: 3)
            ctttttaatcttattc  CT-rich tract
        tttactttttaatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttctcttttctttttaaatttctttttctataaaaaagaatgatttttatctttactttttaatcttattctgtttttctctcgttttcctattttagCCTGTTCAAGAACCAAAAAAGATGACACAAATAATTGTAGATGCTTTGGAGATCACTGGACAGAGGGGCATCATCAATAAAGGATGGGGAGGTCTTGGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG