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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttagctgatttgttatcttaagtggatgaaatgaaacttaaaggtataagatgttaaactgggggttgggctgcgtttttcctttacaatttctttacGTGAATCAAGAGCAGTTCTGATACACCAGTTATCCAAAAAGCTTACGCAAAGACTTCCATTCAAATTACATGGACTTGCTGTTAGGTCAACCTTCCATCC

Basic information

species Glycine max
transcript GLYMA16G00540.1
intron # 8
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G00540.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv00s0227g00060.t01 (Vitis vinifera), 3'ss of exon 14
ttttagctgatttgttatcttaagtggatgaaatgaaacttaaaggtataagatgttaaactgggggttgggctgcgtttttcctttacaatttctttacGTGAATCAAGAGCAGTTCTGATACACCAGTTATCCAAAAAGCTTACGCAAAGACTTCCATTCAAATTACATGGACTTGCTGTTAGGTCAACCTTCCATCC------------
           ||  | ||||  | | ||  | | ||   |  | |  | |    | ||| |   |  |          ||| ||| ||       ||||||||||| |||||| | || || |||||| | || || |||||||| |||||| |||||||||| || ||||| ||| | |||   ||||  || |||||            
---------gctttctctcttctg-gaatatagttaag--tggatgagtgatggctgaaagtaaagaattcatatttacttttcttgacttgggaattacgtgaatctagagCAATACTTATTCACCAGCTCTCTAAGAAGCTTACCCAAAGAATTCCATTCAAGTTGCATGGTCTTCCAGTTTCATCAATTTTTCATCCAACGCGTTCGAT
















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|6454193|gb|AW184806.1|AW184806
EST:     TGTAGAATGGCACCGGAAAGGTGACTACTTTTCGACAGTGATGCCAGCAG                         GTGAATCAAGAGCAGTTCTGATACACCAGTTATCCAAAAAGCTTACGCAAA
genomic: TGTAGAATGGCACCGGAAAGGTGACTACTTTTCGACAGTGATGCCAGCAGatatcctttg ... atttctttacGTGAATCAAGAGCAGTTCTGATACACCAGTTATCCAAAAAGCTTACGCAAA
EST: gi|151411237|gb|EV281048.1|EV281048
EST:     TGTAGAATGGCACCGGAAAGGTGACTACTTTTCGACAGTGATGCCAGCAG                         GTGAATCAAGAGCAGTTCTGATACACCAGTTATCCAAAAAGCTTACGCAAA
genomic: TGTAGAATGGCACCGGAAAGGTGACTACTTTTCGACAGTGATGCCAGCAGatatcctttg ... atttctttacGTGAATCAAGAGCAGTTCTGATACACCAGTTATCCAAAAAGCTTACGCAAA
EST: gi|51337601|gb|CO981467.1|CO981467
EST:     AGTGATGCCAGCAG                         GTGAATCAAGAGCAGTNNNGATACACCAGTTATCCAAAAAGCTTACGCAAA
genomic: AGTGATGCCAGCAGatatcctttg ... atttctttacGTGAATCAAGAGCAGTTCTGATACACCAGTTATCCAAAAAGCTTACGCAAA
EST: gi|7686391|gb|AW757039.1|AW757039
EST:     TGTAGAATGGCACCGGAAAGGTGACTACTTTTCGACAGTGATGCCAGCAG                         GTGAATCAAGAGCAGTTCTGATACACCAGTTATCCAAAAAGCTTACGCAAA
genomic: TGTAGAATGGCACCGGAAAGGTGACTACTTTTCGACAGTGATGCCAGCAGatatcctttg ... atttctttacGTGAATCAAGAGCAGTTCTGATACACCAGTTATCCAAAAAGCTTACGCAAA
EST: gi|18038858|gb|BM307152.1|BM307152
EST:     TGTAGAATGGCACCGGAAAGGTGACTACTTTTCGACAGTGATGCCAGCAG                         GTGAATCAAGAGCAGTTCTGATACACCAGTTATCCAAAAAGCTTACGCAAA
genomic: TGTAGAATGGCACCGGAAAGGTGACTACTTTTCGACAGTGATGCCAGCAGatatcctttg ... atttctttacGTGAATCAAGAGCAGTTCTGATACACCAGTTATCCAAAAAGCTTACGCAAA
EST: gi|23730690|gb|BU763441.1|BU763441
EST:     TGTAGAATGGCACCGGAAAGGTGACTACTTTTCGACAGTGATGCCGGCAG                         GTGAATCAAGAGCAGTTCTGATACACCAGTTATCCAAAAAGCTTACGCAAA
genomic: TGTAGAATGGCACCGGAAAGGTGACTACTTTTCGACAGTGATGCCAGCAGatatcctttg ... atttctttacGTGAATCAAGAGCAGTTCTGATACACCAGTTATCCAAAAAGCTTACGCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtataagatgttaaactgggggttgggctgcgtttttcctttacaatttctttacGTGAATCAAGAGCAGTTCTGATACACCAGTTATCCAAAAAGCTTACGCAAAGACTTCCATTCAAATTACATGGACTTGCTGTTAGGTCAACCTTCCATCC
                                   ttcctttac  putative branch site 
                                tttttcctttacaatt  CT-rich tract
                                       tttacaatttcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttagctgatttgttatcttaagtggatgaaatgaaacttaaaggtataagatgttaaactgggggttgggctgcgtttttcctttacaatttctttacGTGAATCAAGAGCAGTTCTGATACACCAGTTATCCAAAAAGCTTACGCAAAGACTTCCATTCAAATTACATGGACTTGCTGTTAGGTCAACCTTCCATCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT