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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaaatacatctcaaatgaaaattttatttgtaaattacaatggaaattttttttaaatttttttttggtaactatctttactgaacttaatgttttttcagATGGTTGTTTCAGAAGATATAGGAAGACAAATTTTGACATATGGTGAGAG

Basic information

species Glycine max
transcript GLYMA08G03580.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G03580.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv11s0016g02870.t01 (Vitis vinifera), 3'ss of exon 10
gtaagtaaatacatctcaaatgaaaattttatttgtaaattacaatggaaattttttttaaattt---ttttttggtaact------atctttac-tgaactta------atgttt---tttcagATGGTTGTTTCAGAAGATATAGGAAGACAAATTTTGACATATGGTGAGAG
||||  |  | | |   |   |    |||| | | | | ||  | | ||||  || ||||    |   |||||| | ||||      || |||   ||| || |      | ||||   || ||||||||||  |||||||||||||| |||||||| ||||||||||| |||||
gtaaccattttcttgaaattcgtcccttttttattttatttgaatttgaaacattgtttagggctgcatttttttgcaactggtatcatttttgtatgagctcatgatgaaggtttatcttgcagATGGTTGCATCAGAAGATATAGGTAGACAAATCTTGACATATGGAGAGAG
















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|15812744|gb|BI785019.1|BI785019
EST:     GAGCCAAACAGGCTACCAAATTTGCAATTTTGATGAATTTGGAATCAAGA                         ATGGTTGTTTCAGAAGATATAGGAAGACAAATTTTGACATATGGTGAGAG
genomic: GAGCCAAACAGGCTACCAAATCTGCAATTTTGATGAATTTGGAATCAAGAgtaagtaaat ... gttttttcagATGGTTGTTTCAGAAGATATAGGAAGACAAATTTTGACATATGGTGAGAG
EST: gi|5605747|gb|AI899811.1|AI899811
EST:     GAGCCAAACAGGCTACCAAATCTGCAATTTTGATGAATTTGGAATCAAGA                         ATGGTTGTTTCAGAAGATATAGGAAGACAAATTTTGACATATGGTGAGAG
genomic: GAGCCAAACAGGCTACCAAATCTGCAATTTTGATGAATTTGGAATCAAGAgtaagtaaat ... gttttttcagATGGTTGTTTCAGAAGATATAGGAAGACAAATTTTGACATATGGTGAGAG
EST: gi|21675780|gb|BQ628131.1|BQ628131
EST:     GCAATTTTGATGAATTTGGAATCAAGA                         ATGGTTGTTTCAGAAGATATAGGAAGACAAATTTTGACATATGGTGAGAG
genomic: GCAATTTTGATGAATTTGGAATCAAGAgtaagtaaat ... gttttttcagATGGTTGTTTCAGAAGATATAGGAAGACAAATTTTGACATATGGTGAGAG
EST: gi|213599745|gb|DB975810.1|DB975810
EST:     GAGCCAAACAGGCTACCAAATCTGCAATTTTGATGAATTTGGAATCAAGA                         ATGGTTGTTTCAGAAGATATAGGAAGACAAAGAAAT-CCATATGGTGAGAG
genomic: GAGCCAAACAGGCTACCAAATCTGCAATTTTGATGAATTTGGAATCAAGAgtaagtaaat ... gttttttcagATGGTTGTTTCAGAAGATATAGGAAGACAAA-TTTTGACATATGGTGAGAG
EST: gi|20814409|gb|BQ298887.1|BQ298887
EST:     GAGCCAAACAGGCTACCAAATCTGCAATTTTGATGAATTTGGAATCAAGA                         ATGGTTGTTTCAGAAGATATAGGAAGACAAATTTTGACATATGGTGAGAG
genomic: GAGCCAAACAGGCTACCAAATCTGCAATTTTGATGAATTTGGAATCAAGAgtaagtaaat ... gttttttcagATGGTTGTTTCAGAAGATATAGGAAGACAAATTTTGACATATGGTGAGAG
EST: gi|13180739|gb|BG352079.1|BG352079
EST:     GAGCCAAACAGGCTACCAAATCTGCAATTTTGATGAATTTGGAATCAAGA                         ATGGTTGTTTCAGAAGATATAGGAAGACAAATTTTGACATATGGTGAGAG
genomic: GAGCCAAACAGGCTACCAAATCTGCAATTTTGATGAATTTGGAATCAAGAgtaagtaaat ... gttttttcagATGGTTGTTTCAGAAGATATAGGAAGACAAATTTTGACATATGGTGAGAG
EST: gi|254330475|gb|GR841740.1|GR841740
EST:     GAGCCAAACAGGCTACCAAATCTGCAATTTTGATGAATTTGGAATCAAGA                         ATGGTTGTTTCAGAAGATATAGGAAGACAAATTTTGACATATGGTGAGAG
genomic: GAGCCAAACAGGCTACCAAATCTGCAATTTTGATGAATTTGGAATCAAGAgtaagtaaat ... gttttttcagATGGTTGTTTCAGAAGATATAGGAAGACAAATTTTGACATATGGTGAGAG
EST: gi|21638801|gb|BM139847.1|BM139847
EST:     GAGCCAAACAGGCTACCAAATCTGCAATTTTGATGAATTTGGAATCAAGA                         ATGGTTGTTTCAGAAGATATAGGAAGACAAACTTTGACATATGGTGAGAG
genomic: GAGCCAAACAGGCTACCAAATCTGCAATTTTGATGAATTTGGAATCAAGAgtaagtaaat ... gttttttcagATGGTTGTTTCAGAAGATATAGGAAGACAAATTTTGACATATGGTGAGAG
EST: gi|254325529|gb|GR838410.1|GR838410
EST:     GAGCCAAACAGGCTACCAAATCTGCAATTTTGATGAATTTGGAATCAAGA                         ATGGTTGTTTCAGAAGATATAGGAAGACAAATTTTGACATATGGTGAGAG
genomic: GAGCCAAACAGGCTACCAAATCTGCAATTTTGATGAATTTGGAATCAAGAgtaagtaaat ... gttttttcagATGGTTGTTTCAGAAGATATAGGAAGACAAATTTTGACATATGGTGAGAG
EST: gi|8826321|gb|BE210051.1|BE210051
EST:     GAGCCAAACAGGCTACCAAATCTGCAATTTTGATGAATTTGGAATCAAGA                         ATGGTTGTTTCAGAAGATATAGGAAGACAAATTTTGACATATGGTGAGAG
genomic: GAGCCAAACAGGCTACCAAATCTGCAATTTTGATGAATTTGGAATCAAGAgtaagtaaat ... gttttttcagATGGTTGTTTCAGAAGATATAGGAAGACAAATTTTGACATATGGTGAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttttaaatttttttttggtaactatctttactgaacttaatgttttttcagATGGTTGTTTCAGAAGATATAGGAAGACAAATTTTGACATATGGTGAGAG
                                            tgttttttc  CT-rich tract
     tttaaatttttttttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtaaatacatctcaaatgaaaattttatttgtaaattacaatggaaattttttttaaatttttttttggtaactatctttactgaacttaatgttttttcagATGGTTGTTTCAGAAGATATAGGAAGACAAATTTTGACATATGGTGAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA