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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtgtattttgtcatggcatctatcttcagtgtttgtgcactcctatcctattaattttttagtgggcttattcatttttcttttggtgatttctgacagGTCAAGCAAATGTTAATTGCACTTCTTTTTGAGTCGGATATGAAGTTGGCAGATGATGTCATAGAAACAATTCTTGACAAG

Basic information

species Glycine max
transcript GLYMA05G05580.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G05580.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv02s0236g00150.t01 (Vitis vinifera), 3'ss of exon 6
ggtgtattttgtcatggcatctatcttca-----gtgtttgtgcactcctatcctattaattttttagtgggcttattcatttttcttttggtgatttctgacagGTCAAGCAAATGTTAATTGCACTTCTTTTTGAGTCGGATATGAAGTTGGCAGATGATGTCATAGAAACAATTCTTGACAAG
 | | |  ||  || | | | | |||| |     |||||  | || |  | |  |||| |    |   ||    ||  ||| ||  || |  |   || || |||||||| |||||||||||||||||||| |  || || || ||||||||||| |||||   ||| || | ||| ||||| |||
agagaaaatta-caagacttttctcttgattgttgtgttgattcaattatgttttattgaaacctctatg----taggcatcttcattctatttgattttggcagGTCAAACAAATGTTAATTGCACTTCTGTGCGAATCTGAAATGAAGTTGGCTGATGAAACCATCGAGATAATACTTGATAAG

upper sequence: GLYMA05G05580.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv02s0236g00140.t01 (Vitis vinifera), 3'ss of exon 6
ggtgtattttgtcatggcatctatcttca-----gtgtttgtgcactcctatcctattaattttttagtgggcttattcatttttcttttggtgatttctgacagGTCAAGCAAATGTTAATTGCACTTCTTTTTGAGTCGGATATGAAGTTGGCAGATGATGTCATAGAAACAATTCTTGACAAG
 | | |  ||  || | | | | |||| |     |||||  | || |  | |  |||| |    |   ||    ||  ||| ||  || |  |   || || |||||||| |||||||||||||||||||| | ||| || || ||||||||||| |||||   ||| || | ||| ||||| |||
agagaaaatta-caggacttttctcttgattgttgtgttgattcaattatgttttattgaaacctccatg----taggcatcttcattctatttgattttggcagGTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCTGATGAAACCATCGAGATAATACTTGATAAG
















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|213599461|gb|DB980028.1|DB980028
EST:     ATTTAGGCTCTATGATTTGCACAATACTGGCTTTATAGAGCGCCCTGAG                         GTCAAGCAAATGTTAATTGCACTTCCTAACT-AGTCGGATATGAAGTTGGC
genomic: ATTTAGGCTCTATGATTTGCACAATACTGGCTTTATAGAGCGCCCTGAGgtaggatgat ... tttctgacagGTCAAGCAAATGTTAATTGCACTT-CTTTTTGAGTCGGATATGAAGTTGGC
EST: gi|151398929|gb|EV268800.1|EV268800
EST:     CATTTAGGCTCTATGATTTGCACAATACTGGCTTTATAGAGCGCCCTGAG                         GTCAAGCAAATGTTAATTGCACTTCTTTTTGAGTCAGATATGAAGTTGGCA
genomic: CATTTAGGCTCTATGATTTGCACAATACTGGCTTTATAGAGCGCCCTGAGgtaggatgat ... tttctgacagGTCAAGCAAATGTTAATTGCACTTCTTTTTGAGTCGGATATGAAGTTGGCA
EST: gi|151409699|gb|EV279507.1|EV279507
EST:     CATTTAGGCTCTATGATTTGCACAATACTGGCTTTATAGAGCGCCCTGAG                         GTCAAGCAAATGTTAATTGCACTTCTTTTTGAGTCGGATATGAAGTTGGCA
genomic: CATTTAGGCTCTATGATTTGCACAATACTGGCTTTATAGAGCGCCCTGAGgtaggatgat ... tttctgacagGTCAAGCAAATGTTAATTGCACTTCTTTTTGAGTCGGATATGAAGTTGGCA
EST: gi|192316102|gb|FK007163.1|FK007163
EST:     CATTTAGGCTCTATGATTTGCACAATACTGGCTTTATAGAGCGCCCTGAG                         GTCAAGCAAATGTTAATTGCACTTCTTTTTGAGTCGGATATGAAGTTGGCA
genomic: CATTTAGGCTCTATGATTTGCACAATACTGGCTTTATAGAGCGCCCTGAGgtaggatgat ... tttctgacagGTCAAGCAAATGTTAATTGCACTTCTTTTTGAGTCGGATATGAAGTTGGCA
EST: gi|17023266|gb|BM094300.1|BM094300
EST:     CATTTAGGCTCTATGATTTGCACAATACTGGCTTTATAGAGCGCCCTGAG                         GTCAAGCAAATGTTAATTGCACTTCTTTTTGAGTCGGAT
genomic: CATTTAGGCTCTATGATTTGCACAATACTGGCTTTATAGAGCGCCCTGAGgtaggatgat ... tttctgacagGTCAAGCAAATGTTAATTGCACTTCTTTTTGAGTCGGAT
EST: gi|7284862|gb|AW597349.1|AW597349
EST:     CATTTAGGCTCTATGATTTGCACAATACTGGCTTTATAGAGCGCCCTGAG                         GTCAAGCAAATGTTAATTGCACTTCTTTTTGAGTCGGATATGAAGTTGGCA
genomic: CATTTAGGCTCTATGATTTGCACAATACTGGCTTTATAGAGCGCCCTGAGgtaggatgat ... tttctgacagGTCAAGCAAATGTTAATTGCACTTCTTTTTGAGTCGGATATGAAGTTGGCA
EST: gi|151410148|gb|EV279956.1|EV279956
EST:     CATTTAGGCTCTATGATTTGCACAATACTGGCTTTATAGAGCGCCCTGAG                         GTCAAGCAAATGTTAATTGCACTTCTTTTTGAGTCGGATATGAAGTTGGCA
genomic: CATTTAGGCTCTATGATTTGCACAATACTGGCTTTATAGAGCGCCCTGAGgtaggatgat ... tttctgacagGTCAAGCAAATGTTAATTGCACTTCTTTTTGAGTCGGATATGAAGTTGGCA
EST: gi|6726203|gb|AW310557.1|AW310557
EST:     CATTTAGGCTCTATGATTTGCACAATACTGGCTTTATAGAGCGCCCTGAG                         GTCAAGCAAATGTTAATTGCACTTCTTTTTGAGTCGGATATGAAGTTGGCA
genomic: CATTTAGGCTCTATGATTTGCACAATACTGGCTTTATAGAGCGCCCTGAGgtaggatgat ... tttctgacagGTCAAGCAAATGTTAATTGCACTTCTTTTTGAGTCGGATATGAAGTTGGCA
EST: gi|17023184|gb|BM094218.1|BM094218
EST:     CATTTAGGCTCTATGATTTGCACAATACTGGCTTTATAGAGCGCCCTGAG                         GTCAAGCAAATGTTAATTGCACTTCTTTTTGAGTCGGATATGAAGTTGGGA
genomic: CATTTAGGCTCTATGATTTGCACAATACTGGCTTTATAGAGCGCCCTGAGgtaggatgat ... tttctgacagGTCAAGCAAATGTTAATTGCACTTCTTTTTGAGTCGGATATGAAGTTGGCA
EST: gi|213620263|gb|DB961408.1|DB961408
EST:     CATTTAGGCTCTATGATTTGCACAATACTGGCTTTATAGAGCGCCCTGAG                         GTCAAGCAAATGTTAATTGCACTTCTTTTTGAGTCGGA
genomic: CATTTAGGCTCTATGATTTGCACAATACTGGCTTTATAGAGCGCCCTGAGgtaggatgat ... tttctgacagGTCAAGCAAATGTTAATTGCACTTCTTTTTGAGTCGGA
EST: gi|192316103|gb|FK007164.1|FK007164
EST:     CATTTAGGCTCTATGATTTGCACAATACTGGCTTTATAGAGCGCCCTGAG                         GTCAAGCAAATGTTAATTGCACTTCTTTTTGAGTCGGATATGAAGTTGGCA
genomic: CATTTAGGCTCTATGATTTGCACAATACTGGCTTTATAGAGCGCCCTGAGgtaggatgat ... tttctgacagGTCAAGCAAATGTTAATTGCACTTCTTTTTGAGTCGGATATGAAGTTGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcctattaattttttagtgggcttattcatttttcttttggtgatttctgacagGTCAAGCAAATGTTAATTGCACTTCTTTTTGAGTCGGATATGAAGTTGGCAGATGATGTCATAGAAACAATTCTTGACAAG
    tattaat  putative branch site (score: 2)
                                             tttct  putative PPT
                       ttattcatttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtgtattttgtcatggcatctatcttcagtgtttgtgcactcctatcctattaattttttagtgggcttattcatttttcttttggtgatttctgacagGTCAAGCAAATGTTAATTGCACTTCTTTTTGAGTCGGATATGAAGTTGGCAGATGATGTCATAGAAACAATTCTTGACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - catggca
- - - - - - - - - - - - - - -gtgtttg
- - - - - - - - - - - - - - - - - - tgcactc