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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttctgtatgatttcaacttatatttttgtgagagggagactactacccatcttacaatatccaggatcatttactaaccttcaattttgtatcatcagGTCGAAGGTGAAGCTAATATATCATACATATGTTCACGATTCTATCGAGCACCAGAACTTATATTTGGGGCCACAGAGTATACCAGTTCGATTGATATTT

Basic information

species Glycine max
transcript GLYMA06G06850.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G06850.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os05g11730.1 (Oryza sativa), 3'ss of exon 6
---tgttctgtatgatttcaacttatatttttgtgagagggagactactacccatcttacaatatccaggatcatttactaaccttcaattt--tgtatcatcagGTCGAAGGTGAAGCTAATATATCATACATATGTTCACGATTCTATCGAGCACCAGAACTTATATTTGGGGCCACAGAGTATACCAGTTCGATTGATATTT
        | |   |  | |    | || ||||  | |     |||  |    || ||   || |    |  |   || || || | |||||  | |  |||||||||  ||||||| | ||||||||||| ||||| ||||| | ||| |||||||| || || |||||||| || || || ||||| |  || || ||||| |
ttacacctttttccaccttattccagatgtttgctacaattgtacttttgataattttg--atcttactgtcc---taatatccattaatttactattccatcagGTCCCAGGTGAACCCAATATATCATATATATGCTCACGCTACTACCGAGCACCGGAGCTCATATTTGGTGCAACTGAATATACTACATCAATAGATATAT

upper sequence: GLYMA06G06850.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G18710.1 (Arabidopsis thaliana), 3'ss of exon 5
tgttctgtatgatttca--acttatatttttgtgagagggagactactacccatcttacaatatccaggatcatttacta---accttcaattttgtatcatcagGTCGAAGGTGAAGCTAATATATCATACATATGTTCACGATTCTATCGAGCACCAGAACTTATATTTGGGGCCACAGAGTATACCAGTTCGATTGATATTT
      ||| || ||    || ||||   |  |  ||     |    |     | ||     |||  |  |||||||||    |  || | |||||   | ||||||  |||||||||| || || || ||||| || ||||||||||| || ||||| || || |||||||| ||||| ||||| || | ||| |||||||| |
------gtaagactttgtgacatataaactcattcgacttgtagcggttgttgttttctgtgatcttg--tcatttactgttgaaatttacttttg---cttcagGTTAAAGGTGAAGCCAACATTTCTTACATCTGCTCACGATTCTACCGTGCACCCGAGCTCATATTTGGTGCCACTGAGTACACAACTTCTATTGATATCT

upper sequence: GLYMA06G06850.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv10s0003g01480.t01 (Vitis vinifera), 3'ss of exon 6
tgttctgtatgatttcaacttatatttttgtgagagggagactactacccatcttacaatatccaggat------catttactaaccttcaattttgtat-catcagGTCGAAGGTGAAGCTAATATATCATACATATGTTCACGATTCTATCGAGCACCAGAACTTATATTTGGGGCCACAGAGTATACCAGTTCGATTGATATTT
     | | | ||   |     || |   ||  || | |      | |   | ||    | || | |||      ||| |  | ||| | |||    | | ||||||||  |||||||||| || ||||||||||||||||| || ||||| |||||||| ||||| ||||||||||||||||||||||| |  || |||||||| |
-----tctttcatggtagtcagtactca-gtaggaagaaagtctttgcttgtttt-ttctttctatgatatctttcatgttttcaccatgaatccaattttcatcagGTTAAAGGTGAAGCAAACATATCATACATATGTTCTCGTTTCTACCGAGCACCTGAACTCATATTTGGGGCCACAGAGTATACAACCTCAATTGATATAT

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|15815079|gb|BI787354.1|BI787354
EST:     CTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAAGTTCTA                         GTCGAAGGTGAAGCTAATATATCATACATATGTTCACGATTCTATCGAGCA
genomic: CTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAAGTTCTAgtatgttgac ... gtatcatcagGTCGAAGGTGAAGCTAATATATCATACATATGTTCACGATTCTATCGAGCA
EST: gi|12773946|gb|BG238873.1|BG238873
EST:     CTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAAGTTCTA                         GTCGAAGGTGAAGCTAATATATCATACATATGTTCACGATTCTATCGAGCA
genomic: CTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAAGTTCTAgtatgttgac ... gtatcatcagGTCGAAGGTGAAGCTAATATATCATACATATGTTCACGATTCTATCGAGCA
EST: gi|5760433|gb|AI965724.1|AI965724
EST:     CTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAAGTTCTA                         GTCGAAGGTGAAGCTAATATATCATACATATGTTCACGATTCTATCGAGCA
genomic: CTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAAGTTCTAgtatgttgac ... gtatcatcagGTCGAAGGTGAAGCTAATATATCATACATATGTTCACGATTCTATCGAGCA
EST: gi|207772416|gb|GD742672.1|GD742672
EST:     TGCAAAAGTTCTA                         GTTCGAAGGTTGTAAGCTAATATATCATACATATGTTCACGATTCTATCGA
genomic: TGCAAAAGTTCTAgtatgttgac ... gtatcatcagG-TCGAAGG-TG-AAGCTAATATATCATACATATGTTCACGATTCTATCGA
EST: gi|208274892|gb|GE069728.1|GE069728
EST:     CTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAAGTTCTG                         GTCGAAGGTGAAGCTAATATATCATACATATGTTCACGATTCTATCGAGCA
genomic: CTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAAGTTCTAgtatgttgac ... gtatcatcagGTCGAAGGTGAAGCTAATATATCATACATATGTTCACGATTCTATCGAGCA
EST: gi|14990804|gb|BI316477.1|BI316477
EST:     CTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAAGTTCTA                         GTCGAAGGTGAAGCTAATATATCATACATATGTTCACGATTCTATCGAGCA
genomic: CTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAAGTTCTAgtatgttgac ... gtatcatcagGTCGAAGGTGAAGCTAATATATCATACATATGTTCACGATTCTATCGAGCA
EST: gi|6455159|gb|AW185842.1|AW185842
EST:     CTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAAGTTCTA                         GTCGAAGGTGAAGCTAATATATCATACATATGTTCACGATTCTATCGAGCA
genomic: CTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAAGTTCTAgtatgttgac ... gtatcatcagGTCGAAGGTGAAGCTAATATATCATACATATGTTCACGATTCTATCGAGCA
EST: gi|105634210|gb|DW247405.1|DW247405
EST:     CTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAAGTTCTA                         GTCGAAGGTGAAGCTAATATATCATACATATGTTCACGATTCTATCGAGCA
genomic: CTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAAGTTCTAgtatgttgac ... gtatcatcagGTCGAAGGTGAAGCTAATATATCATACATATGTTCACGATTCTATCGAGCA
EST: gi|207797921|gb|GD768499.1|GD768499
EST:     CTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAAGTTCTA                         GTCGAAGGTGAAGCTAATATATCATACATATGTTCACGATTCTATCGAGCA
genomic: CTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAAGTTCTAgtatgttgac ... gtatcatcagGTCGAAGGTGAAGCTAATATATCATACATATGTTCACGATTCTATCGAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacccatcttacaatatccaggatcatttactaaccttcaattttgtatcatcagGTCGAAGGTGAAGCTAATATATCATACATATGTTCACGATTCTATCGAGCACCAGAACTTATATTTGGGGCCACAGAGTATACCAGTTCGATTGATATTT
                            tactaac  putative branch site (score: 0)
                                       aattttgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttctgtatgatttcaacttatatttttgtgagagggagactactacccatcttacaatatccaggatcatttactaaccttcaattttgtatcatcagGTCGAAGGTGAAGCTAATATATCATACATATGTTCACGATTCTATCGAGCACCAGAACTTATATTTGGGGCCACAGAGTATACCAGTTCGATTGATATTT

- - -tgtatga
- - - - - - - - - - - - -ttttgtg
- - - - - - - - - - - - - - - - -gagggag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - accttca