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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cggccagtaattgaatgagataattacctttatatatgcctttatgggatgcattatgatagtcaatgagtttaacttattacactttgacatgacatagGCGGATATAATTCTGCGAGGATACTCTGGTTGGAATTCAAGGCGTGCTGTGCAAGTTCTGGATGAAATTTTCCCTAAG

Basic information

species Glycine max
transcript GLYMA07G18210.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G18210.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0007g02260.t01 (Vitis vinifera), 3'ss of exon 1
cggccagtaattgaatgag-ataattacctttatatatgcctttatgggatgcat-tatgatagt-caatgagtttaacttattacactttgacatga--catagGCGGATATAATTCTGCGAGGATACTCTGGTTGGAATTCAAGGCGTGCTGTGCAAGTTCTGGATGAAATTTTCCCTAAG
     | || |  ||| |  ||  | |  |    | |      ||||  |||    | ||||  |    | | |   ||| |||      ||  ||    ||||||||||| || |  |||| ||||| ||||| ||||| |||||||||||| | |||||||||||  || | || || |||
-----aatactcaaatcaatattgtgaaatggtcaaacagtggtatgaaatgggcgtttgatcctatgtttaatacgactgattttggcgtggaattgttcatagGCGGATGTAGTGTTGCGTGGATATTCTGGGTGGAACTCAAGGCGTGCTCTCCAAGTTCTGGACCAAGTGTTTCCAAAG
















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|151406549|gb|EV276364.1|EV276364
EST:     ACTCTCTCCAGGGTTGGGGCGCTATTCTTGCTCATTTGTATGCTCGCAAG                         GCGGATATAATTCTGCGAGGATACTCTGGTTGGAATTCAAGGCGTGCTGTG
genomic: ACTCTCTCCAAGGTTGGGGCGCTATTCTTGCTCATTTGTATGCTCGCAAGgtatgctacc ... catgacatagGCGGATATAATTCTGCGAGGATACTCTGGTTGGAATTCAAGGCGTGCTGTG
EST: gi|298171010|gb|HO016042.1|HO016042
EST:     ACTCTCTCCAAGGTTGGGGCGCTATTCTTGCTCATTTGTATGCTCGCAAG                         GCGGATATAATTCTGCGAGGATACTCTGGTTGGAATTCAAGGCGTGCTGTG
genomic: ACTCTCTCCAAGGTTGGGGCGCTATTCTTGCTCATTTGTATGCTCGCAAGgtatgctacc ... catgacatagGCGGATATAATTCTGCGAGGATACTCTGGTTGGAATTCAAGGCGTGCTGTG
EST: gi|151398511|gb|EV268382.1|EV268382
EST:     ACTCTCTCCAAGGTTGGGGCGCTATTCTTGCTCATTTGTATGCTCGCAAG                         GCGGATATAATTCTGCGAGGATACTCTGGTTGGAATTCAAGGCGTGCTGTG
genomic: ACTCTCTCCAAGGTTGGGGCGCTATTCTTGCTCATTTGTATGCTCGCAAGgtatgctacc ... catgacatagGCGGATATAATTCTGCGAGGATACTCTGGTTGGAATTCAAGGCGTGCTGTG
EST: gi|7591301|gb|AW707037.1|AW707037
EST:     ACTCTCTCCAAGGTTGGGGCGCTATTCTTGCTCATTTGTATGCTCGCAAG                         GCGGATATAATTCTGCGAGGATACTCTGGTTGGAATTCAAGGCGTGCTGTG
genomic: ACTCTCTCCAAGGTTGGGGCGCTATTCTTGCTCATTTGTATGCTCGCAAGgtatgctacc ... catgacatagGCGGATATAATTCTGCGAGGATACTCTGGTTGGAATTCAAGGCGTGCTGTG
EST: gi|15815106|gb|BI787381.1|BI787381
EST:     ACTCTCTCCAAGGTTGGGGCGCTATTCTTGCTCATTTGTATGCTCGCAAG                         GCGGATATAATTCTGCGAGGATACTCTGGTTGGAATTCAAGGCGTGCTGTG
genomic: ACTCTCTCCAAGGTTGGGGCGCTATTCTTGCTCATTTGTATGCTCGCAAGgtatgctacc ... catgacatagGCGGATATAATTCTGCGAGGATACTCTGGTTGGAATTCAAGGCGTGCTGTG
EST: gi|298169237|gb|HO020597.1|HO020597
EST:     ACTCTCTCCAAGGTTGGGGCGCTATTCTTGCTCATTTGTATGCTCGCAAG                         GCGGATATAATTCTGCGAGGATACTCTGGTTGGAATTCAAGGCGTGCTGTG
genomic: ACTCTCTCCAAGGTTGGGGCGCTATTCTTGCTCATTTGTATGCTCGCAAGgtatgctacc ... catgacatagGCGGATATAATTCTGCGAGGATACTCTGGTTGGAATTCAAGGCGTGCTGTG
EST: gi|151404433|gb|EV274247.1|EV274247
EST:     ACTCTCTCCAAGGTTGGGGCGCTATTCTTGCTCATTTGTATGCTCGCAAG                         GCGGATATAATTCTGCGAGGATACTCTGGTTGGAATTCAAGGCGTGCTGTG
genomic: ACTCTCTCCAAGGTTGGGGCGCTATTCTTGCTCATTTGTATGCTCGCAAGgtatgctacc ... catgacatagGCGGATATAATTCTGCGAGGATACTCTGGTTGGAATTCAAGGCGTGCTGTG
EST: gi|208254011|gb|GE055989.1|GE055989
EST:     ACTCTCTCCAAGGTTGGGGCGCTATTCTTGCTCATTTGTATGCTCGCAAG                         GCGGATATAATTCTGCGAGGATACTCTGGTTGGAATTCAAGGCGTGCTGTG
genomic: ACTCTCTCCAAGGTTGGGGCGCTATTCTTGCTCATTTGTATGCTCGCAAGgtatgctacc ... catgacatagGCGGATATAATTCTGCGAGGATACTCTGGTTGGAATTCAAGGCGTGCTGTG
EST: gi|192327728|gb|FK022035.1|FK022035
EST:     ACTCTCTCCAAGGTTGGGGCGCTATTCTTGCTCATTTGTATGCTCGCAAG                         GCGGATATAATTCTGCGAGGATACTCTGGTTGGAATTCAAGGCGTGCTGTG
genomic: ACTCTCTCCAAGGTTGGGGCGCTATTCTTGCTCATTTGTATGCTCGCAAGgtatgctacc ... catgacatagGCGGATATAATTCTGCGAGGATACTCTGGTTGGAATTCAAGGCGTGCTGTG
EST: gi|151411903|gb|EV281714.1|EV281714
EST:     ACTCTCTCCAAGGTTGGGGCGCTATTCTTGCTCATTTGTATGCTCGCAAG                         GCGGATATAATTCTGCGAGGATACTCTGGTTGGAATTCAAGGCGTGCTGTG
genomic: ACTCTCTCCAAGGTTGGGGCGCTATTCTTGCTCATTTGTATGCTCGCAAGgtatgctacc ... catgacatagGCGGATATAATTCTGCGAGGATACTCTGGTTGGAATTCAAGGCGTGCTGTG
EST: gi|15813377|gb|BI785652.1|BI785652
EST:     ACTCTCTCCAAGGTTGGGGCGCTATTCTTGCTCATTTGTATGCTCGCAAG                         GCGGATATAATTCTGCGAGGATACTCTGGTTGGAATTCAAGGCGTGCTGTG
genomic: ACTCTCTCCAAGGTTGGGGCGCTATTCTTGCTCATTTGTATGCTCGCAAGgtatgctacc ... catgacatagGCGGATATAATTCTGCGAGGATACTCTGGTTGGAATTCAAGGCGTGCTGTG
EST: gi|151394124|gb|EV263995.1|EV263995
EST:     ACTCTCTCCAAGGTTGGGGCGCTATTCTTGCTCATTTGTATGCTCGCAAG                         GCGGATATAATTCTGCGAGGATACTCTGGTTGGAATTCAAGGCGTGCTGTG
genomic: ACTCTCTCCAAGGTTGGGGCGCTATTCTTGCTCATTTGTATGCTCGCAAGgtatgctacc ... catgacatagGCGGATATAATTCTGCGAGGATACTCTGGTTGGAATTCAAGGCGTGCTGTG
EST: gi|298189599|gb|HO038002.1|HO038002
EST:     ACTCTCTCCAAGGTTGGGGCGCTATTCTTGCTCATTTGTATGCTCGCAAG                         GCGGATATAATTCTGCGAGGATACTCTGGTTGGAATTCAAGGCGTGCTGTG
genomic: ACTCTCTCCAAGGTTGGGGCGCTATTCTTGCTCATTTGTATGCTCGCAAGgtatgctacc ... catgacatagGCGGATATAATTCTGCGAGGATACTCTGGTTGGAATTCAAGGCGTGCTGTG
EST: gi|13478430|gb|BG507910.1|BG507910
EST:     ACTCTCTCCAAGGTTGGGGCGCTATTCTTGCTCATTTGTATGCTCGCAAG                         GCGGATATAATTCTGCGAGGATACTCTGGTTGGAATTCAAGGCGTGCTGTG
genomic: ACTCTCTCCAAGGTTGGGGCGCTATTCTTGCTCATTTGTATGCTCGCAAGgtatgctacc ... catgacatagGCGGATATAATTCTGCGAGGATACTCTGGTTGGAATTCAAGGCGTGCTGTG
EST: gi|19053011|gb|BM731678.1|BM731678
EST:     ACTCTCTCCAAGGTTGGGGCGCTATTCTTGCTCATTTGTATGCTCGCAAG                         GCGGATATAATTCTGCGAGGATACTCTGGTTGGAATTCAAGGCGTGCTGTG
genomic: ACTCTCTCCAAGGTTGGGGCGCTATTCTTGCTCATTTGTATGCTCGCAAGgtatgctacc ... catgacatagGCGGATATAATTCTGCGAGGATACTCTGGTTGGAATTCAAGGCGTGCTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggatgcattatgatagtcaatgagtttaacttattacactttgacatgacatagGCGGATATAATTCTGCGAGGATACTCTGGTTGGAATTCAAGGCGTGCTGTGCAAGTTCTGGATGAAATTTTCCCTAAG
                       agtttaacttatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cggccagtaattgaatgagataattacctttatatatgcctttatgggatgcattatgatagtcaatgagtttaacttattacactttgacatgacatagGCGGATATAATTCTGCGAGGATACTCTGGTTGGAATTCAAGGCGTGCTGTGCAAGTTCTGGATGAAATTTTCCCTAAG

- - - - - - gaatgag
- - - - - - - - - - - - - - - - - tatgcct
- - - - - - - - - - - - - - - - - - - - - - - ggatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caatgag