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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgatttttgaaatgaaccattagaatcacttatttgctttgaaatgttgattggtggcattgtttttgataagcacattgatatttggtgacttgcagTTTTCAGGACTGGTGCTGTGAATGCTGCATCTGGATCTGCTTATGCTGAGGTTGGAAATACCAAGGTCATTGTATCAGT

Basic information

species Glycine max
transcript GLYMA12G08170.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G08170.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G27490.1 (Arabidopsis thaliana), 3'ss of exon 2
----------------------------tctgatttttgaaatgaaccattagaatcacttatttgctttgaaatgt------tgattggtggcattgtttttgataagcacattgata-tttggtga---------cttgcagTTTTCAGGACTGGTGCTGTGAATGCTGCATCTGGATCTGCTTATGCTGAGGTTGGAAATACCAAGGTCATTGTATCAGT
                              | ||  ||    |    ||||   |        |||  || | |||       | ||| |||  | |    | |||  | |  ||| |  ||| ||||         ||| ||||  |    ||||||||||||| | |||| ||||| ||||||||||||||| |||| || || || || ||||| |||||
gtaaaaacacctttgattcctctaaattcttaatcgttagggttcttcattgtgaaattacggttggattcatatgactccagttatttgtgagactaaactagatttgaattttgtttcttttgtgaaaaatgcttctttcagTACTTCAAACTGGTGCTGTGAGTTCTGCTTCTGGTTCTGCTTATGCTGAGTTTGGGAACACTAAAGTTATTGTTTCAGT

upper sequence: GLYMA12G08170.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0004g02660.t01 (Vitis vinifera), 3'ss of exon 1
tctgatttttgaaatgaaccattagaatcacttat--ttgctttgaaatgttgattggtggcattgtttttgataagcacattgatatttggtgacttgcagTTTTCAGGACTGGTGCTGTGAATGCTGCATCTGGATCTGCTTATGCTGAGGTTGGAAATACCAAGGTCATTGTATCAGT
| ||  | |    ||    | |||  || | || |  |||| ||  |  ||  | |  ||   |||  ||  | || |  ||   |  |||||| ||||||||| | | |||||||||||||||||||||||| |||||||||||||| ||| |||||||||||||||||||||| || ||
tgtgcatatgtgcattttgctttactatgatttgtaattgcattatagagtgcaattatgat-ttgcattgaagaaacg-ataagttgttggtggcttgcagTTCTGAAGACTGGTGCTGTGAATGCTGCATCAGGATCTGCTTATGCAGAGTTTGGAAATACCAAGGTCATTGTGTCTGT
















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|192307494|gb|FK002026.1|FK002026
EST:     TGGCTCGACCTGATGGCCGCAGTTTCCACCAGTGCGGACCCCCAT                         TTTTCAGGACTGGTGCTGTGAATGCTGCATCTGGATCTGCTTATGCTGAGG
genomic: TGGCTCGACCTGATGGCCGCAGTTTCCACCAGTGCAGACCCGCATgtaagccccc ... tgacttgcagTTTTCAGGACTGGTGCTGTGAATGCTGCATCTGGATCTGCTTATGCTGAGG
EST: gi|298170559|gb|HO019183.1|HO019183
EST:     GGATTTGGCTCGACCTGATGGCCGCAGTTTCCACCAGTGCAGACCCGCAT                         TTTTCAGGACTGGTGCTGTGAATGCTGCATCTGGATCTGCTTATGCTGAGG
genomic: GGATTTGGCTCGACCTGATGGCCGCAGTTTCCACCAGTGCAGACCCGCATgtaagccccc ... tgacttgcagTTTTCAGGACTGGTGCTGTGAATGCTGCATCTGGATCTGCTTATGCTGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttgattggtggcattgtttttgataagcacattgatatttggtgacttgcagTTTTCAGGACTGGTGCTGTGAATGCTGCATCTGGATCTGCTTATGCTGAGGTTGGAAATACCAAGGTCATTGTATCAGT
                                cattgat  putative branch site (score: 4)
               attgtttttgataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgatttttgaaatgaaccattagaatcacttatttgctttgaaatgttgattggtggcattgtttttgataagcacattgatatttggtgacttgcagTTTTCAGGACTGGTGCTGTGAATGCTGCATCTGGATCTGCTTATGCTGAGGTTGGAAATACCAAGGTCATTGTATCAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - aatgaac
- - - - - - - - - - - - - - - - - - tgctttg
- - - - - - - - - - - - - - - - - - - - - - - - - - ttggtgg