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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgatggcttagtacaatacatctggcatttctatgattaaattgcactaaaataacttctagttttgaatcttttaactgtttttttatcaagtattgtgcagtatataatatggcaatgcagtgacgatatggatagttacttttgtgccctttttattaatgcagATTTGTGTCTGGAATACTGATGGATGGGAAAAGCAGAAGTCTAGATTCTTGCAGCTTCCTTCTGGGAGAACACCACCGGCACAGTCAGATACCCGTGTAC

Basic information

species Glycine max
transcript GLYMA07G03180.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G03180.1 (Glycine max), 3'ss of exon 21
lower sequence: Vv09s0002g08370.t01 (Vitis vinifera), 3'ss of exon 22
gtaatgatggcttagtacaatacatctggcatttctatgattaaattgcactaaaataacttctagttttgaatcttttaactgttttt-ttatcaagtattgtgcagtatataatatggcaatgcagtgacgatatggatagttacttttgtgccctttttattaatgcagATTTGTGTCTGGAATACTGATGGATGGGAAAAGCAGAAGTCTAGATTCTTGCAGCTTCCTTCTGGGAGAACACCACCGGCACAGTCAGATACCCGTGTAC
                                                                    ||||  || |||| ||   |  || ||   | | || |  |||          |   |  ||| ||||| |    |||   |  | |   || |||   | ||| ||||||| ||||   ||||||||||||||||||||||||| |||||||| ||| ||||  |||| || ||| || | | ||| |||||||||||||| |
--------------------------------------------------------------------ttgacactattaattgaagtcgttctctgttttggttccttattgtgccaaatagaactttgatgatattgtc--ttatcatgttacatcttctat--gtccagCTTTGTGTGTGGAGCTCTGATGGATGGGAAAAGCAGAAGTCGAGATTCTTACAGGTTCCAGCTGGAAGGACATCAACAGGACAATCAGATACCCGTGTTC
















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|26045637|gb|CA783164.1|CA783164
EST:     CTTTCTCTCATGTATTGAATGTATTAGTTTCATCTGGAGCAGATGCTCAG                         ATTTGTGTCTGGAATACTGATGGATGGGAAAAGCAGAAGTCTAGATTCTTG
genomic: CTTTCTCTCATGTATTGAATGTATTAGTTTCATCTGGAGCAGATGCTCAGgtaatgatgg ... attaatgcagATTTGTGTCTGGAATACTGATGGATGGGAAAAGCAGAAGTCTAGATTCTTG
EST: gi|15285824|gb|BI469715.1|BI469715
EST:     CTTTCTCTCATGTATTGAATGTATTAGTTTCATCTGGAGCAGATGCTCAG                         ATTTGTGTCTGGAATACTGATGGATGGGAAAAGCAGAAGTCTAGATTCTTG
genomic: CTTTCTCTCATGTATTGAATGTATTAGTTTCATCTGGAGCAGATGCTCAGgtaatgatgg ... attaatgcagATTTGTGTCTGGAATACTGATGGATGGGAAAAGCAGAAGTCTAGATTCTTG
EST: gi|4296432|gb|AI442474.1|AI442474
EST:     CTTTCTCTCATGTATTGAATGTATTAGTTTCATCTGGAGCAGATGCTCAG                         ATTTGTGTCTGGAATACTGATGGATGGGAAAAGCAGAAGTCTAGATTCTTG
genomic: CTTTCTCTCATGTATTGAATGTATTAGTTTCATCTGGAGCAGATGCTCAGgtaatgatgg ... attaatgcagATTTGTGTCTGGAATACTGATGGATGGGAAAAGCAGAAGTCTAGATTCTTG
EST: gi|6482439|gb|AW201698.1|AW201698
EST:     CTTTCTCTCATGTATTGAATGTATTAGTTTCATCTGGAGCAGATGCTCAG                         ATTTGTGTCTGGAATACTGATGGATGGGAAAAGCAGAAGTCTAGATTCTTG
genomic: CTTTCTCTCATGTATTGAATGTATTAGTTTCATCTGGAGCAGATGCTCAGgtaatgatgg ... attaatgcagATTTGTGTCTGGAATACTGATGGATGGGAAAAGCAGAAGTCTAGATTCTTG
EST: gi|16346696|gb|BI972291.1|BI972291
EST:     CTTTCTCTCATGTATTGAATGTATTAGTTTCATCTGGAGCAGATGCTCAG                         ATTTGTGTCTGGAATACTGATGGATGGGAAAAGCAGAAGTCTAGATTCTTG
genomic: CTTTCTCTCATGTATTGAATGTATTAGTTTCATCTGGAGCAGATGCTCAGgtaatgatgg ... attaatgcagATTTGTGTCTGGAATACTGATGGATGGGAAAAGCAGAAGTCTAGATTCTTG
EST: gi|207841291|gb|GD810700.1|GD810700
EST:     CTTTCTCTCATGTATTGAATGTATTAGTTTCATCTGGAGCAGATGCTCAG                         ATTTTGTGTCT
genomic: CTTTCTCTCATGTATTGAATGTATTAGTTTCATCTGGAGCAGATGCTCAGgtaatgatgg ... attaatgcagATTT-GTGTCT
EST: gi|4260444|gb|AI416940.1|AI416940
EST:     CTTTCTCTCATGTATTGAATGTATTAGTTTCATCTGGAGCAGATGCTCAG                         ATTTGTGTCTGGAATACTGAT
genomic: CTTTCTCTCATGTATTGAATGTATTAGTTTCATCTGGAGCAGATGCTCAGgtaatgatgg ... attaatgcagATTTGTGTCTGGAATACTGAT
EST: gi|20449020|gb|BQ253144.1|BQ253144
EST:     CTTTCTCTCATGTATTGAATGTATTAGTTTCATCTGGAGCAGATGCTCAG                         ATTTGTGTCTGGAATACTGATGGATGGGAAAAGCAGAAGTCTAGATTCTTG
genomic: CTTTCTCTCATGTATTGAATGTATTAGTTTCATCTGGAGCAGATGCTCAGgtaatgatgg ... attaatgcagATTTGTGTCTGGAATACTGATGGATGGGAAAAGCAGAAGTCTAGATTCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggcaatgcagtgacgatatggatagttacttttgtgccctttttattaatgcagATTTGTGTCTGGAATACTGATGGATGGGAAAAGCAGAAGTCTAGATTCTTGCAGCTTCCTTCTGGGAGAACACCACCGGCACAGTCAGATACCCGTGTAC
                                            tattaat  putative branch site (score: 2)
                                     ccctttttatt  CT-rich tract
                                        tttttattaatgca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgatggcttagtacaatacatctggcatttctatgattaaattgcactaaaataacttctagttttgaatcttttaactgtttttttatcaagtattgtgcagtatataatatggcaatgcagtgacgatatggatagttacttttgtgccctttttattaatgcagATTTGTGTCTGGAATACTGATGGATGGGAAAAGCAGAAGTCTAGATTCTTGCAGCTTCCTTCTGGGAGAACACCACCGGCACAGTCAGATACCCGTGTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA