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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgccactctccacaaatttccatcagtaattagtcttataaatcaaatttggttcattgttttgcctcacctttttggacaaatcatataaggtttattttcaatcgtttttaatcttaatctatttcatttctactagGGAGGAGGATGGTGCAACAATGTCACTACTTGCCTTGCTCGCAAGACCAATCGTTTAGGTTCATCTAAGCAAATGGCCAAGCTAATTGCCTTTTCAGGAA

Basic information

species Glycine max
transcript GLYMA09G35050.4
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G35050.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv02s0087g00400.t01 (Vitis vinifera), 3'ss of exon 3
gtatgccactctccacaaatttccatcagtaattagt--cttataaatcaaatttggttcattgttttgcctcacctttttggacaaatcatataaggtttattttcaatcgtttttaatcttaatctatttcatttctactagGGAGGAGGATGGTGCAACAATGTCACTACTTGCCTTGCTCGCAAGACCAATCGTTTAGGTTCATCTAAGCAAATGGCCAAGCTAATTGCCTTTTCAGGAA
                             | ||| ||  || | |||| | |   ||   || |       |       |    ||| |   |||   | || | ||| || ||| |    ||           ||  ||  |||||||||||||||||||||||| | | |||||||||||||| | |  ||| |||||||||||||| ||||||||||  |||| |||||| || || || |
-----------------------------tgattggtttctcagaaattaga---ggaaaatggaagaaaatttttgagtcatgcaactggcatagcatataatctca-tcatttatggcttt-----------ttgatatcagGGAGGAGGATGGTGCAACAATGCCTCAACTTGCCTTGCTCGTAGGGACAACCGTTTAGGTTCATCGAAGCAAATGGTGAAGCAAATTGCTTTCTCTGGGA
















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|213597073|gb|DB968168.1|DB968168
EST:     TTGATAGGGGATTTGGATCAGGGATTAACAATTGGTTGGTTGCATTTGAG                         GGAGGAGGATGGTGCAACAATGTCACTACTTGCCTTGCTCGCAAGACCAAT
genomic: TTGATAGGGGATTTGGATCAGGGATTAACAATTGGTTGGTTGCATTTGAGgtatgccact ... tttctactagGGAGGAGGATGGTGCAACAATGTCACTACTTGCCTTGCTCGCAAGACCAAT
EST: gi|18733683|gb|BM527753.1|BM527753
EST:     TTGATAGGGGATTTGGATCAGGGATTAACAATTGGTTGGTTGCATTTGAG                         GGAGGAGGATGGTGCAACAATGTCACTACTTGCCTTGCTCGCAAGACCAAT
genomic: TTGATAGGGGATTTGGATCAGGGATTAACAATTGGTTGGTTGCATTTGAGgtatgccact ... tttctactagGGAGGAGGATGGTGCAACAATGTCACTACTTGCCTTGCTCGCAAGACCAAT
EST: gi|21888360|gb|BQ741573.1|BQ741573
EST:     TTGATAGGGGATTTGGATCAGGGATTAACAATTGGTTGGTTGCATTTGAG                         GGAGGAGGATGGTGCAACAATGTCACTACTTGCCTTGCTCGCAAGACCAAT
genomic: TTGATAGGGGATTTGGATCAGGGATTAACAATTGGTTGGTTGCATTTGAGgtatgccact ... tttctactagGGAGGAGGATGGTGCAACAATGTCACTACTTGCCTTGCTCGCAAGACCAAT
EST: gi|9986444|gb|BE660552.1|BE660552
EST:     TTGATAGGGGATTTGGATCAGGGATTAACAATTGGTTGGTTGCATTTGAG                         GGAGGAGGATGGTGCAACAATGTCACTACTTGCCTTGCTCGCAAGACCAAT
genomic: TTGATAGGGGATTTGGATCAGGGATTAACAATTGGTTGGTTGCATTTGAGgtatgccact ... tttctactagGGAGGAGGATGGTGCAACAATGTCACTACTTGCCTTGCTCGCAAGACCAAT
EST: gi|9898765|gb|BE607733.1|BE607733
EST:     CAGGGATTAACAATTGGTTGGTTGCATTTGAG                         GGAGGAGGATGGTGCAACAATGTCACTACTTGCCTTGCTCGCAAGACCAAT
genomic: CAGGGATTAACAATTGGTTGGTTGCATTTGAGgtatgccact ... tttctactagGGAGGAGGATGGTGCAACAATGTCACTACTTGCCTTGCTCGCAAGACCAAT
EST: gi|213614158|gb|DB964902.1|DB964902
EST:     TTGATAGGGGATTTGGATCAGGGATTAACAATTGGTTGGTTGCATTTGAG                         GGAGGAGGATGGTGCAACAATGTCACTACTTGCCTTGCTCGCAAGACCAAT
genomic: TTGATAGGGGATTTGGATCAGGGATTAACAATTGGTTGGTTGCATTTGAGgtatgccact ... tttctactagGGAGGAGGATGGTGCAACAATGTCACTACTTGCCTTGCTCGCAAGACCAAT
EST: gi|9820186|gb|BE555696.1|BE555696
EST:     AACAATTGGTTGGTTGCATTTGAG                         GGAGGAGGATGGTGCAACAATGTCACTACTTGCCTTGCTCGCAAGACCAAT
genomic: AACAATTGGTTGGTTGCATTTGAGgtatgccact ... tttctactagGGAGGAGGATGGTGCAACAATGTCACTACTTGCCTTGCTCGCAAGACCAAT
EST: gi|15287443|gb|BI471334.1|BI471334
EST:     TTGATAGGGGATTTGGATCAGGGATTAACAATTGGTTGGTTGCATTTGAG                         GGAGGAGGATGGTGCAACAATGTCACTACTTGCCTTGCTCGCAAGACCAAT
genomic: TTGATAGGGGATTTGGATCAGGGATTAACAATTGGTTGGTTGCATTTGAGgtatgccact ... tttctactagGGAGGAGGATGGTGCAACAATGTCACTACTTGCCTTGCTCGCAAGACCAAT
EST: gi|15664114|gb|BI701485.1|BI701485
EST:     TTGATAGGGGATTTGGATCAGGGATTAACAATTGGTTGGTTGCATTTGAG                         GGAGGAGGATGGTGCAACAATGTCACTACTTGCCTTGCTCGCAAGACCAAT
genomic: TTGATAGGGGATTTGGATCAGGGATTAACAATTGGTTGGTTGCATTTGAGgtatgccact ... tttctactagGGAGGAGGATGGTGCAACAATGTCACTACTTGCCTTGCTCGCAAGACCAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catataaggtttattttcaatcgtttttaatcttaatctatttcatttctactagGGAGGAGGATGGTGCAACAATGTCACTACTTGCCTTGCTCGCAAGACCAATCGTTTAGGTTCATCTAAGCAAATGGCCAAGCTAATTGCCTTTTCAGGAA
                              tcttaat  putative branch site (score: 3)
                                    tctatttcatttct  CT-rich tract
         tttattttcaatcgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgccactctccacaaatttccatcagtaattagtcttataaatcaaatttggttcattgttttgcctcacctttttggacaaatcatataaggtttattttcaatcgtttttaatcttaatctatttcatttctactagGGAGGAGGATGGTGCAACAATGTCACTACTTGCCTTGCTCGCAAGACCAATCGTTTAGGTTCATCTAAGCAAATGGCCAAGCTAATTGCCTTTTCAGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
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