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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttccgttttcgcttagttgttaacactcacgtgctgtttcgcgtgctctgttatgacttgtgacctaaattgaatgttcctttagcagGTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT

Basic information

species Glycine max
transcript GLYMA08G07230.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G07230.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv03s0017g00540.t01 (Vitis vinifera), 3'ss of exon 2
gttccgttttcgcttagttgttaacactcacgt-gctgtttcgcgtgctctgttatgacttgtgacctaaattgaat----gttcc--------tttagcagGTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT
 || |   |  ||  |||| | || ||| | ||   ||||     || | |    |   | || || |||  ||| |     || |        | | |||| | |||||||||||||||| |||||| ||||||||||| ||
-tttctaatctgcaaagttat-aatacttatgttattgttgtcattgttataaggttcttggtcacataatctgattctaaatttcgatcaacatgttgcagATGTTGGAGTATTGGGCTGGCAGGGGAATGCTGCAGATTTT
















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|6482639|gb|AW201884.1|AW201884
EST:     TCGTGGTCCTCGCCGAGACCGAATGGAGTTTCATCATAAAGTTCTCGAAG                         GTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT
genomic: TCGTGGTCCTCGCCGAGACCGAATGGAGTTTCATCATAAAGTTCTCGAAGgttccgtttt ... cctttagcagGTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT
EST: gi|9259020|gb|BE347167.1|BE347167
EST:     TCGTGGTCCTCGCCGAGACCGAATGGAGTTTCATCATAAAGTTCTCGAAG                         GTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT
genomic: TCGTGGTCCTCGCCGAGACCGAATGGAGTTTCATCATAAAGTTCTCGAAGgttccgtttt ... cctttagcagGTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT
EST: gi|298192683|gb|HO033117.1|HO033117
EST:     TCGTGGTCCTCGCCGAGACCGAATGGAGTTTCATCATAAAGTTCTCGAAG                         GTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT
genomic: TCGTGGTCCTCGCCGAGACCGAATGGAGTTTCATCATAAAGTTCTCGAAGgttccgtttt ... cctttagcagGTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT
EST: gi|15664198|gb|BI701569.1|BI701569
EST:     TCGTGGTCCTCGCCGAGACCGAATGGAGTTTCATCATAAAGTTCTCGAAG                         GTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT
genomic: TCGTGGTCCTCGCCGAGACCGAATGGAGTTTCATCATAAAGTTCTCGAAGgttccgtttt ... cctttagcagGTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT
EST: gi|27425766|gb|CA937286.1|CA937286
EST:     TCGTGGTCCTCGCCGAGACCGAATGGAGTTTCATCATAAAGTTCTCGAAG                         GTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT
genomic: TCGTGGTCCTCGCCGAGACCGAATGGAGTTTCATCATAAAGTTCTCGAAGgttccgtttt ... cctttagcagGTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT
EST: gi|207846957|gb|GD817706.1|GD817706
EST:     TCGTGGTCCTCGCCGAGACCGAATGGAGTTTCATCATAAAGTTCTCGAAG                         GTTTTGGAGTATTGGGCTGCCAAGGGGTAATGCTGCA
genomic: TCGTGGTCCTCGCCGAGACCGAATGGAGTTTCATCATAAAGTTCTCGAAGgttccgtttt ... cctttagcagGTTTTGGAGTATTGGGCTGCCA-GGGGTA-TGCTGCA
EST: gi|5677513|gb|AI938643.1|AI938643
EST:     TCGTGGTCCTCGCCGAGACCGAATGGAGTTTCATCATAAAGTTCTCGAAG                         GTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT
genomic: TCGTGGTCCTCGCCGAGACCGAATGGAGTTTCATCATAAAGTTCTCGAAGgttccgtttt ... cctttagcagGTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT
EST: gi|9564863|gb|BE474372.1|BE474372
EST:     TCGTGGTCCTCGCCGAGACCGAATGGAGTTTCATCATAAAGTTCTCGAAG                         GTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT
genomic: TCGTGGTCCTCGCCGAGACCGAATGGAGTTTCATCATAAAGTTCTCGAAGgttccgtttt ... cctttagcagGTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT
EST: gi|192326392|gb|FK015909.1|FK015909
EST:     TCGTGGTCCTCGCCGAGACCGAATGGAGTTTCATCATAAAGTTCTCGAAG                         GTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT
genomic: TCGTGGTCCTCGCCGAGACCGAATGGAGTTTCATCATAAAGTTCTCGAAGgttccgtttt ... cctttagcagGTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtttcgcgtgctctgttatgacttgtgacctaaattgaatgttcctttagcagGTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT
                             acctaaa  putative branch site (score: 3)
                                         tgttccttt  putative PPT
                                taaattgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttccgttttcgcttagttgttaacactcacgtgctgtttcgcgtgctctgttatgacttgtgacctaaattgaatgttcctttagcagGTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT