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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttaggagaaaactgttatttgtttaggaagttttacttaaaataaattaaaacgaaagggtgattgaatgcaaagatgttgttttgatgctttggcagGTTCTTGTTCTTGATGAATATGACACCAGTATGCCCCTTTGTCAAAGCTTCTCGCCCTGATGATAACAATGCCTCTAAGAAATCTGGCGAAAACTCTATG

Basic information

species Glycine max
transcript GLYMA06G47010.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G47010.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv13s0047g00170.t01 (Vitis vinifera), 3'ss of exon 1
tcttaggagaaaactgttatttgtttaggaa-gttttacttaaaataaattaaaacgaaagggtgattgaatgcaaagatgttgttttgatgctttggcagGTT--CTTGTTCTTGATGAATATGACACCAGTATGCCCCTTTGTCAAAGCTTCTCGCCCTGATGATAACAATGCCTCTAAGAAATCTGGCGAAAACTC-TATG--------
         |   |     ||| ||| || | || ||| |     | | ||  || |||    || |    | |||   | |    |||    | |||    |   |   || ||||| || |||||||| || ||||| |||||||||||| |||| |||||||||  ||   | || | |||| ||   |||  | |  ||         
--------catttcctccctttttttgggtatgtattattcccctttatttttaatgaactc-tgttcccctccaactctttaaagttgtaattgtggtctttgaacagATTGTTGATCAAGATGACACCTGTCTGCCCTTTTGTCAAAGCTGCTCGTCCTGATGATGCCA---CTTCAAGGAAACCTAATGAATGCCCACATAAGCACCAG
















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|208130091|gb|GD927696.1|GD927696
EST:     CAACTTCCAGTTTCTTCTCTCTGTCTCGTTTACCTCGATCCT                         GTTCTTGTTCTTGATGAATATGACACCAGTATGCCCCTTTGTCAAAGCTTC
genomic: CAACTTCCAGTTTCTTCTCTCTGTCTCGTTTACCTCGATCCTgtaatatttt ... gctttggcagGTTCTTGTTCTTGATGAATATGACACCAGTATGCCCCTTTGTCAAAGCTTC
EST: gi|209703747|gb|BW656880.1|BW656880
EST:     GTTCTTTGCAACTTCCAGTTTCTTCTCTCTGTCTCGTTTACCTCGATCCT                         GTTCTTGTTCTTGATGAATATGACACCAGTATGCCCCTTTGTCAAAGCTTC
genomic: GTTCTTTGCAACTTCCAGTTTCTTCTCTCTGTCTCGTTTACCTCGATCCTgtaatatttt ... gctttggcagGTTCTTGTTCTTGATGAATATGACACCAGTATGCCCCTTTGTCAAAGCTTC
EST: gi|298170576|gb|HO019200.1|HO019200
EST:     GTTCTTTGCAACTTCCGGTTTCTTCTCTCTGTCTCGTTTACCTCGATCCT                         GTTCTTGTTCTTGATGAATATGACACCAGTATGCCCCTTTGTCAAAGCTTC
genomic: GTTCTTTGCAACTTCCAGTTTCTTCTCTCTGTCTCGTTTACCTCGATCCTgtaatatttt ... gctttggcagGTTCTTGTTCTTGATGAATATGACACCAGTATGCCCCTTTGTCAAAGCTTC
EST: gi|192323561|gb|FK015327.1|FK015327
EST:     GTTCTTTGCAACTTCCAGTTTCTTCTCTCTGTCTCGTTTACCTCGATCCT                         GTTCTTGTTCTTGATGAATATGACACCAGTATGCCCCTTTGTCAAAGCTTC
genomic: GTTCTTTGCAACTTCCAGTTTCTTCTCTCTGTCTCGTTTACCTCGATCCTgtaatatttt ... gctttggcagGTTCTTGTTCTTGATGAATATGACACCAGTATGCCCCTTTGTCAAAGCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaattaaaacgaaagggtgattgaatgcaaagatgttgttttgatgctttggcagGTTCTTGTTCTTGATGAATATGACACCAGTATGCCCCTTTGTCAAAGCTTCTCGCCCTGATGATAACAATGCCTCTAAGAAATCTGGCGAAAACTCTATG
                                      ttttgat  putative branch site (score: 4)
                   attgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttaggagaaaactgttatttgtttaggaagttttacttaaaataaattaaaacgaaagggtgattgaatgcaaagatgttgttttgatgctttggcagGTTCTTGTTCTTGATGAATATGACACCAGTATGCCCCTTTGTCAAAGCTTCTCGCCCTGATGATAACAATGCCTCTAAGAAATCTGGCGAAAACTCTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - -ggagaaaa
- - - - - - - - - - - - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - -aaacgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaatgca