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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgcatttatattttatgctgattgtcctaattgcacggaatctatgctgttaacacttgcaaacctcctcaaatgttagcttcctgatgttacaatagGTATCAAGGAGTCTGATACTGGATTAGCAGCACCAAGCCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAAGAGCAGCCTCTTCAG

Basic information

species Glycine max
transcript GLYMA16G01810.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g09290.2 (Oryza sativa), 3'ss of exon 2
----gttgcatttatattttatgctgattgtcctaattgcacggaatctat-gctgttaacact-tgcaaacctcctcaaatgttagcttcctga-tgtta-----caatagGTATCAAGGAGTCTGATACTGGATTAGCAGCACCAAGCCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAAGAGCAGCCTCTTCAG
    ||     | | ||| | ||||  |     ||| |  |      |||  | || |  | || | | ||| | ||  ||  |   | ||   | |||||         ||| || || |||||||| |||||||| ||  |||| ||||||||||| ||||| || |||||||| ||||||||||| ||||| || || |||
gtgtgtgctcgtcaaattctttgcttctcaatttaaatataactgtgctacaggtgcttgcgctattccaacttgctgcaacatgctcatctgaactgttaatgaattgcagGAATTAAAGAGTCTGACACTGGATTGGCTCCACCTAGCCAGTGGGACCTTGTATCCGATAAGCAGATGATGCAGGAGGAGCAACCCCTGCAG

upper sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 2
gttgcatttatatt-ttatgctgattgtcctaattgcacggaatctatgctgttaacacttgcaaac----ctcctcaaatgtta-gcttcctgatgttacaatagGTATCAAGGAGTCTGATACTGGATTAGCAGCACCAAGCCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAAGAGCAGCCTCTTCAG
      || | ||  || | | | |||||    |||    ||  ||| |   ||| ||| ||  ||     ||     | || ||  ||   | ||   |    ||| || ||||||||||| |||||  | ||| |||| ||||| |||||||| || || |||||||| |||||||| |||||||| || || || 
-----tttcacatcattgttcagtttgtca-gcttgtttagatgctaggagtttagcacatgttaattggtctatctgactgatatactctttcattaaatcccagGGATTAAGGAGTCTGACACTGGGCTGGCACCACCCAGCCAATGGGATCTAGTATCAGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAA

upper sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 2
gttgcatttatattttatgctgattgtc--ctaattgcacggaatctatgctgttaa--cacttgcaaacctcctcaaatgtta-gcttcctgatgttaca-atagGTATCAAGGAGTCTGATACTGGATTAGCAGCACCAAGCCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAAGAGCAGCCTCTTCAG
     |||| | || |||| || |   |   | ||      |  |  |||||   ||    |||   || |  |  |  ||  | |  | || ||  || |   |||||| |||||||||||||| || || ||  |||| |||||||||||| | ||||| ||||| || |||||||| ||||| || ||  | || 
-----attt-tgttctatgttgttctgcaatttatcagtttgttttaatgctaggaaggtccttttgaatcagcatacctgagatgtgttcttatactaaatgcagGTATAAAGGAGTCTGATACAGGGTTGGCTCCACCTAGCCAGTGGGATTTGGTTTCAGATAAACAGATGATGCAAGAAGAACAACCGTTACAA

upper sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 2
-gttgcat-ttatattttatgctgattgtc--ctaattgcacgg--aatctatgctgttaacacttgcaaacctcctcaaatgttagcttcctgatgttacaatagGTATCAAGGAGTCTGATACTGGATTAGCAGCACCAAGCCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAAGAGCAGCCTCTTCAG
 |||   | | | || || | |   |  ||  ||  ||  | ||  ||      |  ||   | | ||| ||||    | ||||  ||   |  |  | ||   ||| || |||||||||||||| ||  | ||  |||| |||||||||||| | ||||| |||||||| |||||||| ||||| || ||  | || 
agttctctatcaaatgttcttccattcatcagctgctttaaaggttaagaaggtccttttgaattagcatacctg---agatgt--gccctcatacttaacg-cagGGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAA

upper sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 2
------------------------------------------------------------------------------------gttgcatttatattt-tatgctgattgtc--ctaatt--gcacggaatctatgctg-ttaacacttgcaaacctcctca---aatgttagct----tcctgatgttacaatagGTATCAAGGAGTCTGATACTGGATTAGCAGCACCAAGCCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAAGAGCAGCCTCTTCAG
                                                                                    || | |   |   || ||||   | | |     || |  ||| | | | |  |||| |||   |||| | | | | |||   |||  ||||     |  | || ||| || |||||||||||| ||||||||||| ||||| |||||||| |||||||||||||||||||||||||||||||||||||| |||||||||||||||
gtatgtttcttattcgtgatatttccaatgtatagtgctatttgataaactgggcatgtattatgttgatccatgttgaaaatagtagtagccaaggttatatgagaagttttgataaactaggcatgtattatgggctgattatggcttgaataacacttcatgaaattatagcaatgattttcatcttataacagGTATCAAGGAATCTGATACTGGCTTAGCTGCACCAAGTCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAGGAGCAGCCTCTTCAG

upper sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ29161 (Selaginella moellendorffii), 3'ss of exon 2
gttgcatttatattttatgctgattgtcctaattgcacggaatctatgctgttaacac-ttgcaaacctcctcaaatgttagcttcctgatgttacaatagGTATCAAGGAGTCTGATACTGGATTAGCAGCACCAAGCCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAAGAGCAGCCTCTTCAG
                                                         | |||| | | | ||    | ||     | || | || ||   || ||||||||||| || |||||  ||||||| || |||||||||||||| || |||||||||||||||||||| ||||||||||| || || 
------------------------------------------------------gtgcgttgcgatcttgctgggcttttttgagcgtgcttttcca---gGGATCAAGGAGTCCGACACTGGTCTAGCAGCTCCTAGCCAGTGGGATCTGGTGTCTGATAAGCAAATGATGCAAGAAGAGCAGCCACTGCAA

upper sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ13722 (Selaginella moellendorffii), 3'ss of exon 2
gttgcatttatattttatgctgattgtcctaattgcacggaatctatgctgttaacac-ttgcaaacctcctcaaatgttagcttcctgatgttacaatagGTATCAAGGAGTCTGATACTGGATTAGCAGCACCAAGCCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAAGAGCAGCCTCTTCAG
                                                         | |||| |   | ||    | ||     | || | || ||   || ||||||||||| || |||||  ||||||| || |||||||||||||| || |||||||||||||||||||| ||||||||||| || || 
------------------------------------------------------gtgcgttgcgattttgctgggcttttttgagcgtgcttttcca---gGGATCAAGGAGTCCGACACTGGTCTAGCAGCTCCTAGCCAGTGGGATCTGGTGTCTGATAAGCAAATGATGCAAGAAGAGCAGCCACTGCAA

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|213602597|gb|DB968879.1|DB968879
EST:     GGCGGAGAAGGAAATCAAAGATATGGCCAAGAAAGTGAATGACTTATGTG                         GTATCAAGGAGTCTGATACTGGATTAGCAGCACCAAGCCAGTGGGATCTTG
genomic: GGCGGAGAAGGAAATCAAAGATATGGCCAAGAAAGTGAATGACTTATGTGgtacgtgcaa ... gttacaatagGTATCAAGGAGTCTGATACTGGATTAGCAGCACCAAGCCAGTGGGATCTTG
EST: gi|16281984|gb|BI944774.1|BI944774
EST:     AAATCAAAGATATGGCCAAGAAAGTGAATGACTTATGTG                         GTATCAAGGAGTCTGATACTGGATTAGCAGCACCAAGCCAGTGGGATCTTG
genomic: AAATCAAAGATATGGCCAAGAAAGTGAATGACTTATGTGgtacgtgcaa ... gttacaatagGTATCAAGGAGTCTGATACTGGATTAGCAGCACCAAGCCAGTGGGATCTTG
EST: gi|24205597|gb|BU964850.1|BU964850
EST:     GGCGGAGAAGGAAATCAAAGATATGGCCAAGAAAGTGAATGACTTATGTG                         GTATCAAGGAGTCTGATACTGGATTAGCAGCACCAAGCCAGTGGGATCTTG
genomic: GGCGGAGAAGGAAATCAAAGATATGGCCAAGAAAGTGAATGACTTATGTGgtacgtgcaa ... gttacaatagGTATCAAGGAGTCTGATACTGGATTAGCAGCACCAAGCCAGTGGGATCTTG
EST: gi|193388500|gb|FK356213.1|FK356213
EST:     GGCGGAGAAGGAAATCAAAGATATGGCCAAGAAAGTGAATGACTTATGTG                         GCATCAAGGAGTCTGATACTGGATTAGCAGCACCAAGCCAGTGGGATCTTG
genomic: GGCGGAGAAGGAAATCAAAGATATGGCCAAGAAAGTGAATGACTTATGTGgtacgtgcaa ... gttacaatagGTATCAAGGAGTCTGATACTGGATTAGCAGCACCAAGCCAGTGGGATCTTG
EST: gi|254319386|gb|GR829006.1|GR829006
EST:     GGCGGAGAAGGAAATCAAAGATATGGCCAAGAAAGTGAATGACTTATGTG                         GTATCAAGGAGTCTGATACTGGATTAGCAGCACCAAGCCAGTGGGATCTTG
genomic: GGCGGAGAAGGAAATCAAAGATATGGCCAAGAAAGTGAATGACTTATGTGgtacgtgcaa ... gttacaatagGTATCAAGGAGTCTGATACTGGATTAGCAGCACCAAGCCAGTGGGATCTTG
EST: gi|209717050|gb|BW668704.1|BW668704
EST:     GGCGGAGAAGGAAATCAAAGATATGGCCAAGAAAGTGAATGACTTATGTG                         GTATCAAGGAGTCTGATACTGGATTAGCAGCACCAAGCCAGTGGGATCTTG
genomic: GGCGGAGAAGGAAATCAAAGATATGGCCAAGAAAGTGAATGACTTATGTGgtacgtgcaa ... gttacaatagGTATCAAGGAGTCTGATACTGGATTAGCAGCACCAAGCCAGTGGGATCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgctgttaacacttgcaaacctcctcaaatgttagcttcctgatgttacaatagGTATCAAGGAGTCTGATACTGGATTAGCAGCACCAAGCCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAAGAGCAGCCTCTTCAG
                           aaatgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgcatttatattttatgctgattgtcctaattgcacggaatctatgctgttaacacttgcaaacctcctcaaatgttagcttcctgatgttacaatagGTATCAAGGAGTCTGATACTGGATTAGCAGCACCAAGCCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAAGAGCAGCCTCTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- tgcattt
- - - - - - - - -tgctgat
- - - - - - - - - - - - - - - - -tgcacgg
- - - - - - - - - - - - - - - - - - - - - -ctatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - -cacttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttcct