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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cccagagtaaaattctagatctgctttactagtatcttagaaaaatctaaacctttgatttttccttaactatgcatactttttttatattatcattcagGGTACTAGTCGGCCAGCTCATTATCATGTCCTGTGGGATGAAAACAACTTCACAGCAGATGGAATTCAGTCTCTGACAAACAATCTTTGTTATACATATG

Basic information

species Glycine max
transcript GLYMA20G28970.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 20
lower sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 18
----cccagagtaaaattctagatctgctttactagtatcttagaaaaatctaaacctttgatttttccttaactatgcatactttttttatattatcattcagGGTACTAGTCGGCCAGCTCATTATCATGTCCTGTGGGATGAAAACAACTTCACAGCAGATGGAATTCAGTCTCTGACAAACAATCTTTGTTATACATATG
       |   |   ||| || | |     |||| | |||      |     | |   |    || ||| || || | |  |  |   | |  |  |    ||||| || ||| |||| ||||| || |||||||| |||||||| ||||| ||||||||||| | ||| ||  | ||||||||||| ||||| || ||     
ccttttaatcatgtgattgtacagccatggtacttggatcagtagcatgggaatatagtcagattctccgta-ctgtactgaaatgactgacgt-gtgg--cagGGAACAAGTAGGCCCGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAAACACTGACAAACAACCTTTGCTACAC-----

upper sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 20
lower sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 19
cccagagtaaaattctagatct-gctttactagtatcttagaaaaatctaaacct--ttgatttttccttaactatgcatactttttttatat---tatcattcagGGTACTAGTCGGCCAGCTCATTATCATGTCCTGTGGGATGAAAACAACTTCACAGCAGATGGAATTCAGTCTCTGACAAACAATCTTTGTTATACATATG
   |   |   ||| || | ||     |||| | |||  || |  ||   ||  |  |     | ||| || |||| |     |   | || |     |    ||||| || ||| |||| ||||| || |||||||| |||||||| ||||| ||||||||||| | ||| ||| |  |||||||||| ||||| || ||     
---atcatgtgattgtacagcttatggtacttggatc--agtagcatgggaatgtagtcagactctccgta-ctatactggaatgactgatgtgtgagtttgccagGGAACGAGTAGGCCTGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACAC-----

upper sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 20
lower sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 19
-cccagagtaaaattctagatctgctttactagtatcttagaaaaatctaaacctttgatttttccttaactatgcatactttttttatattatcattcagGGTACTAGTCGGCCAGCTCATTATCATGTCCTGTGGGATGAAAACAACTTCACAGCAGATGGAATTCAGTCTCTGACAAACAATCTTTGTTATACATATG
   |  |  ||   || | || | | ||| ||  | |||      | ||| ||   | |         ||  |  |    | | ||| |  ||| ||  |||| || ||  |||| || ||||| ||||| || ||||| || ||||| |||||||||||||| ||||| |||||||| |||||||| |||||||| ||||
gtacgaaacaactatcgaaatatccgttaatatgaccttttccgtaactatacagataa---------aatgacactgtttgtgtttgttgtatgatctagGGAACAAGCAGGCCTGCACATTACCATGTTCTTTGGGACGAGAACAATTTCACAGCAGATGGTATTCAATCTCTGACTAACAATCTCTGTTATACCTATG

upper sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 20
lower sequence: Vv05s0020g04190.t01 (Vitis vinifera), 3'ss of exon 17
----cccagagtaaaattctagatctgctttactagtatcttagaaaaatctaaacctttgatttttccttaactatgcatactttttttatattatcatt-cagGGTACTAGTCGGCCAGCTCATTATCATGTCCTGTGGGATGAAAACAACTTCACAGCAGATGGAATTCAGTCTCTGACAAACAATCTTTGTTATACATATG
    | ||   ||  |     | |||  |||   ||| ||| |  || || |     |  ||  |||    |   |||  |  || |||| | |  |  |  ||||| || ||| |||| |||||||| |||||  | |||||||| ||||| |||||||||||||||||||| ||  |||| ||||||||||| || |||||||
aacactcactttagga----ggctctcatttgtcagtttctaactaacatgtgc-tttcagaacttttggaatggatgagtcattattttctttctttgtggcagGGGACAAGTAGGCCTGCTCATTACCATGTTTTATGGGATGAGAACAATTTCACAGCAGATGGAATTCAATCCTTGACGAACAATCTTTGCTACACATATG

upper sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 20
lower sequence: EFJ24991 (Selaginella moellendorffii), 3'ss of exon 20
cccagagtaaaattctagatctgctttactagtatcttagaaaaatctaaacctttgatttttccttaactatgcatacttttttta--tattatcattcagGGTACTAGTCGGCCAGCTCATTATCATGTCCTGTGGGATGAAAACAACTTCACAGCAGATGGAATTCAGTCTCTGACAAACAATCTTTGTTATACATATG
                                             |   ||         |   | | | |  |  |  |  || |   |   | | | ||||| ||||||||||| || ||||||||||| || |||||||||||||  ||||| || |||||  | |||||  | || ||||| || || || ||     
--------------------------------------------gtacgaaggcacagcgtcaacctgattgaggctgatggttgtgactgcgaccctgcagGGAACTAGTCGGCCGGCACATTATCATGTGCTTTGGGATGAAAACACTTTCACGGCTGATGGTTTGCAGTCATTAACGAACAACCTATGCTACAC-----

upper sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 20
lower sequence: EFJ15357 (Selaginella moellendorffii), 3'ss of exon 20
cccagagtaaaattctagatctgctttactagtatcttagaaaaatctaaacctttgatttttccttaactatgcatacttttttta--tattatcattcagGGTACTAGTCGGCCAGCTCATTATCATGTCCTGTGGGATGAAAACAACTTCACAGCAGATGGAATTCAGTCTCTGACAAACAATCTTTGTTATACATATG
                                             |   ||         ||  | | | |  |  |  |  |  |   |   | | | ||||| ||||||||||| || ||||||||||| || |||||||||||||  ||||| || |||||  | |||||  | || ||||| || || || ||     
--------------------------------------------gtacgaaggcacagcgttaacctgattgaggctgatggtcgtgactgcgaccctacagGGAACTAGTCGGCCGGCACATTATCATGTGCTTTGGGATGAAAACACTTTCACGGCTGATGGTTTGCAGTCATTAACGAACAACCTATGCTACAC-----

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|24205882|gb|BU965135.1|BU965135
EST:     GCCATCCAACAGAATTTGATTTTTATCTCTGCAACCATGCTGGCATCCAG                         GGTACTAGTCGGCCAGCTCATTATCATGTCCTGTGGGATGAAAACAACTTC
genomic: GCCATCCAACAGAATTTGATTTTTATCTCTGCAGCCATGCTGGCATCCAGgtagaagata ... tatcattcagGGTACTAGTCGGCCAGCTCATTATCATGTCCTGTGGGATGAAAACAACTTC
EST: gi|208148115|gb|GD949731.1|GD949731
EST:     GCCATCCAACAGAATTTGATTTTTATCTCTGCAGCCATGCTGGCATCCAG                         GGTACTAGTCGGCCAGCTCATTATCATGTCCTGTGGGATGAAAACAACTT
genomic: GCCATCCAACAGAATTTGATTTTTATCTCTGCAGCCATGCTGGCATCCAGgtagaagata ... tatcattcagGGTACTAGTCGGCCAGCTCATTATCATGTCCTGTGGGATGAAAACAACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctaaacctttgatttttccttaactatgcatactttttttatattatcattcagGGTACTAGTCGGCCAGCTCATTATCATGTCCTGTGGGATGAAAACAACTTCACAGCAGATGGAATTCAGTCTCTGACAAACAATCTTTGTTATACATATG
                  ccttaac  putative branch site (score: 3)
                    ttaactatgcatactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cccagagtaaaattctagatctgctttactagtatcttagaaaaatctaaacctttgatttttccttaactatgcatactttttttatattatcattcagGGTACTAGTCGGCCAGCTCATTATCATGTCCTGTGGGATGAAAACAACTTCACAGCAGATGGAATTCAGTCTCTGACAAACAATCTTTGTTATACATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - -tctgctt
- - - - - - - - - - - - - - - - - - - agaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatact