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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcacgccatatttcagtacaaaaaatacccttgatatttgatcagaacttattgttgatttaatatgtacactgatatcatgccatcccttttatacagGTATGTTGACGTGATTCTTCAATTAATTGACAAGGCCGGAGATTTTGTTAGCGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGAC

Basic information

species Glycine max
transcript GLYMA17G05410.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 12
-gtcacgccatattt-cagtacaaaaaatacccttgatatttgatcagaacttattgttgatttaat-atgtacactgatatcatgccatcccttttatacagGTATGTTGACGTGATTCTTCAATTAATTGACAAGGCCGGAGATTTTGTTAGCGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGAC
 ||   |   ||  |  || | |  || |     |   ||| ||  ||   ||  |||  | || || || | |||  ||||| |  | |   |||| || |||||||| || || ||||| ||  | || ||||| || ||||||||||| || ||||| ||||||| ||| ||||| || ||||| || ||||||||||| 
agttctgaactacctgtaggatagtaactctagctagcattggactag--ttttatgtgaaattgatgatttccaccaatatc-taactttttttttctatagGTATGTCGATGTTATTCTGCAGCTGATAGACAAAGCAGGAGATTTTGTAAGTGATGATATATGGTATCGAGTGGTACAATTTGTCACCAACAATGAAGAT

upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 13
gtcacgccatatttcagtacaaaaaatacccttgatatttgatcagaacttattgttgatttaatatgtacac---tgatatcatgccatccct--------tttatacagGTATGTTGACGTGATTCTTCAATTAATTGACAAGGCCGGAGATTTTGTTAGCGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGAC
               | |  |  ||||    |||  | ||         || |  || ||  ||| |   |||   |||  |  ||| ||  ||        ||| |  ||||||||||| || ||||||||| | || ||||| || ||||||||||| || ||||| ||||||| ||| ||||| || |||||||| ||||| ||||||
-----------aacaactgtagcaaattgtgttgtcagttctgtgtgcattttaatttatgcaatttcgtcaccattgagtttttgctatatctgatttgtatttgtgtagGTATGTTGATGTTATTCTTCAACTTATAGACAAAGCTGGAGATTTTGTAAGTGATGATATATGGTATCGAGTGGTACAATTTGTTACGAACAACGAAGAC

upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 12
lower sequence: AT5G22780.1 (Arabidopsis thaliana), 3'ss of exon 12
-------------gtcacgccatatttcagtaca-----aaaaatacccttgatatttgatcagaacttattgttgattta-atatgtacactgat--atcatgccatcccttttatac--agGTATGTTGACGTGATTCTTCAATTAATTGACAAGGCCGGAGATTTTGTTAGCGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGAC
             | || |   ||| |    |       |   | ||  | || |  ||  | |  |   ||      ||| | | | | | || |  |  |||  |    |  | | |  |||||||| || ||||| ||||| || || |||||||| || |||||||||||||||||||| |||||||| |||||||||||||| ||||| |||||||||
gtaaagagaactcgacaagaagtatatgtacattttttcatgcacactatagagacatgtgctgtgccctttagatccttacacaagca-attggtcaaagatgttaattttgatgttctcagGTATGTAGATGTGATCCTTCAGTTGATCGACAAGGCTGGGGATTTTGTTAGCGATGACATTTGGTTTCGTGTGGTTCAGTTTGTAACAAATAATGAAGAC

upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 12
lower sequence: AT5G22770.2 (Arabidopsis thaliana), 3'ss of exon 13
-------------------------------------gtcacgc---catatttcagtacaaaaa-atacccttgatatttgatcagaacttattgttgatttaatatgtacactgatatcatgccatccct--tttatacagGTATGTTGACGTGATTCTTCAATTAATTGACAAGGCCGGAGATTTTGTTAGCGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGAC
                                      ||| ||   || ||||   ||||  || || |  |    ||||| |  || ||| | | |  ||  | ||  ||      |  |||  |    |  | | | |||||||||||| ||||| ||||| || || |||||||| || ||||||||||||||||||||||||||||| |||||||||||||| ||||| |||||||||
gtgaggataactcgatacgaagtatatgtacacttcattcatgcacacaaatttggttacagtaacatgcattatccatttggtgtgacctt-tagatccttgcaaatcaactggttaaagatgttaattttgatgttttcagGTATGTTGATGTGATCCTTCAGTTGATCGACAAGGCTGGGGATTTTGTTAGCGATGACATATGGTTTCGTGTGGTTCAGTTTGTAACAAATAATGAAGAC

upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 12
gtcacgccatatttcagtacaaaaaatacccttgatatttgatcagaacttattgttgatttaatatgtacactgatat-catgccatcccttttatacagGTATGTTGACGTGATTCTTCAATTAATTGACAAGGCCGGAGATTTTGTTAGCGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGAC
||     ||| |   ||     ||   |   |||    ||||    |    ||  |  | |   ||| ||   ||  ||  || |      | | || ||||||||| |||||||| || || || ||||||||||| ||||||||||| || ||||||||||||||||| || || ||||||||||||||||||||||||
gtgctttcat-tggaaggttggaagcaattgttgcctgttgaagcaacaagatcttctactgtttatatatgttgtcatgtattcttcaattgtcatgcagGTATGTGGACGTGATCCTACAGTTGATTGACAAGGCAGGAGATTTTGTCAGTGATGACATATGGTTTCGTGTTGTGCAGTTTGTTACAAACAATGAAGAC

upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 12
lower sequence: PP1S26_36V6.1 (Physcomitrella patens), 3'ss of exon 12
gtcacgccatatttcagtacaaaaaatacccttgatatttgatcagaactta--ttgttgatttaatatg-tacactgatat----catgccatcccttttat-acagGTATGTTGACGTGATTCTTCAATTAATTGACAAGGCCGGAGATTTTGTTAGCGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGAC
          |  |   ||   ||  |  | |||  | ||  | |  || ||   |  |    || | || || | |||  |     ||    |   |   ||  |||||| ||||| || ||  | ||  | ||||| ||||| || ||||||||||| ||||| |||||||  || |||||||| |||||||| |||||||| || 
-------ttgaccttgatatggaatgt-tcattgtgagttattgattacctagacttctagaatactgtgctaaagtgaagtgctttatattgtgattgggatcgcagGTACGTTGATGTCATATTACAGCTTATTGAGAAGGCTGGTGATTTTGTTAGTGATGATATATGGTACCGAGTGGTTCAATTTGTTACCAACAATGATGAT

upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 12
lower sequence: PP1S507_6V6.1 (Physcomitrella patens), 3'ss of exon 12
--gtcacgccatatttcagtacaaaaaatacccttgatatttgatcagaacttattgttgatttaatatgtacactgatatcatgccatcccttttatacagGTATGTTGACGTGATTCTTCAATTAATTGACAAGGCCGGAGATTTTGTTAGCGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGAC
       |      |||  |     | |||    |  |  |   | | |  |      ||   ||||      |    ||    |  |  |   || |  |||||||| || || ||  | ||| | || || || || || |||||||| || |||||||| |||| |||||| || ||||||||||| ||| ||||| ||
attctgtgtttatattcgttgtggtatatagtgatacttgtcagtgaaacttggcgcctggaataatccactaaactctacttggaaactctcattgt--agGTATGTGGATGTCATATTGCAACTCATCGAGAAAGCTGGTGATTTTGTAAGTGATGACATTTGGTATCGGGTTGTACAGTTTGTTACCAACGATGAACAC

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|193557084|gb|FK512727.1|FK512727
EST:     TCACTTAAAGCAGCTATTCTTGCTGAGAAGTTTGCACCAGACCTTTCATG                         GTATGTTGACGTGATTCTTCAATTAATTGACAAGGCCGGAGATTTTGTTAG
genomic: TCACTTAAAGCAGCTATTCTTGCTGAGAAGTTTGCACCAGACCTTTCATGgtaatgcaat ... ttttatacagGTATGTTGACGTGATTCTTCAATTAATTGACAAGGCCGGAGATTTTGTTAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaacttattgttgatttaatatgtacactgatatcatgccatcccttttatacagGTATGTTGACGTGATTCTTCAATTAATTGACAAGGCCGGAGATTTTGTTAGCGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGAC
                         cactgat  putative branch site (score: 3)
                                      ccatccctttt  putative PPT
     tattgttgatttaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcacgccatatttcagtacaaaaaatacccttgatatttgatcagaacttattgttgatttaatatgtacactgatatcatgccatcccttttatacagGTATGTTGACGTGATTCTTCAATTAATTGACAAGGCCGGAGATTTTGTTAGCGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- cacgcca
- - - - - - - - - - aaaaaat
- - - - - - - - - - - - - - cccttga
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgtac