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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCTgtatgtcctgactcctgagaatcctattccttccaatggttttggtgtcctaacttgtagtaaatttattaccaaaatcaaattggaaaaataagtagaa...

Basic information

species Glycine max
transcript GLYMA01G43470.4
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G43470.4 (Glycine max), 5'ss of exon 16
lower sequence: LOC_Os01g46750.1 (Oryza sativa), 5'ss of exon 16
TATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCTgtatgtc-ctgact-cctgagaatcctat-tccttccaatggttttggtgtcctaacttgtagtaaatttattaccaaaatcaaat--tggaaaaataagtagaa--------------------------------------------------------------
 || ||||| || |||||||| || ||||||||||||||||||||||| || || |||||  ||||||| ||||| ||||  |||||| |||| || || |||| |  ||  || | | | | | || |   | |  |||   ||  | | | |   || | |    |||  || || ||   | |  |||   | ||  |                                                                  
CATAGATCGCAAAAAGAATATCTTCAAGCTTTCACAAGGAGAATATGTAGCAGTAGAAAATTTGGAGAACATTTATGGTCTTGTTTCTGCTATAGATTCGgtatatggctatctgctttaaagttctctgctccttaaatttattctgcgacattgttttt-gcctttttggtatcataaatgactgatgggtcattaccttctgtttctgctaaaacaatttgaaaaactttcctctgttttttttttttttgaacatctgttcag

upper sequence: GLYMA01G43470.4 (Glycine max), 5'ss of exon 16
lower sequence: LOC_Os01g48910.1 (Oryza sativa), 5'ss of exon 16
TATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCTgtatgtcctgactcctgagaatcctattccttccaatggttttggtgtcctaacttgtagtaaatttattaccaaaatcaaattgga--aaaataagtagaa-----------
 |||||||| |||||||| || || ||||| || |||||||||||||| ||||| || ||  ||||||| || | |||||||| | ||  | |||| || |||    ||||   |  ||  | |  || ||   ||   ||||    |  ||||   |  ||  |||           ||   ||        | | | ||            
CATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAATTTGGAGAACATATTCGGTCAAGCTCCTGGTGTTGATTCGgtacaatctgataacctagctttcatttgctcaaaaccttttttccattataaccgatcttacgtttccatatgttgacatgctgactcgccgttatttgacaatctctccag

upper sequence: GLYMA01G43470.4 (Glycine max), 5'ss of exon 16
lower sequence: GRMZM5G861300_T01 (Zea mays), 5'ss of exon 16
TATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCTgtatgtcctgactcctgagaatcctattccttccaatggttttgg-tgtcctaacttgtagtaaatttattaccaaaatcaaattggaaaaataagtagaa-----------------------------------------------------------
 || || || || ||||||||||| || |||||||| || |||||||| || || |||||  |||||||| |||| ||||  |||||| |||| || || ||||||  ||       |  ||  || |  |||   |  |||    | | ||    | ||  ||||     |  |||| || ||||      | ||    |                                                           
CATAGACCGTAAAAAGAATATATTCAAACTTTCACAGGGTGAATATGTGGCAGTTGAAAATTTGGAGAATGTTTATGGTCTTGTTTCTGCTATAGACTCGgtatgtaatggac----aacattttaatttttctggtcttttcaaattttctgtagtctatgaaatgcg--aataaaaccagattgattttcttaggcttatgtcctagttgttctgctgaaggaacatgaattggcttcaatctttttgaattttttag

upper sequence: GLYMA01G43470.4 (Glycine max), 5'ss of exon 16
lower sequence: AT4G23850.1 (Arabidopsis thaliana), 5'ss of exon 16
TATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCTgtatgtcctgactcctgagaatcctattccttccaatggttttggtgtcctaacttgtagtaaattta-ttaccaaaatcaaattggaaaaataagtagaa
 |||||  ||||||||||||| ||||| || ||||||||||| |||||||| || || ||| | || || || |||||| ||||     || |||| || ||| ||      |    ||  | || |  | |    | | |      ||  | ||  |  |||    | | || | | |   |||   ||| | | |||  
AATTGACAGGAAGAAGAATATCTTTAAACTCTCACAAGGAGAGTATGTTGCGGTGGAGAACATAGAAAACATATACGGTGAAGTACAAGCTGTTGATTCCgtaagtaaccgatttgtagttttctctctcataggtttggtaaatattctcatctactgataatcacaatcacaatatttccattc--aaatttattag--

upper sequence: GLYMA01G43470.4 (Glycine max), 5'ss of exon 16
lower sequence: Vv02s0025g01410.t01 (Vitis vinifera), 5'ss of exon 16
TATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCTgtatgtcctgactcctgagaatcctattccttccaatggttttggtgtcctaacttgtagtaaatttattaccaaaatcaaattggaaaaataagtagaa
||| || || |||||||| ||||| |||||||||||||||||||| ||||| || || ||| |||| || ||||| ||||  ||||||  |||||| || ||||| |             ||| ||    || |     |||     ||||   ||       ||||     |    |||  ||       || |     
TATCGACCGCAAGAAGAACATATTCAAGCTTTCACAAGGAGAATACGTTGCCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCGgtatgcctctcaaatgtgtcatcatacgttttacctgaatttatcactcctttttttcccctgattttggttctctctcagtttcattgtgtatgcctct

upper sequence: GLYMA01G43470.4 (Glycine max), 5'ss of exon 16
lower sequence: PP1S108_163V6.1 (Physcomitrella patens), 5'ss of exon 16
TATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCTgtatgtcctgactcctgagaatcctattccttccaatggttttggtgtcctaacttgtagtaaatttattaccaaaatcaaattggaaaaataagtagaa
|||||| || ||||||||||| || |||||||| || ||||||||| |||| |||||||| ||||| ||| | |||  |||   | || || | ||  | |||  | || |  |   |  || ||  |       |     |   |   | ||    |  |  | ||  |      |||   |||| |   |    |   
TATTGACCGTAAGAAGAATATTTTCAAGCTTTCTCAGGGAGAATATATTGCAGTCGAAAAGCTGGAAAATGTGTACAATCAGTCTGCTGCTGTGGATGCGgtacatgcttaacctcaatgattctggtgaacatcagtaactgatttctcaaaagcattttcgagttgctcgttgcatcgttttggcacgttttccatcc

upper sequence: GLYMA01G43470.4 (Glycine max), 5'ss of exon 16
lower sequence: PP1S47_161V6.1 (Physcomitrella patens), 5'ss of exon 16
TATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCTgtatgtcctgactcctgagaatcctattccttccaat--ggttttggtgtcctaacttgtag--taaatttattaccaaaatcaaattggaaaaataagtagaa
||||||||| |||||||| || || |||||||| ||||||||||| ||||| ||||||||||| || ||| | |||  | |    || ||| ||||  | |||||  |   | | | |  || ||  |  |   |||   ||| | |   ||  |      |  | |    ||| | |    |  |||     | || ||    
TATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCGgtatgagc-atcactttacgattctgctgttcataatctagttcttgcaaccacatgcactgctttagcagatttcgatctacccatttcggtactaggtt---

upper sequence: GLYMA01G43470.4 (Glycine max), 5'ss of exon 16
lower sequence: PP1S218_19V6.1 (Physcomitrella patens), 5'ss of exon 17
TATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCTgtat----gtcctgact--cctgagaatcctattccttccaatggttttggtgtcctaacttgtagtaaatttattaccaaa-atcaaa---ttggaaaaataagtagaa---------------------------------------------------------------------------------
 || ||  |||||||||| || || ||| | ||||| || ||||| ||||||||||| ||||| |||| |||||| ||||||  |    |||| ||    ||||    |   ||||   |    |  ||  | |   | |||     ||       |   ||     |  || || ||||     ||||   ||    |     | | |                                                                                  
CATCGACAGGAAGAAGAACATCTTCAAGTTGTCACAGGGTGAATACGTTGCTGTCGAGAACCTTGAGAGTATTTATGGTCAATGTGAAGCTATCGATCAGgtattagagctgtgaccagctcttgcctctcactatgttcaacatcatttccacgtttgtttactccaggttaatgaccatgtgccaaaatcttctctagccttgcaaagctttactgattacttggggtagtagctcattttgcgctacttatatgtgacagtgaactgattagtactttcattgatcag

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|254347181|gb|GR856851.1|GR856851
EST:     CTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCT                         ATATGGGTTTATGGAAACAGTTTTGAGGCCTTCCTTGTGGCTGTTGTTAAC
genomic: CTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCTgtatgtcctg ... tctatttcagATATGGGTTTATGGAAACAGTTTTGAGGCCTTCCTTGTGGCTGTTGTTAAC
EST: gi|58025423|gb|CX712164.1|CX712164
EST:     CTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCT                         ATATGGGTTTATGGAAACAGTTTTGAGGCCTTCCTTGTGGCTGTTGTTAAC
genomic: CTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCTgtatgtcctg ... tctatttcagATATGGGTTTATGGAAACAGTTTTGAGGCCTTCCTTGTGGCTGTTGTTAAC
EST: gi|21676990|gb|BQ629341.1|BQ629341
EST:     CTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCT                         ATATGGGTTTATGGAAACAGTTTTGAGGCCTTCCTTGTGGCTGTTGTTAAC
genomic: CTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCTgtatgtcctg ... tctatttcagATATGGGTTTATGGAAACAGTTTTGAGGCCTTCCTTGTGGCTGTTGTTAAC
EST: gi|208127888|gb|GD924920.1|GD924920
EST:     TGTCGAAAACCTAGGNGAATATTTACGGTCAAGTTTCTTCTATTGAATCT                         ATATGGGTTTA
genomic: TGTCGAAAACCT-GGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCTgtatgtcctg ... tctatttcagATATGGGTTTA
EST: gi|193354695|gb|FK323347.1|FK323347
EST:     TGTTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCT                         ATATGGGTTTATGGAAACAGTTTTGAGGCCTTCCTTGTGGCTGTTGTTAAC
genomic: TG-TCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCTgtatgtcctg ... tctatttcagATATGGGTTTATGGAAACAGTTTTGAGGCCTTCCTTGTGGCTGTTGTTAAC
EST: gi|209712294|gb|BW668488.1|BW668488
EST:     AAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCT                         ATATGGGTTTATGGAAACAGTTTTGAGGCCTTCCTTGTGGCTGTTGTTAAC
genomic: AAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCTgtatgtcctg ... tctatttcagATATGGGTTTATGGAAACAGTTTTGAGGCCTTCCTTGTGGCTGTTGTTAAC
EST: gi|11275038|gb|BF325362.1|BF325362
EST:     CTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCT                         ATATGGGTTTATGGAAACAGTTTTGAGGCCTTCCTTGTGGCTGTTGTTAAC
genomic: CTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCTgtatgtcctg ... tctatttcagATATGGGTTTATGGAAACAGTTTTGAGGCCTTCCTTGTGGCTGTTGTTAAC
EST: gi|193554869|gb|FK513130.1|FK513130
EST:     CTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTNTTGAATCT                         ATATGGGTTTATGGAAACAGTTTTGAGGCCTTCCTTGTGGCTGTTGTTAAC
genomic: CTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCTgtatgtcctg ... tctatttcagATATGGGTTTATGGAAACAGTTTTGAGGCCTTCCTTGTGGCTGTTGTTAAC
EST: gi|151396024|gb|EV265901.1|EV265901
EST:     CTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCT                         ATATGGGTTTATGGAAACAGTTTTGAGGCCTTCCTTGTGGCTGTTGTTAAC
genomic: CTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCTgtatgtcctg ... tctatttcagATATGGGTTTATGGAAACAGTTTTGAGGCCTTCCTTGTGGCTGTTGTTAAC
EST: gi|208076877|gb|GD877402.1|GD877402
EST:     CAGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCT                         ATATGGGTTTATGGAAACAGTTTTGAGGCCTTCCTTGTGGC
genomic: CTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCTgtatgtcctg ... tctatttcagATATGGGTTTATGGAAACAGTTTTGAGGCCTTCCTTGTGGC
EST: gi|208119453|gb|GD917386.1|GD917386
EST:     CGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCT                         ATATGGGTTTATGGAAACAGTTTTGAGGCCTTCCTTGTGGCTGTTGTTAAC
genomic: CGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCTgtatgtcctg ... tctatttcagATATGGGTTTATGGAAACAGTTTTGAGGCCTTCCTTGTGGCTGTTGTTAAC
EST: gi|213605729|gb|DB976168.1|DB976168
EST:     CGAAAACCTGGAGAATATTTACGGTCAAGTTAAGGCTATTGAATCT                         ATATGGGTTTATGGAAACAGTTTTGAGGCCTTCCTTGTGGCTGTTGTTAAC
genomic: CGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCTgtatgtcctg ... tctatttcagATATGGGTTTATGGAAACAGTTTTGAGGCCTTCCTTGTGGCTGTTGTTAAC
EST: gi|192295718|gb|FG990572.1|FG990572
EST:     CTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCT                         ATATGGGTTTATGGAAACAGTTTTGAGGCCTTCCTTGTGGCTGTTGTTAAC
genomic: CTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCTgtatgtcctg ... tctatttcagATATGGGTTTATGGAAACAGTTTTGAGGCCTTCCTTGTGGCTGTTGTTAAC
EST: gi|193323732|gb|FK291256.1|FK291256
EST:     CTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCT                         ATATGGGTTTATGGAAACAGTTTTGAGGCCTTCCTTGTGGCTGTTGTTAAC
genomic: CTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCTgtatgtcctg ... tctatttcagATATGGGTTTATGGAAACAGTTTTGAGGCCTTCCTTGTGGCTGTTGTTAAC
EST: gi|254347182|gb|GR856852.1|GR856852
EST:     CTGTCGAAAA-CTGGAGAATATTTACGGTCAAG-TTCTTCTATTGAATCT                         ATATGGGTTTATGGAAACAGTTTTGAGGCCTTCCTTGTGGCTGTTGTTAAC
genomic: CTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCTgtatgtcctg ... tctatttcagATATGGGTTTATGGAAACAGTTTTGAGGCCTTCCTTGTGGCTGTTGTTAAC
EST: gi|120533313|gb|EH261446.1|EH261446
EST:     CTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCT                         ATATGGGTTCATGG
genomic: CTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCTgtatgtcctg ... tctatttcagATATGGGTTTATGG
EST: gi|51342594|gb|CO983564.1|CO983564
EST:     CTGTCGAAAATCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCT                         ATATGGGTTTATGGAAACAGTTTTGAGGCCTTCCTTGTGGCTGTTGTTAAC
genomic: CTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCTgtatgtcctg ... tctatttcagATATGGGTTTATGGAAACAGTTTTGAGGCCTTCCTTGTGGCTGTTGTTAAC
EST: gi|19270925|gb|BM887181.1|BM887181
EST:     CTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCT                         ATATGGGTTTATGGAAACAGTTTTGAGGCCTTCCTTGTGGCTGTTGTTAAC
genomic: CTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCTgtatgtcctg ... tctatttcagATATGGGTTTATGGAAACAGTTTTGAGGCCTTCCTTGTGGCTGTTGTTAAC
EST: gi|15661796|gb|BI699167.1|BI699167
EST:     TTACGGTCAAGTTTCTTCTATTGAATCT                         ATATGGGTTTATGGAAACAGTTTTGAGGCCTTCCTTGTGGCTGTTGTTAAC
genomic: TTACGGTCAAGTTTCTTCTATTGAATCTgtatgtcctg ... tctatttcagATATGGGTTTATGGAAACAGTTTTGAGGCCTTCCTTGTGGCTGTTGTTAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCTgtatgtcctgactcctgagaatcctattccttccaatggttttggtgtcctaacttgtagtaaatttattaccaaaatcaaattggaaaaataagtagaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA