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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAAGAAGATCCGCCTCGAGCAGGAGGACGAGGGCGTCCCGTCCACCGCCATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctttggttttatgcaacagcgggtaggtgtcgttttaggatgggattcgtttgctcgatggaaatgatggtgcgtatgtatgcaatcaagtaaaagtcagacgcaattttgatgctgcgatgccctgtagtgttggtacgctgacaagctttatactctcctaagtgcag

Basic information

species Zea mays
transcript GRMZM2G143213_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143213_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g02680.1 (Oryza sativa), 5'ss of exon 1
TCAAGAAGATCCGCCTCGAGCAGGAGGACGAGGGCGTCCCGTCCACCGCCATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctttggttttatgcaacagcgggtaggtgtcgttttaggatgggattcgtttgctcgatggaaatgatggtgcgtatgtatgcaatcaagtaaaagtcagacgcaattttgatgctgcgatgccctgtagtgttggtacgctgacaagctttatactctcctaagtgcag
||||||||||||| || ||||||||||| ||||||||||| |||||||| |||||||||||||| ||||||||||||||| | ||||||||||||||||||||| || |  |   |  |    |  | ||||       || |||| |  |  ||   | ||     | |||| |   |  ||  ||  ||  | | |  |   ||                                                                     
TCAAGAAGATCCGGCTTGAGCAGGAGGATGAGGGCGTCCCCTCCACCGCAATCCGCGAGATCTCGCTCCTCAAGGAGATGCATCACGGCAACATCGTCAGgtcctctctattaacactctgttgttgttagga-----ctttggattgactaagtcatcacggactgattgattggttgcctgattg--attgactgattgattgat--------------------------------------------------------------------

upper sequence: GRMZM2G143213_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g01850.1 (Oryza sativa), 5'ss of exon 3
TCAAGAAGATCCGCCTCGAGCAGGAGGACGAGGGCGTCCCGTCCACCGCCATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctttggttttatgcaacagcgggtaggtgtcgttttaggatgggattcgtttgctcgatggaaatgatggtgcgtatgtatgcaatcaagtaaaagtcagacgcaattttgatgctgcgatgccctgtagtgttggtacgctgacaagctttatactctcctaagtgcag
||||||||||||| || ||||||||||| ||||| ||||| ||||||||||||||||||||||| ||||||||||||||| | ||| ||||||||||||||||| || |    |||  ||||     |  | | | ||||  |  |  |     ||  ||   | | | |  |  |    | | |    ||  | | |  |   || |                                                                   
TCAAGAAGATCCGGCTTGAGCAGGAGGATGAGGGTGTCCCCTCCACCGCCATCCGCGAGATCTCGCTCCTCAAGGAGATGCATCACCGCAACATCGTCAGgtcctctcta---ttaaccaaccctctgctgctcttgtttaggactttgg---attcacttattaggagtagtcat---cacggac-tgattgattcattgattgatgtg-----------------------------------------------------------------

upper sequence: GRMZM2G143213_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA05G25320.1 (Glycine max), 5'ss of exon 1
TCAAGAAGATCCGCCTCGAGCAGGAGGACGAGGGCGTCCCGTCCACCGCCATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctttggttttatgcaacagcgggtaggtgtcgttttaggatgggattcgtttgctcgatggaaatgatggtgcgtatgtatgcaatcaagtaaaagtcagacgcaattttgatgctgcgatgccctgtagtgttggtacgctgacaagctttatactctcctaagtgcag
| |||||||| ||||||||||||||||| ||||| || ||   ||||||||| |||||||| |||||| | || || ||| | ||| | ||||| || ||||      |   | |    || |  | || |||    ||  |   ||  |||| | ||||       |||  |      |||| | | | |   ||| || | |||   |||                                                               
TGAAGAAGATTCGCCTCGAGCAGGAGGATGAGGGGGTTCCCAGCACCGCCATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAGgtatataatatatctg---aagaatgtgttggtc---ttcaattgtgcaattcatgtgctgagaaagaatatta-----tatggacgtagt--ggtagaaattagaaa-aatag-------------------------------------------------------------

upper sequence: GRMZM2G143213_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA15G14390.1 (Glycine max), 5'ss of exon 2
TCAAGAAGATCCGCCTCGAGCAGGAGGACGAGGGCGTCCCGTCCACCGCCATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctttggttttatgcaacagcgggtaggtgtcgttttaggatgggattcgtt-tgctcgatggaaatgatggtgcgtatgtatgcaatcaagtaaaagtcagacgcaattttgatgctgcgatgccctgtagtgttggtacgctgacaagctttatactctcctaagtgcag
|||||||||| |||||||||||||||||||| ||||| ||   ||||||||| |||||||| ||||||||||| |||||| | ||  | ||||| || ||||         | | ||  ||   |   |     |    || | |||  ||  ||| |  ||||||   |   ||| | ||        ||| | ||    | |  || | ||||                                                             
TCAAGAAGATTCGCCTCGAGCAGGAGGACGAAGGCGTTCCCAGCACCGCCATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAGgt--------atatcatctaattcc---ttctcctttcattggaatgcaatgtgttgttgtcgatgatgaaattggagggt-------taataatgttgtcgccgcactctatttgtc----------------------------------------------------------

upper sequence: GRMZM2G143213_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA09G03470.1 (Glycine max), 5'ss of exon 2
TCAAGAAGATCCGCCTCGAGCAGGAGGACGAGGGCGTCCCGTCCACCGCCATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctttggttttatgcaacagcgggtaggtgtcgttttaggatgggattcgtttgct--cgatggaaatgatggtgcgtatgtatgcaatcaagtaaaagtcagacgcaattttgatgctgcgatgccctgtagtgttggtacgctgacaagctttatactctcctaagtgcag
| |||||||| |||||||||||||||||||| ||||| ||   ||||||||| |||||||| ||||| ||||| |||||| | ||  | ||||| || ||||           | || ||    |       | || ||| |        |    |||     |||| || | ||| |   |  ||  || ||        | |  |                                                                      
TGAAGAAGATTCGCCTCGAGCAGGAGGACGAAGGCGTTCCCAGCACCGCCATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAGgttta--------tcatccatttcccttctcctttcatttgaatgcaatgtgttgttgtcgatgatgaaattaatgttttatccgtgcgctatttgtcgtgaatttgt---------------------------------------------------------------------

upper sequence: GRMZM2G143213_T02 (Zea mays), 5'ss of exon 2
lower sequence: EFJ15022 (Selaginella moellendorffii), 5'ss of exon 2
TCAAGAAGATCCGCCTCGAGCAGGAGGACGAGGGCGTCCCGTCCACCGCCATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctttggttttatgcaacagcgggtaggtgtcgttttaggatgggattcgtttgctcgatggaaatgatggtgcgtatgtatgcaatcaagtaaaagtcagacgcaattttgatgctgcgatgccctgtagtgttggtacgctgacaagctttatactctcctaagtgcag
||||||||||||| || || ||||||||||||||||||||   ||| || |||||||| || || ||||||||||| ||| | ||||||||||| || |||| ||  |    ||       | | |  | | | || |   | ||   |||| |  ||| |                                                                                                                  
TCAAGAAGATCCGACTGGACCAGGAGGACGAGGGCGTCCCCAGCACGGCGATCCGCGAAATATCGCTCCTCAAGGAAATGCAGCACGGCAACATTGTGAGgtgcgtgtccacttccattctctg-gaatggatttc-taaaacgaatcgattgggctgcccag----------------------------------------------------------------------------------------------------------------

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|61118495|gb|DN559456.1|DN559456
EST:     ATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAG                         GTTACATGATGTTGTCCACAGCGAGAAGCGGATATACCTCGTCTTCGAGTA
genomic: ATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctttg ... ctaagtgcagGTTACATGATGTTGTCCACAGCGAGAAGCGGATATACCTCGTCTTCGAGTA
EST: gi|21390004|gb|BQ528053.1|BQ528053
EST:     ATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAG                         GTTACATGATGTTGTCCACAGCGAGAAGCGGATATACCTCGTCTTCGAGTA
genomic: ATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctttg ... ctaagtgcagGTTACATGATGTTGTCCACAGCGAGAAGCGGATATACCTCGTCTTCGAGTA
EST: gi|60397283|gb|DN230099.1|DN230099
EST:     ATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAG                         GTTACATGATGTTGTCCACAGCGAGAAGCGGATATACCTCGTCTTCGAGTA
genomic: ATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctttg ... ctaagtgcagGTTACATGATGTTGTCCACAGCGAGAAGCGGATATACCTCGTCTTCGAGTA
EST: gi|6020558|gb|AW065591.1|AW065591
EST:     CTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAG                         GTTACATGATGTTGTCCACAGCGAGAAGCGGATATACCTCGTCTTCGAGTA
genomic: CTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctttg ... ctaagtgcagGTTACATGATGTTGTCCACAGCGAGAAGCGGATATACCTCGTCTTCGAGTA
EST: gi|22542162|gb|BU092600.1|BU092600
EST:     ATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAG                         GTTACATGATGTTGTCCACAGCGAGAAGCGGATATACCTCGTCTTCGAGTA
genomic: ATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctttg ... ctaagtgcagGTTACATGATGTTGTCCACAGCGAGAAGCGGATATACCTCGTCTTCGAGTA
EST: gi|60398446|gb|DN231262.1|DN231262
EST:     ATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAG                         GTTACATGATGTTGTCCACAGCGAGAAGCGGATATACCTCGTCTTCGAGTA
genomic: ATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctttg ... ctaagtgcagGTTACATGATGTTGTCCACAGCGAGAAGCGGATATACCTCGTCTTCGAGTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAAGAAGATCCGCCTCGAGCAGGAGGACGAGGGCGTCCCGTCCACCGCCATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctttggttttatgcaacagcgggtaggtgtcgttttaggatgggattcgtttgctcgatggaaatgatggtgcgtatgtatgcaatcaagtaaaagtcagacgcaattttgatgctgcgatgccctgtagtgttggtacgctgacaagctttatactctcctaagtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG