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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttcccttggcattaaaatccttctttgtatctgcattccttcctgctccaaagtacagtaactgatattctatgatttttttag

Basic information

species Zea mays
transcript GRMZM2G375002_T03
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G375002_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g58730.2 (Oryza sativa), 5'ss of exon 2
GACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtc---tcttcccttggcattaa--aatccttctttgtatct----gcattccttcctgctccaaagt----acagtaactgata-ttctatgatttttttag------
||||||||||||||||| || || ||||||||||| ||||||||||| || ||||||||||| ||||||||  |||||||||||||||||      ||||| |    ||||   || | |   |  | ||      || | | |    | ||  ||    | | ||| | | | ||  |  | |||   ||      
GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctactttcccctccttttaatggatgcatgcgtaaacctccttatatacatccacctttcacggtcatcaaaataaataaaaatttgacaaatttaacaggacaag

upper sequence: GRMZM2G375002_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g58730.1 (Oryza sativa), 5'ss of exon 2
GACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtct---cttcccttggcattaa--aatccttctttgtatctgc----attccttcctgctccaaagt----acagtaactgata-ttctatgatttttttag
||||||||||||||||| || || ||||||||||| ||||||||||| || ||||||||||| ||||||||  |||||||||||||||||      ||||| |    ||||   || | |   |  | || |    || | | |    | ||  ||    | | ||| | | | ||  |  | |||   ||
GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctactttcccctccttttaatggatgcatgcgtaaacctccttatatacatccacctttcacggtcatcaaaataaataaaaatttgacaaatttaacag

upper sequence: GRMZM2G375002_T03 (Zea mays), 5'ss of exon 2
lower sequence: AT4G35020.3 (Arabidopsis thaliana), 5'ss of exon 4
GACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttcccttggcattaaaatccttctttgtatctgcattccttcctgctccaaagtacagtaactgatattctatgatttttttag----
|| ||||| |||||||||||||| || ||||||||||||||  | ||||| || | |||| ||||||||||  |||||||||| |||||    ||          |   ||  || | | | | || ||| | ||||  |||| ||   ||| | |  | || | ||| ||  | |     
GATTATGTGCCAACTGTGTTCGATAATTTCAGTGCCAATGTGATTGTTGATGGCAACACTATCAACTTGGGATTGTGGGATACTGCAGgcaagttgttac----cttggatttttttgtct-tttgaatttcctcctcttccagag---agtcatttgtgtttt-tgacttggtgaaacag

upper sequence: GRMZM2G375002_T03 (Zea mays), 5'ss of exon 2
lower sequence: PP1S257_74V6.1 (Physcomitrella patens), 5'ss of exon 2
GACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc--------ttggcattaaaatccttctttgt-atctgcattccttcctgctccaaagtacagtaactgatattctatgatttttttag--
|| || || || ||||| |||||||||||||| || ||||| ||||| || ||||  || |||||| |||| || |||||||||||||||  |   |         | | | | | | | |    |||| |  |||| |  |   || |    |   | ||   |  |   || ||||||  | |   
GATTACGTCCCTACTGTATTCGACAACTTCAGCGCGAATGTCGTGGTCGATGGGAATACCGTCAACCTGGGACTATGGGATACAGCAGgtaacacacgcaataggatagacttcacagttcgcggttgtcagttgcactggtagttggtgaggaagtcggtgtttattcacctgtgatttagtgaaag

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|211163171|gb|FK955398.1|FK955398
EST:     TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG                         GACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
genomic: TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
EST: gi|211164770|gb|FK955409.1|FK955409
EST:     TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG                         GACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
genomic: TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
EST: gi|14242930|gb|BG840265.2|BG840265
EST:     TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG                         GACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
genomic: TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
EST: gi|211163177|gb|FK955404.1|FK955404
EST:     TGTTGTGGTTGACGGGAGCACTGTCAACTTNGGTCTGTGGGATACAGCAG                         GACAAGAAGATTACRATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
genomic: TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
EST: gi|211164778|gb|FK955417.1|FK955417
EST:     TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG                         GACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
genomic: TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
EST: gi|32909548|gb|CF014360.1|CF014360
EST:     TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG                         GACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCG
genomic: TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCG
EST: gi|211236584|gb|FK955431.1|FK955431
EST:     TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG                         GACAAGAAGATTACAATATGACTGCGTCCGTTGAGCTATCGTGGTGCTGAT
genomic: TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATA-GACTGCGTCCGTTGAGCTATCGTGGTGCTGAT
EST: gi|211236576|gb|FK955423.1|FK955423
EST:     TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG                         GACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
genomic: TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
EST: gi|211163178|gb|FK955405.1|FK955405
EST:     TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG                         GACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
genomic: TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
EST: gi|211164773|gb|FK955412.1|FK955412
EST:     TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG                         GACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
genomic: TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
EST: gi|211163176|gb|FK955403.1|FK955403
EST:     TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG                         GACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
genomic: TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
EST: gi|211164772|gb|FK955411.1|FK955411
EST:     TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG                         GACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
genomic: TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
EST: gi|211163179|gb|FK955406.1|FK955406
EST:     TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG                         GACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTA
genomic: TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTA
EST: gi|32827834|gb|CD967512.1|CD967512
EST:     TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG                         GACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
genomic: TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
EST: gi|211163175|gb|FK955402.1|FK955402
EST:     TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG                         GACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
genomic: TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
EST: gi|12047201|gb|BF729340.1|BF729340
EST:     TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG                         GACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
genomic: TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
EST: gi|32858427|gb|CD998108.1|CD998108
EST:     TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG                         GACAAGAAGATTACAATAGACTTGCGTCCGTTG
genomic: TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACT-GCGTCCGTTG
EST: gi|32936373|gb|CF041192.1|CF041192
EST:     TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG                         GACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
genomic: TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
EST: gi|211385329|gb|FL304291.1|FL304291
EST:     TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG                         GACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
genomic: TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
EST: gi|211236582|gb|FK955429.1|FK955429
EST:     TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG                         GACAAGAAGAT-ACAATAGACTGCG
genomic: TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACTGCG
EST: gi|211164771|gb|FK955410.1|FK955410
EST:     TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG                         GACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
genomic: TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
EST: gi|31558461|gb|CD527673.1|CD527673
EST:     TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG                         GACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
genomic: TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
EST: gi|33467050|gb|CF244099.1|CF244099
EST:     TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACCGCAG                         GACAAGAAGATTACAATAGACTGCGTCC
genomic: TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACTGCGTCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttcccttggcattaaaatccttctttgtatctgcattccttcctgctccaaagtacagtaactgatattctatgatttttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA