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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATGTTTTTCTGCTCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGTCTCTAAGAAGgcaataatctttccctgcccactttcttgccccggccccggtttaatgcattcttatttattttagcttcttgacttgcatttcttgcatattacctgtgcatgtcgttttttccag

Basic information

species Zea mays
transcript GRMZM2G375002_T03
intron # 3
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 3
lower sequence: LOC_Os02g58730.2 (Oryza sativa), 5'ss of exon 3
TTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATGTTTTTCTGCTCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGTCTCTAAGAAGgcaataatctttccctgcccactttcttgccccggccccggtttaatgcattcttatttattttagcttcttgacttgcatttcttgcatattacctgtgcatgtcgttttttccag
 |||||||| || || ||||||||||||||||| ||||||||||| ||||| ||||||||||| |||||||||||||||||||||||||| ||||| ||||||||||  | |  | ||||||||||||  | |   | |  |  | | |   ||||  |   | | | | ||  ||||||   ||  || || |  | |   ||| ||         
CTACAATAGGCTACGCCCGTTGAGCTATCGTGGCGCTGATGTTTTCCTGCTGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaatcttgccgcccactttctttgctctctctccatgaagtac---cttagcttagtcaacctgttatcttgca---ctgacacat-atatatttctgttgtcag------

upper sequence: GRMZM2G375002_T03 (Zea mays), 5'ss of exon 3
lower sequence: PP1S165_55V6.1 (Physcomitrella patens), 5'ss of exon 3
TTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATGTTTTTCTGCTCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGTCTCTAAGAAGgcaataatctttccctgcc-cactttcttgccccggcccc---ggtttaatgcattcttatttattttagcttcttgacttgcatttcttgcatattacctgtgcatgtcgttttttccag
||| || || || || ||  |||| ||  | ||||||||||||||||| || || || ||||||||||||||||| || ||||||||  |||| ||||||| | ||  | |   |  |       ||        | ||    |  |  ||||       |||  || |  | ||  ||| |  |   ||||||     |||   || |  |   |  |||
TTATAACAGGCTTCGACCTCTGAGTTACAGGGGTGCTGATGTTTTTCTACTAGCATTCTCTCTTATCAGCAAAGCTAGTTATGAGAACATCTCAAAGAAGgtactagccctctgcatcagtggcctcacatttgtgtcctaaggagtagatgcgcgaccgtttggttga-ttgctgtactcg-gtggattgcattgattctgacgatttattacatggcag

upper sequence: GRMZM2G375002_T03 (Zea mays), 5'ss of exon 3
lower sequence: PP1S126_126V6.2 (Physcomitrella patens), 5'ss of exon 4
TTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATGTTTTTCTGCTCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGTCTCTAAGAAGgcaataatctttc-------cctgcccactttcttgccccggc--cccggtttaatgcattcttatttattttagcttcttgac--ttgcatttcttgcatattacctgtgcatgtcgttttttccag
|||||| ||||| || ||  |||| ||  | || |||||||||||||| || || ||||||||||||||||| || || ||||| ||| |||| ||||||| | | || |          | || |  | |  | |    | |  |  | || ||    ||   |  ||    | |   | ||   |   ||||    ||||||  |||    ||   |   || |||
TTACAACAGACTTCGACCTCTGAGTTACAGAGGCGCTGATGTTTTTCTTCTAGCATTTTCTCTTATCAGCAAGGCTAGTTATGAAAATATCTCAAAGAAGgtagttatttccttgacgatcttgtcttcgtgttagggttgacgacttgcttgaaaatgtttcaaagtagagaaccgcgtagagggtgctatttacgtcatattttctgatattgcattgcattgcag

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:     TCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGTCTCTAAGAAG                         TGGGTTCCTGAATTAAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTT
genomic: TCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGTCTCTAAGAAGgcaataatct ... ttttttccagTGGGTTCCTGAATTAAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTT
EST: gi|211164770|gb|FK955409.1|FK955409
EST:     TCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGTCTCTAAGAAG                         TGGGTTCCTGAATTAAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTT
genomic: TCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGTCTCTAAGAAGgcaataatct ... ttttttccagTGGGTTCCTGAATTAAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTT
EST: gi|14242930|gb|BG840265.2|BG840265
EST:     TCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGTCTCTAAGAAG                         TGGGTTCCTGAATTAAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTT
genomic: TCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGTCTCTAAGAAGgcaataatct ... ttttttccagTGGGTTCCTGAATTAAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTT
EST: gi|211164778|gb|FK955417.1|FK955417
EST:     TCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGTCTCTAAGAAG                         TGGGTTCCTGAATTAAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGNT
genomic: TCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGTCTCTAAGAAGgcaataatct ... ttttttccagTGGGTTCCTGAATTAAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTT
EST: gi|211236576|gb|FK955423.1|FK955423
EST:     TCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGTCTCTAAGAAG                         TGGGTTCCTGAATTAAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGGT
genomic: TCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGTCTCTAAGAAGgcaataatct ... ttttttccagTGGGTTCCTGAATTAAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTT
EST: gi|211163178|gb|FK955405.1|FK955405
EST:     TCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGTCTCTAAGAAG                         TGGGTTCCTGAATTAAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTT
genomic: TCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGTCTCTAAGAAGgcaataatct ... ttttttccagTGGGTTCCTGAATTAAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTT
EST: gi|211164773|gb|FK955412.1|FK955412
EST:     TCGCCNTTNCTCTTATCAGCANAGCAAGCTATGANAATGTCTCTAAGAAG                         TGGGTTCCTTGAATTAAGGCACTATGCTCCTG-CGTGCCCATAATCCTTGT
genomic: TCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGTCTCTAAGAAGgcaataatct ... ttttttccagTGGGTTCCT-GAATTAAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGT
EST: gi|211163176|gb|FK955403.1|FK955403
EST:     TCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGTCTCTAAGAAG                         TGGGTTCCTGAATTAAGGCACTATGCT
genomic: TCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGTCTCTAAGAAGgcaataatct ... ttttttccagTGGGTTCCTGAATTAAGGCACTATGCT
EST: gi|211164772|gb|FK955411.1|FK955411
EST:     TCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGTCTCTAAGAAG                         TGGGTTCCTGAATTAAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTT
genomic: TCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGTCTCTAAGAAGgcaataatct ... ttttttccagTGGGTTCCTGAATTAAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTT
EST: gi|32827834|gb|CD967512.1|CD967512
EST:     TCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGTCTCTAAGAAG                         TGGGTTCCTGAATTA
genomic: TCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGTCTCTAAGAAGgcaataatct ... ttttttccagTGGGTTCCTGAATTA
EST: gi|211163175|gb|FK955402.1|FK955402
EST:     TCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGTCTCTAAGAAG                         TGGGTTCCTGAATTAAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTT
genomic: TCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGTCTCTAAGAAGgcaataatct ... ttttttccagTGGGTTCCTGAATTAAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTT
EST: gi|32936373|gb|CF041192.1|CF041192
EST:     TCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGTCTCTAAGAAG                         TGGGTTCCTGAATTA
genomic: TCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGTCTCTAAGAAGgcaataatct ... ttttttccagTGGGTTCCTGAATTA
EST: gi|211385329|gb|FL304291.1|FL304291
EST:     TCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGTCTCTAAGAAG                         TGGGTTCCTGAATTAAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTT
genomic: TCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGTCTCTAAGAAGgcaataatct ... ttttttccagTGGGTTCCTGAATTAAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTT
EST: gi|211164771|gb|FK955410.1|FK955410
EST:     TCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGTCTCTAAGAAG                         TGGGTTCCTGAATTAAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTT
genomic: TCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGTCTCTAAGAAGgcaataatct ... ttttttccagTGGGTTCCTGAATTAAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTT
EST: gi|31558461|gb|CD527673.1|CD527673
EST:     TCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGTCTCTAAGAAG                         TGGGTTCCTGAATTAAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTT
genomic: TCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGTCTCTAAGAAGgcaataatct ... ttttttccagTGGGTTCCTGAATTAAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATGTTTTTCTGCTCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGTCTCTAAGAAGgcaataatctttccctgcccactttcttgccccggccccggtttaatgcattcttatttattttagcttcttgacttgcatttcttgcatattacctgtgcatgtcgttttttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG