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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAACGAGAACAGGAACGACAAAGGCAGGAAAAACTTGCTGAAGTTGGTCGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAGgtaattaaaccaatcatttttatgtcagtttgtttttttccttcttcattggataattgtgctaagcatgtggatttgttgacctcaatagaagtcattt...

Basic information

species Zea mays
transcript GRMZM2G022061_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G022061_T03 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os03g27840.1 (Oryza sativa), 5'ss of exon 11
------AGAAACGAGAACAGGAACGACAAAGGCAGGAAAAACTTGCTGAAGTTGGTCGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAGgtaattaaacc-aatcatttttatgtcagtttgtttttttccttcttcattggataattgtgctaagcatgtggatttgttgacctcaatagaagtcattt--
      ||||||||||||||||||| |||||||||||||||||||| || || ||||| |||| | |||| |||      || || |||||||| || |||||||||||||| ||   ||||| | ||   |||  |   |    || ||   |||   |   | | |||  | ||      |  |||    | | | || |||     
TAGCAAAGAAACGAGAACAGGAACGCCAAAGGCAGGAAAAACTTGCGGAGGTAGGTCGGTACAGGGGTCGAAGC------AGGAGCCTTAGCCGATCTCCACCAAGgtaattgaattgaatcagtatt-catcacatcaatgcaatc-ttggacatgaaactgtagggctgtg-atagaatctgcttgcttcctaaataattcaagctg
















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|6918688|gb|AW400218.1|AW400218
EST:     CGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAG                         AAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA
genomic: CGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAGgtaattaaac ... cctagcacagAAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA
EST: gi|37388853|gb|CF631641.1|CF631641
EST:     CGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAG                         AAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA
genomic: CGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAGgtaattaaac ... cctagcacagAAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA
EST: gi|89250973|gb|DY622759.1|DY622759
EST:     CGATACAAGCGTCGTAGCCGCAGTAGAAGTTTTAGCCGTTCCCCACCAAG                         AAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA
genomic: CGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAGgtaattaaac ... cctagcacagAAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA
EST: gi|37385048|gb|CF629639.1|CF629639
EST:     CGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAG                         AAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA
genomic: CGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAGgtaattaaac ... cctagcacagAAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA
EST: gi|24767845|gb|CA402981.1|CA402981
EST:     CGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAG                         AAGGTGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA
genomic: CGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAGgtaattaaac ... cctagcacagAAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA
EST: gi|113684467|gb|DW836849.1|DW836849
EST:     CCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAG                         AAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA
genomic: CCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAGgtaattaaac ... cctagcacagAAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA
EST: gi|211251413|gb|FL479559.1|FL479559
EST:     CGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAG                         AAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAAAAGCCCAAGAAGGTA
genomic: CGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAGgtaattaaac ... cctagcacagAAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA
EST: gi|60400201|gb|DN233008.1|DN233008
EST:     CGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAG                         AAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA
genomic: CGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAGgtaattaaac ... cctagcacagAAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA
EST: gi|40335728|gb|CK369798.1|CK369798
EST:     CGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAG                         AAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA
genomic: CGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAGgtaattaaac ... cctagcacagAAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA
EST: gi|31360537|gb|CD444894.1|CD444894
EST:     CGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAG                         AAGGTGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA
genomic: CGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAGgtaattaaac ... cctagcacagAAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA
EST: gi|211429291|gb|FL073230.1|FL073230
EST:     CGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAG                         AAGGCGGCGATATAGCAGAAGCCGTAGTAGGA
genomic: CGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAGgtaattaaac ... cctagcacagAAGGCGGCGATATAGCAGAAGCCGTAGTAGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAACGAGAACAGGAACGACAAAGGCAGGAAAAACTTGCTGAAGTTGGTCGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAGgtaattaaaccaatcatttttatgtcagtttgtttttttccttcttcattggataattgtgctaagcatgtggatttgttgacctcaatagaagtcattt

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