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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCAAGTAATGTTCTCTATATCCCCTCAAGAACATTATTTTGACTGCCCATACCAGATAAGCTCAGAGGCAGAGGGTCAAACATATAAGGATGCATTGgtatgtaccttcttttactaattcgtttttatttattatgtttagtcaccatcaatatgatacatccatgtaaaggtttaagcttaaaggtggtgactag...

Basic information

species Zea mays
transcript GRMZM2G003096_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G003096_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g07090.1 (Oryza sativa), 5'ss of exon 7
GGCAAGTAATGTTCTCTATATCCCCTCAAGAACATTATTTTGACTGCCCATACCAGATAAGCTCAGAGGCAGAGGGTCAAACATATAAGGATGCATTGgtatgtaccttcttttactaattcgtttttatttattatgtttagtcaccatcaatatgatacatccatgtaaaggtttaagcttaaaggtggtgactag
| |||||||||||||||| ||  |||||||||||||| |||||||||||||||||| ||||||| || |||   |||||||| |||  ||||||| |||||||| |||| || ||        |  |       | ||| |    |   |     |   | |  ||  |  ||||    ||  | | ||    || ||
GCCAAGTAATGTTCTCTACATGTCCTCAAGAACATTACTTTGACTGCCCATACCAGTTAAGCTCTGAAGCAATTGGTCAAACGTATCTGGATGCACTGgtatgtgccttattgtaggtcagaataatagagctgtgtgtgtgacgattgttttattagcatactcagttctaggtggttgcccatatgttacaacgag
















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|50334525|gb|CO529651.1|CO529651
EST:     CATACCAGATAAGCTCAGAGGCAGAGGGTCAAACATATAAGGATGCATTG                         GTTTGCAGTGTAAATCTTATGGAGGGTGATATAATTGTGAGTGGTTCAGAT
genomic: CATACCAGATAAGCTCAGAGGCAGAGGGTCAAACATATAAGGATGCATTGgtatgtacct ... ggtctgtcagGTTTGCAGTGTAAATCTTATGGAGGGTGATATAATTGTGAGTGGTTCAGAT
EST: gi|89249663|gb|DY621449.1|DY621449
EST:     CATACCAGATAAGCTCAGAGGCAGAGGGTCAAACATATAAGGATGCATTG                         GTTTGCAGTGTAAATCTTATGGAGGGTGATATAATTGTGAGTGGTTCAGAT
genomic: CATACCAGATAAGCTCAGAGGCAGAGGGTCAAACATATAAGGATGCATTGgtatgtacct ... ggtctgtcagGTTTGCAGTGTAAATCTTATGGAGGGTGATATAATTGTGAGTGGTTCAGAT
EST: gi|50334526|gb|CO529652.1|CO529652
EST:     CATACCAGATAAGCTCAGAGGCAGAGGGTCAAACATATAAGGATGCATTG                         GTTTGCAGTGTAAATCTTA
genomic: CATACCAGATAAGCTCAGAGGCAGAGGGTCAAACATATAAGGATGCATTGgtatgtacct ... ggtctgtcagGTTTGCAGTGTAAATCTTA
EST: gi|211439719|gb|FL188857.1|FL188857
EST:     CATACCAGATAAGCTCAGAGGCAGAGGGTCAAACATATAAGGATGCATTG                         GTTTGCAGTGTAAATCTCATGGAGGGTGATATAATTGTGAGTGGTTCAGAT
genomic: CATACCAGATAAGCTCAGAGGCAGAGGGTCAAACATATAAGGATGCATTGgtatgtacct ... ggtctgtcagGTTTGCAGTGTAAATCTTATGGAGGGTGATATAATTGTGAGTGGTTCAGAT
EST: gi|16378003|gb|BI992233.1|BI992233
EST:     CATACCAGATAAGCTCAGAGGCAGAGGGTCAAACATATAAGGATGCATTG                         GTTTGCAGTGTAAATCTTATGGAGGGTGATATAATTGTGAGTGGTTCAGAT
genomic: CATACCAGATAAGCTCAGAGGCAGAGGGTCAAACATATAAGGATGCATTGgtatgtacct ... ggtctgtcagGTTTGCAGTGTAAATCTTATGGAGGGTGATATAATTGTGAGTGGTTCAGAT
EST: gi|211439722|gb|FL188860.1|FL188860
EST:     CATACCAGATAAGCTCAGAGGCAGAGGGTCAAACATATAAGGATGCATTG                         GTTTGCAGTGTAAATCTCATGGAGGGTGATATAATTGTGAGTGGTTCAGAT
genomic: CATACCAGATAAGCTCAGAGGCAGAGGGTCAAACATATAAGGATGCATTGgtatgtacct ... ggtctgtcagGTTTGCAGTGTAAATCTTATGGAGGGTGATATAATTGTGAGTGGTTCAGAT
EST: gi|211322726|gb|FL462750.1|FL462750
EST:     CATACCAGATAAGCTCAGAGGCAGAGGGTCAAACATATAAGGATGCATTG                         GTTTGCAGTGTAAATCTCATGGAGGGTGATATAATTGTGAGTGGTTCAGAT
genomic: CATACCAGATAAGCTCAGAGGCAGAGGGTCAAACATATAAGGATGCATTGgtatgtacct ... ggtctgtcagGTTTGCAGTGTAAATCTTATGGAGGGTGATATAATTGTGAGTGGTTCAGAT
EST: gi|211439720|gb|FL188858.1|FL188858
EST:     CATACCAGATAAGCTCAGAGGCAGAGGGTCAAACATATAAGGATGCATTG                         GTTTGCAGTGTAAATCTCATGGAGGGTGATATAATTGTGAGTGGTTCAGAT
genomic: CATACCAGATAAGCTCAGAGGCAGAGGGTCAAACATATAAGGATGCATTGgtatgtacct ... ggtctgtcagGTTTGCAGTGTAAATCTTATGGAGGGTGATATAATTGTGAGTGGTTCAGAT
EST: gi|211537751|gb|FL446842.1|FL446842
EST:     CATACCAGATAAGCTCAGAGGCAGAGGGTCAAACATATAAGGATGCATTG                         GTTTGCAGTGTAAATCTCATGGAGGGTGATATAATTGTGAGTGGTTCAGAT
genomic: CATACCAGATAAGCTCAGAGGCAGAGGGTCAAACATATAAGGATGCATTGgtatgtacct ... ggtctgtcagGTTTGCAGTGTAAATCTTATGGAGGGTGATATAATTGTGAGTGGTTCAGAT
EST: gi|211439718|gb|FL188856.1|FL188856
EST:     CATACCAGATAAGCTCAGAGGCAGAGGGTCAAACATATAAGGATGCATTG                         GTTTGCAGTGTAAATCTCATGGAGGGTGATATAATTGTGAGTGGTTCAGAT
genomic: CATACCAGATAAGCTCAGAGGCAGAGGGTCAAACATATAAGGATGCATTGgtatgtacct ... ggtctgtcagGTTTGCAGTGTAAATCTTATGGAGGGTGATATAATTGTGAGTGGTTCAGAT
EST: gi|76281783|gb|DV021351.1|DV021351
EST:     CATCCCAGATAAGCTCAGAGGCAGAGGGTCAAACATATAAGGATGCATTG                         GTTTGCAGTGTAAATCTTATGGAGGGTGATATAATTGTGAGTGGTTCAGAT
genomic: CATACCAGATAAGCTCAGAGGCAGAGGGTCAAACATATAAGGATGCATTGgtatgtacct ... ggtctgtcagGTTTGCAGTGTAAATCTTATGGAGGGTGATATAATTGTGAGTGGTTCAGAT
EST: gi|89249664|gb|DY621450.1|DY621450
EST:     CATACCAGATAAGCTCAGAGGCAGAAGGTCAAACATATAAGGATGCATTG                         GTTTGCAGTGTAAATCCTATGGAAGGTGATAT
genomic: CATACCAGATAAGCTCAGAGGCAGAGGGTCAAACATATAAGGATGCATTGgtatgtacct ... ggtctgtcagGTTTGCAGTGTAAATCTTATGGAGGGTGATAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCAAGTAATGTTCTCTATATCCCCTCAAGAACATTATTTTGACTGCCCATACCAGATAAGCTCAGAGGCAGAGGGTCAAACATATAAGGATGCATTGgtatgtaccttcttttactaattcgtttttatttattatgtttagtcaccatcaatatgatacatccatgtaaaggtttaagcttaaaggtggtgactag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG