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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCTCCCCTCCCCCATGGCGCTCAAGCAGAAGGACACCGACGCCGCCGCCACCGCCACCGGTACCAAGAAGCGCCGCCGCGTCTTCTTCTCCGACACCGgtaccaaactcgatctacgcatcaccctctcatttccggcgattcgtgcgtctggctgcgagtcaggcgctgcagatcccattcgtgttgtgacgcgcct...

Basic information

species Zea mays
transcript GRMZM5G851405_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G851405_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os09g17850.1 (Oryza sativa), 5'ss of exon 1
--GTCCTCCCCTCCC-------CCATGGCGCTCAAGCAGAAGGACACCGACGCCGCCGCCACCGCCACCGGTACCAAGAAGCGCCGCCGCGTCTTCTTCTCCGACACCGgtaccaaactcgatctacgcatcaccctctcatttccggcgattcgtgcgtctggctgcgagtc--aggcgctgc--agatcccattcgtgttgtgacgcgcct---
   ||||||||  ||       |||||||||||||||||||||  |||||||||||||||         |   ||||||||||||||||||||  |||||||| || ||||||   || |      | | ||  | ||||   |||  ||||||| | |  |  || || ||    ||||| |    | |  || ||||| || | |||||     
TCCTCCTCCCCCTCCGCACCAGCCATGGCGCTCAAGCAGAAGGGGACCGACGCCGCCGCC---------GACCCCAAGAAGCGCCGCCGCGTCGGCTTCTCCGGCATCGgtacggcacccagct--cccttcgtcttctc---tcc--cgattcgcgggatttccttcgtgttttgggcgcgggtggggtggcaatcgtggtgcggcgcgctcttc
















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|211157917|gb|FL378567.1|FL378567
EST:     CACCGCGACCGGTACCAAGAAGCGCCGCCGCGTCTTCTTCTCCGACACCG                         ATGCTGGTGTTGAGGCAAATGAGTGTATGAAAGTGTTTCTAG
genomic: CACCGCCACCGGTACCAAGAAGCGCCGCCGCGTCTTCTTCTCCGACACCGgtaccaaact ... tgttgtgcagATGCTGGTGTTGAGGCAAATGAGTGTATGAAAGTGTTTCTAG
EST: gi|76290309|gb|DV029877.1|DV029877
EST:     CACCGCCACCGGTACCAAGAAGCGCCGCCGCGTCTTCTTCTCCGACACCG                         ATGCTGGTGTTGAGGCAAATGAGTGTATGA
genomic: CACCGCCACCGGTACCAAGAAGCGCCGCCGCGTCTTCTTCTCCGACACCGgtaccaaact ... tgttgtgcagATGCTGGTGTTGAGGCAAATGAGTGTATGA
EST: gi|211393307|gb|FL420230.1|FL420230
EST:     CACCGCCACCGGTACCAAGAAGCGCCGCCGCGTCTTCTTCTCCGACACCG                         ATGCTGGTGTTGAGGCAAATGAGTGTATGAAAGTGTTTCTAGTATGGAAT
genomic: CACCGCCACCGGTACCAAGAAGCGCCGCCGCGTCTTCTTCTCCGACACCGgtaccaaact ... tgttgtgcagATGCTGGTGTTGAGGCAAATGAGTGTATGAAAGTGTTTCTAGTATGGAAT
EST: gi|211343698|gb|FL394268.1|FL394268
EST:     CACCGCCACCGGTACCAAGAAGCGCCGCCGCGTCTTCTTCTCCGACACCG                         ATGCTGGTGTTGAGGCAAATGAGTGTATGAAAGTGTTTCTAGTATGGAAT
genomic: CACCGCCACCGGTACCAAGAAGCGCCGCCGCGTCTTCTTCTCCGACACCGgtaccaaact ... tgttgtgcagATGCTGGTGTTGAGGCAAATGAGTGTATGAAAGTGTTTCTAGTATGGAAT
EST: gi|211437212|gb|FL420722.1|FL420722
EST:     CACCGCCACCGGTACCAAKAAGCGCCGCCGCGTCTTCTTCTCCGACACCG                         ATGCTGGTGTTGAGGCAAATGAGTGTATGAAAGTGTTTCTAG
genomic: CACCGCCACCGGTACCAAGAAGCGCCGCCGCGTCTTCTTCTCCGACACCGgtaccaaact ... tgttgtgcagATGCTGGTGTTGAGGCAAATGAGTGTATGAAAGTGTTTCTAG
EST: gi|71766135|gb|DR964072.1|DR964072
EST:     CACCGCCACCGGTACCAAGAAGCGCCGCCGCGTCTTCTTCTCCGACACCG                         ATGCTGGTGTTGAGGCAAATGAGTGTATGAAAGTGTTTCTAG
genomic: CACCGCCACCGGTACCAAGAAGCGCCGCCGCGTCTTCTTCTCCGACACCGgtaccaaact ... tgttgtgcagATGCTGGTGTTGAGGCAAATGAGTGTATGAAAGTGTTTCTAG
EST: gi|211202431|gb|FL416111.1|FL416111
EST:     CACCGCCACCGGTACCAAGAAGCGCCGCCGCGTCTTCTTCTCCGACACCG                         ATGCTGGTGTTGAGGCAAATGAGTGTATGAAAGTGTTTCTAG
genomic: CACCGCCACCGGTACCAAGAAGCGCCGCCGCGTCTTCTTCTCCGACACCGgtaccaaact ... tgttgtgcagATGCTGGTGTTGAGGCAAATGAGTGTATGAAAGTGTTTCTAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCTCCCCTCCCCCATGGCGCTCAAGCAGAAGGACACCGACGCCGCCGCCACCGCCACCGGTACCAAGAAGCGCCGCCGCGTCTTCTTCTCCGACACCGgtaccaaactcgatctacgcatcaccctctcatttccggcgattcgtgcgtctggctgcgagtcaggcgctgcagatcccattcgtgttgtgacgcgcct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC