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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggctgaatctactttttgcagaattcggaagatttatgagtgtcactaccgtttgctcattttcttgcttcttttggccaattcttttgacatcaccatgcagGTCAACAGTGGGGTATTAAGTGTGTGCACTGCATTCTTATCTGGCGAGCCAGCAACTAGGCTCAGATCCCAAGAACTGCAGCAGCTCATCGCCGCATTGC

Basic information

species Zea mays
transcript GRMZM2G462803_T04
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G462803_T04 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g21080.1 (Oryza sativa), 3'ss of exon 11
-------gtgaggctgaatctactttttgcagaattcggaagattt---atgagtgtcactaccgtttgctcattttcttgcttcttttggccaattcttttga---catcaccatgcagGTCAACAGTGGGGTATTAAGTGTGTGCACTGCATTCTTATCTGGCGAGCCAGCAACTAGGCTCAGATCCCAAGAACTGCAGCAGCTCATCGCCGCATTGC
       || || ||| | ||   || ||||||||| | |  ||||   | || || |   |   | ||||| | |  || |||  ||| || || | ||   |   | | || |||||||| || ||||| |||||||||||||||||||||||||||||||| ||||| |||||||||||| |||| ||||||||||||||||||||||| |||||||
gtaagctgtaagcctgtaact--cttgtgcagaatttgaaccattttttaagaatgccttgagtatatgctcctctattttctttcttttgctaacttttacaaaaacctgacgatgcagGTAAATAGTGGTGTATTAAGTGTGTGCACTGCATTCTTATCTGGTGAGCCCGCAACTAGGCTCCGATCTCAAGAACTGCAGCAGCTCATCGCTGCATTGC

upper sequence: GRMZM2G462803_T04 (Zea mays), 3'ss of exon 7
lower sequence: AT4G16340.1 (Arabidopsis thaliana), 3'ss of exon 29
gtgaggctgaatctactttttgcagaattcggaagatttatgagtgtcactaccgtttgctcattttcttgcttcttttggccaattcttttgacatcaccatgcagGTCAACAGTGGGGTATTAAGTGTGTGCACTGCATTCTTATCTGGCGAGCCAGCAACTAGGCTCAGATCCCAAGAACTGCAGCAGCTCATCGCCGCATTGC
       ||  | |   |     |  ||  |      ||||   |     |       |   |  | ||    || | ||       ||||  |    |  |||||||| ||||||||||| || || |||||||| || |||||||| || ||||| ||||| ||  |  | || || ||||||||||| || ||||| ||| |||
------gtgggtttttctcccataatatctgtg----ttatagattgtgttgtaaaacgtagaaatgctca--tcatatg------cctttccatggaaatatgcagGTGAACAGTGGGGTGTTGAGCGTGTGCACAGCTTTCTTATCAGGAGAGCCTGCAACGAGATTGCGTTCACAGGAACTGCAGCAACTAATCGCGGCACTGC
















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|32164851|gb|CD670169.1|CD670169
EST:     CAAGGCTTCAAAGCTTGCAAAGGATACTCCAAGGAAGTGTGGCTGTGCAG                         GTCAACAGTGGGGTATTAAGTGTGTGCACTGCATTCTTATCTGGCGAGCCA
genomic: CAAGGCTTCAAAGCTTGCAAAGGATACTCCAAGGAAGTGTGGCTGTGCAGgtgaggctga ... caccatgcagGTCAACAGTGGGGTATTAAGTGTGTGCACTGCATTCTTATCTGGCGAGCCA
EST: gi|32832902|gb|CD972580.1|CD972580
EST:     CAAGGCTTCAAAGCTTGCAAAGGATACTCCAAGGAAGTGTGGCTGTGCAG                         GTCAACAGTGGGGTATTAAGTGTGTGCACTGCATTCTTATCTGGCGAGCCA
genomic: CAAGGCTTCAAAGCTTGCAAAGGATACTCCAAGGAAGTGTGGCTGTGCAGgtgaggctga ... caccatgcagGTCAACAGTGGGGTATTAAGTGTGTGCACTGCATTCTTATCTGGCGAGCCA
EST: gi|83278442|gb|DV942450.1|DV942450
EST:     CAAGGCTTCAAAGCTTGCAAAGGATACTCCAAGGAAGTGTGGCTGTGCAG                         GTCAACAGTGGGGTATTAAGTGTGTGCACTGCATTCTTATCTGGCGAGCCA
genomic: CAAGGCTTCAAAGCTTGCAAAGGATACTCCAAGGAAGTGTGGCTGTGCAGgtgaggctga ... caccatgcagGTCAACAGTGGGGTATTAAGTGTGTGCACTGCATTCTTATCTGGCGAGCCA
EST: gi|37401321|gb|CF638023.1|CF638023
EST:     CAAGGCTTCAAAGCTTGCAAAGGATACTCCAAGGAAGTGTGGCTGTGCAG                         GTCAACAGTGGGGTATTAAGTGTGTGCACTGCATTCTTATCTGGCGAGCCA
genomic: CAAGGCTTCAAAGCTTGCAAAGGATACTCCAAGGAAGTGTGGCTGTGCAGgtgaggctga ... caccatgcagGTCAACAGTGGGGTATTAAGTGTGTGCACTGCATTCTTATCTGGCGAGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgtttgctcattttcttgcttcttttggccaattcttttgacatcaccatgcagGTCAACAGTGGGGTATTAAGTGTGTGCACTGCATTCTTATCTGGCGAGCCAGCAACTAGGCTCAGATCCCAAGAACTGCAGCAGCTCATCGCCGCATTGC
                                    ttttgac  putative branch site (score: 3)
                               aattctttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggctgaatctactttttgcagaattcggaagatttatgagtgtcactaccgtttgctcattttcttgcttcttttggccaattcttttgacatcaccatgcagGTCAACAGTGGGGTATTAAGTGTGTGCACTGCATTCTTATCTGGCGAGCCAGCAACTAGGCTCAGATCCCAAGAACTGCAGCAGCTCATCGCCGCATTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA