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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcgtaccgatggtccatgcatgcactaagcttgttggtttctgaatggaaggagcgacgtgtggagcttgttctgaaccccaaagcttgctgcttgcagGTTGCGCCGGTGAAAAGCCAGCTGAGCAACGCCGCGGAGCAGATGCAGGTCACGCTGGCTCCTCACTCCTTCACCGCCTTCGATCTGGCGCTGGCTGAGC

Basic information

species Zea mays
transcript GRMZM2G006130_T05
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006130_T05 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os11g03730.3 (Oryza sativa), 3'ss of exon 17
gtatgcgtaccgatggtccatgcatgcactaagcttgttg-gtttctgaatggaaggagcgacgtgtggagcttgt--tctgaaccccaaagcttgctgct---------tgcagGTTGCGCCGGTGAAAAGCCAGCTGAGCAACGCCGCGGAGCAGATGCAGGTCACGCTGGCTCCTCACTCCTTCACCGCCTTCGATCTGGCGCTGGCTGAGC
||| ||  ||  ||     |    |  |||     |  ||    | | ||||    |       |||||   | ||  |||||| || ||   |||||  |         |||||||||  || || |||||||||||   ||| || || ||||||||||| |||||||| ||||||||||| ||| || | |||||||| ||||| ||  || 
gtaagcaaac--atttctgacttct-tactggatgtaatgcacatatcaatgtctagtagagtttgtggttttggtcatctgaagccaaagctttgctcatgacaaccaatgcagGTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTCACGCTTGCTCCTCACTCTTTCTCCTCATTCGATCTTGCGCTTGCCCAGT

upper sequence: GRMZM2G006130_T05 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 16
gtatgcgtaccgatggtccatgcatgcactaagcttgttg-gtttctgaatggaaggagcgacgtgtggagcttgt--tctgaaccccaaagcttgctgct---------tgcagGTTGCGCCGGTGAAAAGCCAGCTGAGCAACGCCGCGGAGCAGATGCAGGTCACGCTGGCTCCTCACTCCTTCACCGCCTTCGATCTGGCGCTGGCTGAGC
||| ||  ||  ||     ||   |  |||     |  ||    | | ||||    |       |||||   | ||  |||||| || ||   |||||  |         |||||||||  || || |||||||||||   ||| || || ||||||||||| |||||||| ||||||||||| ||| || | |||||||| ||||| ||  || 
gtaagcaaac--atttctgatttct-tactggatgtaatgcacatatcaatgtctagtagagtttgtggttttggtcatctgaagccaaagctttgctcatgataaccaatgcagGTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTCACGCTTGCTCCTCACTCTTTCTCCTCATTCGATCTTGCGCTTGCCCAGT
















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|4647310|gb|AI622385.1|AI622385
EST:     TCACGTCTGGCAACGTCATGGACGAGAACTCCTTCAGTAACCCGAACAAG                         GTTGCGCCGGTGAAAAGCCAGCTGAGCAACGCCGCGGAGCAGATGCAGGTC
genomic: TCACGTCTGGCAACGTCATGGACGAGAACTCCTTCAGTAACCCGAACAAGgtatgcgtac ... ctgcttgcagGTTGCGCCGGTGAAAAGCCAGCTGAGCAACGCCGCGGAGCAGATGCAGGTC
EST: gi|30086983|gb|CB885191.1|CB885191
EST:     TCACGTCTGGCAACGTCATGGACGAGAACTCCTTCAGTAACCCGAACAAG                         GTTGCGCCGGTGAAAAGCCAGCTGAGCAACGCCGCGGAGCAGATGCAGGTC
genomic: TCACGTCTGGCAACGTCATGGACGAGAACTCCTTCAGTAACCCGAACAAGgtatgcgtac ... ctgcttgcagGTTGCGCCGGTGAAAAGCCAGCTGAGCAACGCCGCGGAGCAGATGCAGGTC
EST: gi|211146564|gb|FL325013.1|FL325013
EST:     TCACGTYTGGCAACGTCATGGACGAGAACTCCTTCAGTAACCCGAACAAG                         GTTGCGCCGGTGAAAAGCCAGCTGAGCAACGCCGCGGAGCAGATGCAGGTC
genomic: TCACGTCTGGCAACGTCATGGACGAGAACTCCTTCAGTAACCCGAACAAGgtatgcgtac ... ctgcttgcagGTTGCGCCGGTGAAAAGCCAGCTGAGCAACGCCGCGGAGCAGATGCAGGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcgtaccgatggtccatgcatgcactaagcttgttggtttctgaatggaaggagcgacgtgtggagcttgttctgaaccccaaagcttgctgcttgcagGTTGCGCCGGTGAAAAGCCAGCTGAGCAACGCCGCGGAGCAGATGCAGGTCACGCTGGCTCCTCACTCCTTCACCGCCTTCGATCTGGCGCTGGCTGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGCCGCGG