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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAAAGAAGAGGATCAAGTCTGATACAGATTCTGCACGATTTTCTGCTGCATCTATGAGGAATCAACTTGACCAAGCTGCAAGCCTTAAAGGAGAGCAGgttcaacttcagatttatttaataacatcaattagtttttatatttcttgttttcatcagtgcatgctttattaggccagcttctaccttccatgtagga...

Basic information

species Zea mays
transcript GRMZM5G862959_T04
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G862959_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os12g19350.1 (Oryza sativa), 5'ss of exon 4
GAAAAAGAAGAGGATCAAGTCTGATACAGATTCTGCACGATTTTCTGCTGCATCTATGAGGAATCAACTTGACCAAGCTGCAAGCCTTAAAGGAGAGCAGgtt-caacttcagatttatttaataacatcaattagtttttatatttc--ttgttttcatcagtgcatgctttattaggccagc--ttctaccttccatgtagga
||||||||||||||| ||||||||||||||| || ||||||| ||  |||||||||||||||  ||||||||||||||| ||| ||| |||||||| |||||| ||||||||| |  ||||   || |||| ||||||||| ||||||   |||||     |  |||    | || |    | |  |||||| |||||||     
GAAAAAGAAGAGGATGAAGTCTGATACAGATACTACACGATTCTCCTCTGCATCTATGAGGAGCCAACTTGACCAAGCTACAAACCTGAAAGGAGAACAGgtttcaacttcagctgaatttggaaatatcagttagtttttgtatttcagctgtttgtgctacagcaacgctgatgaaaaaaacacttctactttccatg-----
















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|148981020|gb|EE027383.2|EE027383
EST:     AAAGGAGAGCAG                         GTTGCTGCTAGGGTAAAATCAGATGACGAAAAAGATGAGTGGTTTGTCGTG
genomic: AAAGGAGAGCAGgttcaacttc ... accatttcagGTTGCTGCTAGGGTAAAATCAGATGACGAAAAAGATGAGTGGTTTGTCGTG
EST: gi|74236008|gb|DT643922.1|DT643922
EST:     TGCAAACCTTAAAGGAGAGCAG                         GTTGCTGCTGGGGTAAAATCAGATGACGAAAAAGATGAGTGGTTTGTCGTG
genomic: TGCAAGCCTTAAAGGAGAGCAGgttcaacttc ... accatttcagGTTGCTGCTAGGGTAAAATCAGATGACGAAAAAGATGAGTGGTTTGTCGTG
EST: gi|74244628|gb|DT652542.1|DT652542
EST:     AAGCTGCAAGCCTTAAAGGAGAGCAG                         GTTGCTGCTAGGGTAAAATCAGATGACGAAAAAGATGAGTGGTTTGTCGTG
genomic: AAGCTGCAAGCCTTAAAGGAGAGCAGgttcaacttc ... accatttcagGTTGCTGCTAGGGTAAAATCAGATGACGAAAAAGATGAGTGGTTTGTCGTG
EST: gi|71332525|gb|DR803228.1|DR803228
EST:     CATCTATGAGGAATCAACTTGACCAAGCTGCAAGCCTTAAAGGAGAGCAG                         GTTGCTGCTAGGGTAAAATCAGATGACGAAAAAGATGAGTGGTTTGTCGTG
genomic: CATCTATGAGGAATCAACTTGACCAAGCTGCAAGCCTTAAAGGAGAGCAGgttcaacttc ... accatttcagGTTGCTGCTAGGGTAAAATCAGATGACGAAAAAGATGAGTGGTTTGTCGTG
EST: gi|71439819|gb|DR820869.1|DR820869
EST:     CATCTATGAGGAATCAACTTGACCAAGCTGCAAGCCTTAAAGGAGAGCAG                         GTTGCTGCTAGGGTAAAATCAGATGACGAAAAAGATGAGTGGTTTGTCGTG
genomic: CATCTATGAGGAATCAACTTGACCAAGCTGCAAGCCTTAAAGGAGAGCAGgttcaacttc ... accatttcagGTTGCTGCTAGGGTAAAATCAGATGACGAAAAAGATGAGTGGTTTGTCGTG
EST: gi|93283255|gb|EB675519.1|EB675519
EST:     CATCTATGAGGAATCAACTTGACCAAGCTGCAAGCCTTAAAGGAGAGCAG                         GTTGCTGCTAGGGTAAAATCAGATGACGAAAAAGATGAGTGGTTTGTCGTG
genomic: CATCTATGAGGAATCAACTTGACCAAGCTGCAAGCCTTAAAGGAGAGCAGgttcaacttc ... accatttcagGTTGCTGCTAGGGTAAAATCAGATGACGAAAAAGATGAGTGGTTTGTCGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAAAAGAAGAGGATCAAGTCTGATACAGATTCTGCACGATTTTCTGCTGCATCTATGAGGAATCAACTTGACCAAGCTGCAAGCCTTAAAGGAGAGCAGgttcaacttcagatttatttaataacatcaattagtttttatatttcttgttttcatcagtgcatgctttattaggccagcttctaccttccatgtagga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG