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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATACGACCAAAGAAATTGGCCTTAAAATTAGCATTTACTTTACCAACATCATGCTACGCTACAATGGCTATCCGGGAGCTTCTGAAGACTTCCACCTCAgtatgttcatacattttttttaatttttttacctgtagttgtttgttgcttagaaatcccctttcagaatctgtttcataatctccttgattgcctgcag

Basic information

species Zea mays
transcript GRMZM2G096553_T02
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G096553_T02 (Zea mays), 5'ss of exon 18
lower sequence: LOC_Os05g43374.1 (Oryza sativa), 5'ss of exon 13
TATACGACCAAAGAAATTGGCCTTAAAATTAGCATTTACTTTACCAACATCATGCTACGCTACAATGGCTATCCGGGAGCTTCTGAAGACTTCCACCTCAgtatgttcatacatttttttta-------atttttttacctgtagttgtttgttgcttagaaatcccctttcagaatctgtttcataatctccttgattgcctgcag
|||   | ||| |||||||||| ||||||||||||||||| ||||| |||| | ||| ||||||||||||||  ||||| | ||||||||||| ||||| |||||||  |  | |  | |||       ||| ||||||  | | ||   || || | |     | |  || |   | |  | |||| |      || ||| |    
TATGTTAGCAAGGAAATTGGCCATAAAATTAGCATTTACTCTACCAGCATCCTCCTATGCTACAATGGCTATTAGGGAGTTGCTGAAGACTTCAACCTCGgtatgtttctcaactaatattatattactattcttttactagaatttaaatgatgttaaatggactctgtttatggtgttatgcatagttaa---gaatgcat----
















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|67025158|gb|CO453907.1|CO453907
EST:     CATGCTACGCTACAATGGCTATCCGGGAGCTTCTGAAGACTTCCACCTCA                         GTTGCATATCAGAAAACACTCAGCTGCTAGATTCTGTTTGGAAGACATTCC
genomic: CATGCTACGCTACAATGGCTATCCGGGAGCTTCTGAAGACTTCCACCTCAgtatgttcat ... ttgcctgcagGTTGCATATCAGAAAACACTCAGCTGCTAGATTCTGTTTGGAAGACATTCC
EST: gi|60352877|gb|DN219850.1|DN219850
EST:     ATGGCTATCCGGGAGCTTCTGAAGACTTCCACCTCA                         GTTGCATATCAGAAAACACTCAGCTGCTAGATTCTGTTTGGAAGACATTCC
genomic: ATGGCTATCCGGGAGCTTCTGAAGACTTCCACCTCAgtatgttcat ... ttgcctgcagGTTGCATATCAGAAAACACTCAGCTGCTAGATTCTGTTTGGAAGACATTCC
EST: gi|211224590|gb|FL216904.1|FL216904
EST:     CATGCTACGCTACAATGGCTATCCGGGAGCTTCTGAAGACTTCCACCTCA                         GTTGCATATCAGAAAACACTCAGCTGCTAGATTCTGTTTGGAAGACATTCC
genomic: CATGCTACGCTACAATGGCTATCCGGGAGCTTCTGAAGACTTCCACCTCAgtatgttcat ... ttgcctgcagGTTGCATATCAGAAAACACTCAGCTGCTAGATTCTGTTTGGAAGACATTCC
EST: gi|60347237|gb|DN214210.1|DN214210
EST:     CATGCTACGCTACAATGGCTATCCGGGAGCTTCTGAAGACTTCCACCTCA                         GTTGCATATCAGAAAACACTCAGCTGCTAGATTCTGTTTGGAAGACATTCC
genomic: CATGCTACGCTACAATGGCTATCCGGGAGCTTCTGAAGACTTCCACCTCAgtatgttcat ... ttgcctgcagGTTGCATATCAGAAAACACTCAGCTGCTAGATTCTGTTTGGAAGACATTCC
EST: gi|86465812|gb|DY232185.1|DY232185
EST:     CATGCTACGCTACAATGGCTATCCGGGAGCTTCTGAAGACTTCCACCTCA                         GTTGCATATCAGAAAACACTCAGCTGCTAGATTCTGTTTGGAAGACATTCC
genomic: CATGCTACGCTACAATGGCTATCCGGGAGCTTCTGAAGACTTCCACCTCAgtatgttcat ... ttgcctgcagGTTGCATATCAGAAAACACTCAGCTGCTAGATTCTGTTTGGAAGACATTCC
EST: gi|13149317|gb|BG319639.1|BG319639
EST:     CATS-TACGCTACAATGGCTATCCGGGAGCTTCTGAAGACTTCCACCTCA                         GTTGCATATCAGAAAACACTCAGCTGCTAGATTCTGTTTGGAAGACATTCC
genomic: CATGCTACGCTACAATGGCTATCCGGGAGCTTCTGAAGACTTCCACCTCAgtatgttcat ... ttgcctgcagGTTGCATATCAGAAAACACTCAGCTGCTAGATTCTGTTTGGAAGACATTCC
EST: gi|60397731|gb|DN230547.1|DN230547
EST:     CATGCTACGCTACAATGGCTATCCGGGAGCTTCTGAAGACTTCCACCTCA                         GTTGCATATCAGAAAACACTCAGCTGCTAGATTCTGTTTGGAAGACATTCC
genomic: CATGCTACGCTACAATGGCTATCCGGGAGCTTCTGAAGACTTCCACCTCAgtatgttcat ... ttgcctgcagGTTGCATATCAGAAAACACTCAGCTGCTAGATTCTGTTTGGAAGACATTCC
EST: gi|5740555|gb|AI948245.1|AI948245
EST:     CATGNTACGCTACAATGGCTATCCGGGAGCTTCTGAAGACTTCCACCTCA                         GTTGCATATCAGAAAACACTCAGCTGCTAGATTCTGTTTGGAAGACATTCC
genomic: CATGCTACGCTACAATGGCTATCCGGGAGCTTCTGAAGACTTCCACCTCAgtatgttcat ... ttgcctgcagGTTGCATATCAGAAAACACTCAGCTGCTAGATTCTGTTTGGAAGACATTCC
EST: gi|60349430|gb|DN216403.1|DN216403
EST:     CATGCTACGCTACAATGGCTATCCGGGAGCTTCTGAAGACTTCCACCTCA                         GTTGCATATCAGAAAACACTCAGCTGCTAGATTCTGTTTGGAAGACATTCC
genomic: CATGCTACGCTACAATGGCTATCCGGGAGCTTCTGAAGACTTCCACCTCAgtatgttcat ... ttgcctgcagGTTGCATATCAGAAAACACTCAGCTGCTAGATTCTGTTTGGAAGACATTCC
EST: gi|161584306|gb|EY955983.1|EY955983
EST:     CGGGAGCTTCTGAAGACTTCCACCTCA                         GTTGCATATCAGAAAACACTCAGCTGCTAGATTCTGTTTGGAAGACATTCC
genomic: CGGGAGCTTCTGAAGACTTCCACCTCAgtatgttcat ... ttgcctgcagGTTGCATATCAGAAAACACTCAGCTGCTAGATTCTGTTTGGAAGACATTCC
EST: gi|71773678|gb|DR971575.1|DR971575
EST:     CATGCTACGCTACAATGGCTATCCGGGAGCTTTTGAAGACTTCCACCTCA                         GTTGCATATCAGAAAACACTCAGCTGCTAGATTTTGTTTGGAAGACATTCC
genomic: CATGCTACGCTACAATGGCTATCCGGGAGCTTCTGAAGACTTCCACCTCAgtatgttcat ... ttgcctgcagGTTGCATATCAGAAAACACTCAGCTGCTAGATTCTGTTTGGAAGACATTCC
EST: gi|211224589|gb|FL216903.1|FL216903
EST:     CATGCTACGCTACAATGGCTATCCGGGAGCTTCTGAAGACTTCCACCTCA                         GTTGCATATCAGAAAACACTCAGCTGCTAGATTCTGTTTGGAAGACATTCC
genomic: CATGCTACGCTACAATGGCTATCCGGGAGCTTCTGAAGACTTCCACCTCAgtatgttcat ... ttgcctgcagGTTGCATATCAGAAAACACTCAGCTGCTAGATTCTGTTTGGAAGACATTCC
EST: gi|211067559|gb|FL462521.1|FL462521
EST:     CATG-TACGCTACAATGGCTATCCGGGAGCTTCTGAAGACTTCCACCTCA                         GTTGCATATCAGAAAACACTCAGCTGCTAGATTCTGTTTGGAAGACATTCC
genomic: CATGCTACGCTACAATGGCTATCCGGGAGCTTCTGAAGACTTCCACCTCAgtatgttcat ... ttgcctgcagGTTGCATATCAGAAAACACTCAGCTGCTAGATTCTGTTTGGAAGACATTCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATACGACCAAAGAAATTGGCCTTAAAATTAGCATTTACTTTACCAACATCATGCTACGCTACAATGGCTATCCGGGAGCTTCTGAAGACTTCCACCTCAgtatgttcatacattttttttaatttttttacctgtagttgtttgttgcttagaaatcccctttcagaatctgtttcataatctccttgattgcctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA