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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAATCCCAGGCGGGCGGGTCGTTCACTGTTACTCGTGACACGTCTGGGGAGCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCAGgtatgcaggaagctggatcaatcaaagctcgttattatggtatctgttgcattgcttgatgtaatctgttctaattgcataacccaagtatgcctgtgtt...

Basic information

species Zea mays
transcript GRMZM2G069651_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069651_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os09g30412.1 (Oryza sativa), 5'ss of exon 2
GGAATCCCAGGCGGGCGGGTCGTTCACTGTTACTCGTGACACGTCTGGGGAGCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCAGgtatg-----caggaagctggatcaatcaaagctcgttat---tatggtatctgttgcattgcttgatgtaatctgttctaattgcataacccaagtatgcctgtgtt
||| || ||||| || ||||| ||||||||||| ||||| || ||||| |||||||||||  ||||||||||||| || || | ||||||||| ||||||||||      ||| |   |       | ||  |   |||    | || ||| ||||||  | |   |||| || | || |   | || |||   ||     |||    
GGAGTCACAGGCCGGTGGGTCCTTCACTGTTACACGTGATACCTCTGGTGAGCAGCTTGGACGGGGTACTAAGATCACCCTCTACCTCAAGGATGATCAGgtataagattcagcacatttctcttgtgaattcctattacttgtgtgatatatgttgctgtcc---atgtgatgttttttttgt-cagaactttagatgttctg----
















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|32934806|gb|CF039618.1|CF039618
EST:     ACTAAGATTACACTTTTCCTCAAGGAAGATCAG                         TTAGAATACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCACTCT
genomic: ACTAAGATTACACTTTTCCTCAAGGAAGATCAGgtatgcagga ... tctcttgcagTTAGAATACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCACTCT
EST: gi|89250451|gb|DY622237.1|DY622237
EST:     AGCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCAG                         TTAGAATACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCACTCT
genomic: AGCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCAGgtatgcagga ... tctcttgcagTTAGAATACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCACTCT
EST: gi|32936795|gb|CF041614.1|CF041614
EST:     AGCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCAG                         TTAGAATACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCACTCT
genomic: AGCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCAGgtatgcagga ... tctcttgcagTTAGAATACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCACTCT
EST: gi|4775968|gb|AI664971.1|AI664971
EST:     AGCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCAG                         TTAGAATACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCACTCT
genomic: AGCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCAGgtatgcagga ... tctcttgcagTTAGAATACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCACTCT
EST: gi|211225431|gb|FL262920.1|FL262920
EST:     AGCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCAG                         TTAGAATACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCACTCT
genomic: AGCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCAGgtatgcagga ... tctcttgcagTTAGAATACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCACTCT
EST: gi|67039888|gb|CO466143.1|CO466143
EST:     AGCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCAG                         TTAGAATACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCACTCT
genomic: AGCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCAGgtatgcagga ... tctcttgcagTTAGAATACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCACTCT
EST: gi|67012785|gb|CO441534.1|CO441534
EST:     AGCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCANGGAAGATCAG                         TTAAGA-TACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCACTC
genomic: AGCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCAGgtatgcagga ... tctcttgcagTTA-GAATACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCACTC
EST: gi|67011477|gb|CO440226.1|CO440226
EST:     AGCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCAG                         TTAGAATACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCACTCT
genomic: AGCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCAGgtatgcagga ... tctcttgcagTTAGAATACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCACTCT
EST: gi|32943090|gb|CF047909.1|CF047909
EST:     ACTAAGATTGCACTTTTCCTCAAGGAAGATCAG                         TTAGAATACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCACTCT
genomic: ACTAAGATTACACTTTTCCTCAAGGAAGATCAGgtatgcagga ... tctcttgcagTTAGAATACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCACTCT
EST: gi|18171368|gb|BM341208.1|BM341208
EST:     AGCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCAG                         TTAGAATACATAGAG-AGCGTCGCCTCAAGGATTTGGTCAAGAAGCACTCT
genomic: AGCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCAGgtatgcagga ... tctcttgcagTTAGAATACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCACTCT
EST: gi|89762811|gb|DY690255.1|DY690255
EST:     AGCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCAG                         TTAGAATACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCACTCT
genomic: AGCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCAGgtatgcagga ... tctcttgcagTTAGAATACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCACTCT
EST: gi|211171946|gb|FL098009.1|FL098009
EST:     AGCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCAG                         TTAGAATACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCACTCT
genomic: AGCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCAGgtatgcagga ... tctcttgcagTTAGAATACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCACTCT
EST: gi|211321105|gb|FL262989.1|FL262989
EST:     GCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCANG                         T-AGAATACCTTGNAGGAGCGTCGCCTCAAGGATTTGGGTCA-GAAGCAC
genomic: GCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCA-Ggtatgcagga ... tctcttgcagTTAGAATACCTTG-AGGAGCGTCGCCTCAAGGATTTGG-TCAAGAAGCAC
EST: gi|12968224|gb|BG265170.1|BG265170
EST:     AGCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCAG                         TTAGAATACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCACTCT
genomic: AGCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCAGgtatgcagga ... tctcttgcagTTAGAATACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCACTCT
EST: gi|166417512|gb|EG256450.1|EG256450
EST:     AGCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCAG                         TTAGAATACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCAC
genomic: AGCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCAGgtatgcagga ... tctcttgcagTTAGAATACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCAC
EST: gi|19351881|gb|BM896413.1|BM896413
EST:     AGCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCAG                         TTAGAATACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCACTCT
genomic: AGCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCAGgtatgcagga ... tctcttgcagTTAGAATACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCACTCT
EST: gi|16377473|gb|BI991947.1|BI991947
EST:     AGCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCAG                         TTAGAATACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCACTCT
genomic: AGCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCAGgtatgcagga ... tctcttgcagTTAGAATACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCACTCT
EST: gi|67039274|gb|CO465529.1|CO465529
EST:     AGCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCAG                         TTAGAATACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCACTCT
genomic: AGCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCAGgtatgcagga ... tctcttgcagTTAGAATACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCACTCT
EST: gi|28910310|gb|CB331375.1|CB331375
EST:     AGCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCAG                         TTAGAATACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCACTCT
genomic: AGCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCAGgtatgcagga ... tctcttgcagTTAGAATACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCACTCT
EST: gi|4874318|gb|AI673838.1|AI673838
EST:     AGCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCAG                         TTAGAATACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCACTCT
genomic: AGCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCAGgtatgcagga ... tctcttgcagTTAGAATACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCACTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAATCCCAGGCGGGCGGGTCGTTCACTGTTACTCGTGACACGTCTGGGGAGCAGCTTGGCAGGGGTACTAAGATTACACTTTTCCTCAAGGAAGATCAGgtatgcaggaagctggatcaatcaaagctcgttattatggtatctgttgcattgcttgatgtaatctgttctaattgcataacccaagtatgcctgtgtt

- - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA