Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGCGAAACGGACCTCCCGCCCAACCTGTACAGAATATACAATATTTATGAATTCTGAAAATTTATCTAGGTCAAGCAAAATGTACATTGGAAAGCTGAGgtactaactcatgcattggccattattttaggaattacataattctctagtatttgtgtatcactaacaaaggcctggtgcagtggtgagaactatctca...

Basic information

species Zea mays
transcript GRMZM2G001272_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G001272_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os12g06630.2 (Oryza sativa), 5'ss of exon 3
GTGCGAAACGGACCTCCCGCCCAACCTGTACAGAATATACAATATTTATGAATTCTGAAAATTTATCTAGGTCAAGCAAAATGTACATTGGAAAGCTGAGgtactaactcatg-cattggccattat-tttaggaattacataattctctagtatttgtgtatcactaacaaaggcctggtgcagtggtgagaactatctca
  |||||| |   ||||||  |||||||||||||||||||||||||||||| | |||| |||  ||||||||||||||| ||||||||||||||  ||||||| |||| ||    | |||| | | | |||||  |    | |       ||| |||   |   |  | |  |    |  | | ||| ||   ||| |    
CGGCGAAAAGATACTCCCGTGCAACCTGTACAGAATATACAATATTTATGAGTGCTGACAATACATCTAGGTCAAGCAACATGTACATTGGAAAATTGAGgtaataacccaaaataatggcaactttgtttagagaaggtacatcgtctaagtgttttaatggtataatctgatatatt-tactgtgttgg--acttttag-
















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|21330563|gb|BQ485944.1|BQ485944
EST:     AATTCTGAAAATTTATCTAGGTCAAGCAAAATGTACATTGGAAAGCTGAG                         GTCGAATCTCCTCGGCACAAAGTTTGCAATATATGATACCCAGCCCCCATG
genomic: AATTCTGAAAATTTATCTAGGTCAAGCAAAATGTACATTGGAAAGCTGAGgtactaactc ... acatctatagGTCGAATCTCCTCGGCACAAAGTTTGCAATATATGATACCCAGCCCCCATG
EST: gi|50335303|gb|CO530429.1|CO530429
EST:     AATTCTGAAAATTTATCTAGGTCAAGCAAAATGTACATTGGAAAGCTGAG                         GTCGAATCTCCTCGGCACAAAGTTTGCAATATATGATACCCAGCCCCCATG
genomic: AATTCTGAAAATTTATCTAGGTCAAGCAAAATGTACATTGGAAAGCTGAGgtactaactc ... acatctatagGTCGAATCTCCTCGGCACAAAGTTTGCAATATATGATACCCAGCCCCCATG
EST: gi|87154671|gb|DY399460.1|DY399460
EST:     AATTCTGAAAATTTATCTAGGTCAAGCAAAATGTACATTGGAAAGCTGAG                         GTCGAATCTCCTCGGCACAAAGTTTGCAATATATGATACCCAGCCCCCATG
genomic: AATTCTGAAAATTTATCTAGGTCAAGCAAAATGTACATTGGAAAGCTGAGgtactaactc ... acatctatagGTCGAATCTCCTCGGCACAAAGTTTGCAATATATGATACCCAGCCCCCATG
EST: gi|149077539|gb|EE166236.2|EE166236
EST:     AATTCTGAAAATTTATCTAGGTCAAGCAAAATGTACATTGGAAAGCTGAA                         GTCGAATCTCCTCGGCACAAAGTTTGCAATATATGATACCCAGCCC
genomic: AATTCTGAAAATTTATCTAGGTCAAGCAAAATGTACATTGGAAAGCTGAGgtactaactc ... acatctatagGTCGAATCTCCTCGGCACAAAGTTTGCAATATATGATACCCAGCCC
EST: gi|21481553|gb|BQ578236.1|BQ578236
EST:     AATTCTGAAAATTTATCTAGGTCAAGCAAAATGTACATTGGAAAGCTGAG                         GTCGAATCTCCTCGGCACAAAGTTTGCAATATATGATACCCAGCCCCCATG
genomic: AATTCTGAAAATTTATCTAGGTCAAGCAAAATGTACATTGGAAAGCTGAGgtactaactc ... acatctatagGTCGAATCTCCTCGGCACAAAGTTTGCAATATATGATACCCAGCCCCCATG
EST: gi|148955113|gb|EC900627.2|EC900627
EST:     ATTCTNGAAA-TTTATCTAGGTCAAGCAAAATGTACATTGGAAAGCTGAG                         GTCGAATCTCCTCGGCACAAAGTTTGCAATATATGA
genomic: ATTCT-GAAAATTTATCTAGGTCAAGCAAAATGTACATTGGAAAGCTGAGgtactaactc ... acatctatagGTCGAATCTCCTCGGCACAAAGTTTGCAATATATGA
EST: gi|33098000|gb|CF057960.1|CF057960
EST:     AATTCTGAAAATTTATCTAGGTCAAGCAAAATGTACATTGGAAAGCTGAG                         GTCGAATCTCCTCGGCACAAAGTTTGCAATATATGATACCCAGCCCCCATG
genomic: AATTCTGAAAATTTATCTAGGTCAAGCAAAATGTACATTGGAAAGCTGAGgtactaactc ... acatctatagGTCGAATCTCCTCGGCACAAAGTTTGCAATATATGATACCCAGCCCCCATG
EST: gi|93014712|gb|EB640232.1|EB640232
EST:     AATTCTGAAAATTTATCTAGGTCAAGCAAAATGTACATTGGAAAGCTGAG                         GTCGAATCTCCTCGGCACAAAGTTTGCAATATATGATACCCAGCCCCCATG
genomic: AATTCTGAAAATTTATCTAGGTCAAGCAAAATGTACATTGGAAAGCTGAGgtactaactc ... acatctatagGTCGAATCTCCTCGGCACAAAGTTTGCAATATATGATACCCAGCCCCCATG
EST: gi|149111854|gb|EE191009.2|EE191009
EST:     AATTCTGAAAATTTATCTAGGTCAAGCAAAATGTACATTGGAAAGCTGAG                         GTCGAATCTCCTCGGCACAAAGTTTGCCATATATGATACCCAGCCCCCATG
genomic: AATTCTGAAAATTTATCTAGGTCAAGCAAAATGTACATTGGAAAGCTGAGgtactaactc ... acatctatagGTCGAATCTCCTCGGCACAAAGTTTGCAATATATGATACCCAGCCCCCATG
EST: gi|7137562|gb|AW499156.1|AW499156
EST:     GGAAAGCTGAG                         GTCGAATCTCCTCGGCACAAAGTTTGCAATATATGATACCCAGCCCCCATG
genomic: GGAAAGCTGAGgtactaactc ... acatctatagGTCGAATCTCCTCGGCACAAAGTTTGCAATATATGATACCCAGCCCCCATG
EST: gi|86468999|gb|DY235369.1|DY235369
EST:     AATTCTGAAAATTTATCTAGGTCAAGCAAAATGTACATTGGAAAGCTGAG                         GTCGAATCTCCTCGGCACAAAGTTTGCAATATATGATACCCACCCCCCATG
genomic: AATTCTGAAAATTTATCTAGGTCAAGCAAAATGTACATTGGAAAGCTGAGgtactaactc ... acatctatagGTCGAATCTCCTCGGCACAAAGTTTGCAATATATGATACCCAGCCCCCATG
EST: gi|78085094|gb|DV513487.1|DV513487
EST:     AATTCTGAAAATTTATCTAGGTCAAGCAAAATGTACATTGGAAAGCTGAG                         GTCGAATCTCCTCGGCACAAAG
genomic: AATTCTGAAAATTTATCTAGGTCAAGCAAAATGTACATTGGAAAGCTGAGgtactaactc ... acatctatagGTCGAATCTCCTCGGCACAAAG
EST: gi|26455022|gb|CA826605.1|CA826605
EST:     AATTCTGAAAATTTATCTAGGTCAAGCAAAATGTACATTGGAAAGCTGAG                         GTCGAATCTCCTCGGCACAAAGTTTGCAATATATGATACCCAGCCCCCATG
genomic: AATTCTGAAAATTTATCTAGGTCAAGCAAAATGTACATTGGAAAGCTGAGgtactaactc ... acatctatagGTCGAATCTCCTCGGCACAAAGTTTGCAATATATGATACCCAGCCCCCATG
EST: gi|50333305|gb|CO528431.1|CO528431
EST:     AATTCTGAAAATTTATCTAGGTCAAGCAAAATGTACATTGGAAAGCTGAG                         GTCGAATCTCCTCGGCACAAAGTTTGCAATATATGATACCCAGCCCCCATG
genomic: AATTCTGAAAATTTATCTAGGTCAAGCAAAATGTACATTGGAAAGCTGAGgtactaactc ... acatctatagGTCGAATCTCCTCGGCACAAAGTTTGCAATATATGATACCCAGCCCCCATG
EST: gi|21891490|gb|BQ744703.1|BQ744703
EST:     AATTCTGAAAATTTATCTAGGTCAAGCAAAATGTACATTGGAAAGCTGAG                         GTCGAATCTCCTCGGCACAAAGTTTGCAATATATGATACCCAGCCCCCATG
genomic: AATTCTGAAAATTTATCTAGGTCAAGCAAAATGTACATTGGAAAGCTGAGgtactaactc ... acatctatagGTCGAATCTCCTCGGCACAAAGTTTGCAATATATGATACCCAGCCCCCATG
EST: gi|148940279|gb|EC885058.2|EC885058
EST:     AATTCTGAAAATTTATCTAGGTCAAGCAAAATGTACATTGGAAAGCTGAG                         GTCGAATCTCCTCGGCACAAAGTTTGCAATATATGATACCCAGCCCCCATG
genomic: AATTCTGAAAATTTATCTAGGTCAAGCAAAATGTACATTGGAAAGCTGAGgtactaactc ... acatctatagGTCGAATCTCCTCGGCACAAAGTTTGCAATATATGATACCCAGCCCCCATG
EST: gi|149014539|gb|EE044173.2|EE044173
EST:     AATTCTGAAAATTTATCTAGGTCAAGCAAAATGTACATTGGAAAGCTGAG                         GTCGAATCTCCTCGGCACAAAGTTTGCAATATATGATACCCAGCCCCCATG
genomic: AATTCTGAAAATTTATCTAGGTCAAGCAAAATGTACATTGGAAAGCTGAGgtactaactc ... acatctatagGTCGAATCTCCTCGGCACAAAGTTTGCAATATATGATACCCAGCCCCCATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGCGAAACGGACCTCCCGCCCAACCTGTACAGAATATACAATATTTATGAATTCTGAAAATTTATCTAGGTCAAGCAAAATGTACATTGGAAAGCTGAGgtactaactcatgcattggccattattttaggaattacataattctctagtatttgtgtatcactaacaaaggcctggtgcagtggtgagaactatctca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA