Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctaattgaaagtaaaaaaaatagctgggtatgttgataggcttttgtgttaaatcgtcttggtgacttaatggtgttatacatgtgtttttcaatgcagGCTCGATATATTTCAGAGGAAGTGAAGGACAAAAGTAACAGAGTAATCAACACCAGTTTGTGGCATGAAGAGCTAGTTGATATTCCTTTACAGCGGAATG

Basic information

species Zea mays
transcript GRMZM5G849959_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G849959_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g22400.1 (Oryza sativa), 3'ss of exon 6
-cctaattgaaa-gtaaaaaaaatagctgggtatgttgataggcttttgtgttaaatcgtcttggtgacttaatggtgttatacatgtgtttttcaat-gcagGCTCGATATATTTCAGAGGAAGTGAAGGACAAAAGTAACAGAGTAATCAACACCAGTTTGTGGCATGAAGAGCTAGTTGAT---ATTCCTTTACAGCGGAATG
   | ||| |   ||    ||  | | |   |   |  | |  |||    |||| |   |   |  | ||||   || || ||  ||||  |  || |  |||||| |||||||| ||||||||||||||||||| ||||| | ||  ||| |||| |     ||||| |||||| ||||||||   |||||||| ||||  |   
gtttcattaatgtgttgctaagcttgtttaatccatcaa-atacttgca-gttacagatttgagtgggcttacctgtattttat-tgtgcatgccactcacagGCTAGATATATTGCAGAGGAAGTGAAGGACAAGAGTAATAAAGAGATCGACACAAACACTTGGCACGAAGAGTTAGTTGATGATATTCCTTTGCAGCAAA---
















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|74241159|gb|DT649073.1|DT649073
EST:     AGTTTCTTGATTCCCTTGGTGGCATGGATCATAATGTACCAAAAGTACTG                         GCTCGATATTTTTCAGAGGAAGTGAAGGACAAAAGTAACAGAGGTAATCAA
genomic: AGTATCTTGATTCCCTTGGTGGCATGGATCATAATGTACCAAAAGTACTGgtaagcataa ... ttcaatgcagGCTCGATATATTTCAGAGGAAGTGAAGGACAAAAGTAACAGA-GTAATCAA
EST: gi|113845654|gb|DW957590.1|DW957590
EST:     AGTATCTTGATTCCCTTGGTGGCATGGATCATAATGT-CCAAAAGTACTG                         GCTCGATANATTTCAGAGGAAGTG
genomic: AGTATCTTGATTCCCTTGGTGGCATGGATCATAATGTACCAAAAGTACTGgtaagcataa ... ttcaatgcagGCTCGATATATTTCAGAGGAAGTG
EST: gi|166444165|gb|EG132079.1|EG132079
EST:     AGTATCTTGATTCCCTTGGTGGCATGGATCATAATGTACCAAAAGTACTG                         GCTCGATATATTTCAGAGGAAGTGAAGGACAAAAGTAACAGAGTAA
genomic: AGTATCTTGATTCCCTTGGTGGCATGGATCATAATGTACCAAAAGTACTGgtaagcataa ... ttcaatgcagGCTCGATATATTTCAGAGGAAGTGAAGGACAAAAGTAACAGAGTAA
EST: gi|71309671|gb|DR791114.1|DR791114
EST:     AGTATCTTGATTCCCTTGGTGGCATGGATCATAATGTACCAAAAGTACTG                         GCTCGATATATTTCAGAGGAAGTGAAGGACAAAAGTAACAGAGTAATCAAC
genomic: AGTATCTTGATTCCCTTGGTGGCATGGATCATAATGTACCAAAAGTACTGgtaagcataa ... ttcaatgcagGCTCGATATATTTCAGAGGAAGTGAAGGACAAAAGTAACAGAGTAATCAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgttaaatcgtcttggtgacttaatggtgttatacatgtgtttttcaatgcagGCTCGATATATTTCAGAGGAAGTGAAGGACAAAAGTAACAGAGTAATCAACACCAGTTTGTGGCATGAAGAGCTAGTTGATATTCCTTTACAGCGGAATG
                    acttaat  putative branch site (score: 4)
                                        tgtttttc  putative PPT
                                          tttttcaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctaattgaaagtaaaaaaaatagctgggtatgttgataggcttttgtgttaaatcgtcttggtgacttaatggtgttatacatgtgtttttcaatgcagGCTCGATATATTTCAGAGGAAGTGAAGGACAAAAGTAACAGAGTAATCAACACCAGTTTGTGGCATGAAGAGCTAGTTGATATTCCTTTACAGCGGAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT