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'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtggtacttaaattaatctcccattgtgtcgtggatgctgtttttaaattatgtagccgtgaaagtgacttagttttccatttttaaaccccattttcagGTTGAGAGCGAATTTCAAAAAGCTTATGACAATGGATTGCCAAAATCAAA

Basic information

species Zea mays
transcript GRMZM2G064023_T03
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064023_T04 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os11g33240.3 (Oryza sativa), 3'ss of exon 8
gtggtacttaaattaa-tctcccattgtgtcgtggatgctgtttttaaattatgtagcc----gtgaaagtgacttagttttccatttttaaaccccattttcagGTTGAGAGCGAATTTCAAAAAGCTTATGACAATGGATTGCCAAAATCAAA
     | ||||   ||  |    |     ||||  ||       ||  |||     |||    || |   | | |||| | | |  ||||||  |  |||||||||||||||| || |||||||||||||| ||||| ||| |||||||||||||
-----aattaaccaaaaccatttaaaaaatcgttaataaaagccttgtatttctctgccttttgtaattcttatttagctcttctattttaactcttattttcagGTTGAGAGTGAGTTTCAAAAAGCTTACGACAAAGGAATGCCAAAATCAAA

upper sequence: GRMZM2G064023_T04 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 9
gtggtacttaaattaa--tctcccattgtgtcgtggatgctgtttttaaattatgtagccgtgaaagtgacttagttttccatttttaaaccccattttcagGTTGAGAGCGAATTTCAAAAAGCTTATGACAATGGATTGCCAAAATCAAA
    | | |  || ||   |||  ||| ||  ||   |  |  |||  |  | |  |  | |  || | | ||   ||| |  ||||||  |  |||| ||||| ||||| || ||||||||||| |||||||| ||| || ||||||||||
aaaatccattgataaaaccctcttattttgctgtttgtaattctttctaggtctccacactt--aattaatttgccttttctattttaattcttatttgcagGTGGAGAGTGAGTTTCAAAAAGCCTATGACAAAGGAATGTCAAAATCAAA
















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|211399063|gb|FL099822.1|FL099822
EST:     TAACTGCACATCCTATGACACAGTTTACCACGGGAGTAATGGCTCTTCAG                         GTTGAGAGCGAATTTCAAAAAGCTTATGANCA-TGGATTGCCAAAATCAAA
genomic: TAACTGCACATCCTATGACACAGTTTACCACGGGAGTAATGGCTCTTCAGgtgagtcctt ... ccattttcagGTTGAGAGCGAATTTCAAAAAGCTTATGA-CAATGGATTGCCAAAATCAAA
EST: gi|76287895|gb|DV027463.1|DV027463
EST:     TAACTGCACATCCTATGACACAGTTTACCACGGGAGTAATGGCTCTTCAG                         GTTGAGAGCGAATTTCAAAAAGCTTATGACAATGGATTGCCAAAATCAAA
genomic: TAACTGCACATCCTATGACACAGTTTACCACGGGAGTAATGGCTCTTCAGgtgagtcctt ... ccattttcagGTTGAGAGCGAATTTCAAAAAGCTTATGACAATGGATTGCCAAAATCAAA
EST: gi|4609628|gb|AI600467.1|AI600467
EST:     TAACTGCACATCCTATGACACAGTTTACCACGGGAGTAATGGCTCTTCAG                         GTTGAGAGCGAATTTCAAAAAGCTTATGACAATGGA
genomic: TAACTGCACATCCTATGACACAGTTTACCACGGGAGTAATGGCTCTTCAGgtgagtcctt ... ccattttcagGTTGAGAGCGAATTTCAAAAAGCTTATGACAATGGA
EST: gi|149082725|gb|EE171943.2|EE171943
EST:     TAACTGCACATCCTATGACACAGTTTACCACGGGAGTAATGGCTCTTCAG                         GTTGAGAGCGAATTTCAAAAAGCTTATGACAATGGATTGCCAAAATCAAA
genomic: TAACTGCACATCCTATGACACAGTTTACCACGGGAGTAATGGCTCTTCAGgtgagtcctt ... ccattttcagGTTGAGAGCGAATTTCAAAAAGCTTATGACAATGGATTGCCAAAATCAAA
EST: gi|71450120|gb|DR831170.1|DR831170
EST:     TAACTGCACATCCTATGACACAGTTTACCACGGGAGTAATGGCTCTTCAG                         GTTGAGAGCGAATTTCAAAAAGCTTATGACAATGGATTGCCAAAATCAAA
genomic: TAACTGCACATCCTATGACACAGTTTACCACGGGAGTAATGGCTCTTCAGgtgagtcctt ... ccattttcagGTTGAGAGCGAATTTCAAAAAGCTTATGACAATGGATTGCCAAAATCAAA
EST: gi|31361054|gb|CD445411.1|CD445411
EST:     TAACTGCACATCCTATGACACAGTTTACCACGGGAGTAATGGCTCTTCAG                         GTTGAGAGCGAATTTCAAAAAGCTTATGACAATGGATTACCAAAATCAAA
genomic: TAACTGCACATCCTATGACACAGTTTACCACGGGAGTAATGGCTCTTCAGgtgagtcctt ... ccattttcagGTTGAGAGCGAATTTCAAAAAGCTTATGACAATGGATTGCCAAAATCAAA
EST: gi|213174510|gb|FM184748.1|FM184748
EST:     TAACTGCACATCCTATGACACAGTTTACCACGGGAGTAATGGCTCTTCAG                         GTTGAGAGCGAATTTCAAAAAGCTTATGACAATGGATTGCCAAAATCAAA
genomic: TAACTGCACATCCTATGACACAGTTTACCACGGGAGTAATGGCTCTTCAGgtgagtcctt ... ccattttcagGTTGAGAGCGAATTTCAAAAAGCTTATGACAATGGATTGCCAAAATCAAA
EST: gi|149077813|gb|EE166538.2|EE166538
EST:     TAACTGCACATCCTATGACACAGTTTACCACGGGAGTAATGGCTCTTCAG                         GTTGAGAGCGAATTTCAAAAAGCTTATGACAATGGATTGCCAAAATCAAA
genomic: TAACTGCACATCCTATGACACAGTTTACCACGGGAGTAATGGCTCTTCAGgtgagtcctt ... ccattttcagGTTGAGAGCGAATTTCAAAAAGCTTATGACAATGGATTGCCAAAATCAAA
EST: gi|211269893|gb|FL099813.1|FL099813
EST:     CTGCACATCCTATGACACAGTTTTACCACGGGAAGTA-TGGCCTCTTCAG                         GTTGAGAGCGATTTTCAAAAAGCTTATGACCATGGATTGCCAAAATCAA
genomic: CTGCACATCCTATGACACAGTTT-ACCACGGGA-GTAATGGC-TCTTCAGgtgagtcctt ... ccattttcagGTTGAGAGCGAATTTCAAAAAGCTTATGACAATGGATTGCCAAAATCAA
EST: gi|32859373|gb|CD999054.1|CD999054
EST:     TAACTGCACATCCTATGACACAGTTTACCACGGGAGTAATGGCTCTTCAG                         GTTGAGAGCGAATTTCAAAAAGCTTATGACAATGGATTGCCAAAATCAAA
genomic: TAACTGCACATCCTATGACACAGTTTACCACGGGAGTAATGGCTCTTCAGgtgagtcctt ... ccattttcagGTTGAGAGCGAATTTCAAAAAGCTTATGACAATGGATTGCCAAAATCAAA
EST: gi|149090362|gb|EE179668.2|EE179668
EST:     TAACTGCACATCCTATGACACAGTTTACCACGGGAGTAATGGCTCTTCAG                         GTTGAGAGCGAATTTCAAAAAGCTTATGACAATGGATTGCCAAAATCAAAG
genomic: TAACTGCACATCCTATGACACAGTTTACCACGGGAGTAATGGCTCTTCAGgtgagtcctt ... ccattttcagGTTGAGAGCGAATTTCAAAAAGCTTATGACAATGGATTGCCAAAATCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaattatgtagccgtgaaagtgacttagttttccatttttaaaccccattttcagGTTGAGAGCGAATTTCAAAAAGCTTATGACAATGGATTGCCAAAATCAAA
                                           ccccattttc  CT-rich tract
                            ttttccatttttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggtacttaaattaatctcccattgtgtcgtggatgctgtttttaaattatgtagccgtgaaagtgacttagttttccatttttaaaccccattttcagGTTGAGAGCGAATTTCAAAAAGCTTATGACAATGGATTGCCAAAATCAAA

-tggtact
- - - - - - - - - - - - - - - - -gatgctg