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

TGGTGGCTTGCGAGAGTTGATTGTTGGGAAGGATGATGAGATCCTGAAAACAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcatacagtggaagacacgtaactgtagatccatgcttttctcaaactcttgtgaaagtgctaactctatagtttgattgatctgtggctttcctatgcag

Basic information

species Zea mays
transcript GRMZM2G047219_T03
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047219_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os05g01970.1 (Oryza sativa), 5'ss of exon 6
TGGTGGCTTGCGAGAGTTGATTGTTGGGAAGGATGATGAGATCCTGAAAACAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcata-cagtggaagacacgtaactgtagatccatgcttttctcaaactcttgtgaaagtgctaactctatagtttgattgatctgtggctttcctatgcag
||||||  |||| |||||| ||||||||||||||||||||||| |||| |||||||||| ||||||  |||| || |||||||||||||||||  |||||||| ||||| | | ||||| |||| || |||||  ||  |  || | |||      || || |  | | |  |||   || |    || |  ||  |   |||     
TGGTGGTGTGCGGGAGTTGCTTGTTGGGAAGGATGATGAGATCTTGAAGACAGAAACAAAAACTATTACCAGAGCAGATGTTGCAGAAGTTTGTTTACAGgtaccttcacaactgtggatgacatgttactgttcat--aatctctgctcggtgaattttgcatctaccatgtctgatgtctccgagaacaatg-ttaatcta-----
















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|148955762|gb|EC901460.2|EC901460
EST:     CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAG                         GCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
EST: gi|17931616|gb|BM268576.1|BM268576
EST:     CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAG                         GCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
EST: gi|13381992|gb|BG458667.1|BG458667
EST:     CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAG                         GCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
EST: gi|32940932|gb|CF045751.1|CF045751
EST:     CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAG                         GCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
EST: gi|148966373|gb|EE017367.2|EE017367
EST:     CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATCCAG                         GCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
EST: gi|89762676|gb|DY690164.1|DY690164
EST:     CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAG                         GCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTTATCTGGCATCAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAA
EST: gi|6742502|gb|AW313317.1|AW313317
EST:     CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAG                         GCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
EST: gi|91055640|gb|EB166058.1|EB166058
EST:     CAGAAACA-GAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAG                         GCATTGCTATTCGAAGAGTCAAAAGTT-AAGGCATTTGATCTGCCATCAAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAA-GTTTAAGGCATTTGATCTGGCATCAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTGGCTTGCGAGAGTTGATTGTTGGGAAGGATGATGAGATCCTGAAAACAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcatacagtggaagacacgtaactgtagatccatgcttttctcaaactcttgtgaaagtgctaactctatagtttgattgatctgtggctttcctatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT