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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCGAATTCTGCTGCTGTGGCCATTACAACTACAGACCTTGTTAGCAAGAGCATTGCTGTCCAGACTGAGgtttgagtctcttggtttacttattgttatttccttagattttattgtcatatttttttttttgttcaaaactag

Basic information

species Zea mays
transcript GRMZM2G044237_T03
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044237_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g17120.1 (Oryza sativa), 5'ss of exon 8
TGCGAATTCTGCTGCTGTGGCCATTACAACTACAGACCTTGTTAGCAAGAGCATTGCTGTCCAGACTGAGgtttgagtctcttggtttacttattgttatttccttagattttattgtcatatttttttttttgttcaaaactag------------------
||| |||||||| ||||||||||||||||||||||||||||||||||||||||| ||||| ||||| ||||||||| | |||| |  | | |||| ||   || |||| |||  |||   |    || | |||||||  | |                     
TGCAAATTCTGCAGCTGTGGCCATTACAACTACAGACCTTGTTAGCAAGAGCATCGCTGTACAGACAGAGgtttgactttcttagcct-cgtattatt--ctcattaggtttatttggtttgacattatctttgttcttatcatctctttattgaaaagttag

upper sequence: GRMZM2G044237_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA13G19450.1 (Glycine max), 5'ss of exon 9
TGCGAATTCTGCTGCTGTGGCCATTACAACTACAGACCTTGTTAGCAAGAGCATTGCTGTCCAGACTGAGgt--------ttgagtctcttggtttacttattgttatttccttagatt--ttattgtcatatttttttttttgttcaaaactag---------------
 ||  ||||||| |||||||| || || |||||||| ||||||||||||||  | ||  |  || ||  |||        ||     | || | | |||| || | | ||  |   | |  ||  | |   | | |||| || |  || |   |                
GGCAGATTCTGCAGCTGTGGCAATCACCACTACAGATCTTGTTAGCAAGAGTGTGGCAATTGAGTCTCTGgtatttcttgttactattttttgctcacttgttttaagttgatacaactagtttgtatgtaactgttttattagcacacatacatatatagataaacgca
















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|71298836|gb|DR785405.1|DR785405
EST:     CCATTACAACTACAGACCTTGGTAGCAAGAGCATTGCTGTCTAGACTGAG                         ATTGGAGGAGTGGCTATTAGAATAGGTGGGATGGCTAAAGGTTCTG
genomic: CCATTACAACTACAGACCTTGTTAGCAAGAGCATTGCTGTCCAGACTGAGgtttgagtct ... tcaaaactagATTGGAGGAGTGGCTATTAGAATAGGTGGGATGGCTAAAGGTTCTG
EST: gi|148956344|gb|EC902151.2|EC902151
EST:     CCATTACAACTACAGACCTTGTTAGCAAGAGCATTGCTGTCCAGACTGAG                         ATTGGAGGAGTGGCTATT
genomic: CCATTACAACTACAGACCTTGTTAGCAAGAGCATTGCTGTCCAGACTGAGgtttgagtct ... tcaaaactagATTGGAGGAGTGGCTATT
EST: gi|78092275|gb|DV520649.1|DV520649
EST:     CCATTACAACTACAGACCTTGTTAGCAAGAGCATTGCTGTCCAGACTGAG                         ATTGGAGGAGTGGCTATTAGAATAGGTGGGATGGCTAAAGGTTCTGGAATG
genomic: CCATTACAACTACAGACCTTGTTAGCAAGAGCATTGCTGTCCAGACTGAGgtttgagtct ... tcaaaactagATTGGAGGAGTGGCTATTAGAATAGGTGGGATGGCTAAAGGTTCTGGAATG
EST: gi|149009106|gb|EE041258.2|EE041258
EST:     CATTACAACTACAGACCTTGTTAGCAAGAGCATTGCTGCTC-AGACTGAG                         ATTGCAGGAGTGGCTATTAGAATAGGTGGGATGGCTAAACGTTCTGGAATG
genomic: CATTACAACTACAGACCTTGTTAGCAAGAGCATTGCTG-TCCAGACTGAGgtttgagtct ... tcaaaactagATTGGAGGAGTGGCTATTAGAATAGGTGGGATGGCTAAAGGTTCTGGAATG
EST: gi|148932140|gb|EC875563.2|EC875563
EST:     CCATTACAACTACAGACCTTGTTAGCAAGAGCATTGCTGTCCAGACTGAG                         ATTGGAGGAGTGGCT
genomic: CCATTACAACTACAGACCTTGTTAGCAAGAGCATTGCTGTCCAGACTGAGgtttgagtct ... tcaaaactagATTGGAGGAGTGGCT
EST: gi|76917242|gb|DV166726.1|DV166726
EST:     GCATTGCTGTCCAGACTGAG                         ATTGGAGGAGTGGCTATTAGAATAGGTGGGATGGCTAAAGGTTCTGGAATG
genomic: GCATTGCTGTCCAGACTGAGgtttgagtct ... tcaaaactagATTGGAGGAGTGGCTATTAGAATAGGTGGGATGGCTAAAGGTTCTGGAATG
EST: gi|60348874|gb|DN215847.1|DN215847
EST:     CCATTACAACTACAGACCTTGTTAGCAAGAGCATTGCTGTCCAGACTGAG                         ATTGGAGGAGTGGCTATTAGAATAGGTGGGATGGCTAAAGGTTCTGGAATG
genomic: CCATTACAACTACAGACCTTGTTAGCAAGAGCATTGCTGTCCAGACTGAGgtttgagtct ... tcaaaactagATTGGAGGAGTGGCTATTAGAATAGGTGGGATGGCTAAAGGTTCTGGAATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCGAATTCTGCTGCTGTGGCCATTACAACTACAGACCTTGTTAGCAAGAGCATTGCTGTCCAGACTGAGgtttgagtctcttggtttacttattgttatttccttagattttattgtcatatttttttttttgttcaaaactag

- - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - -  AGAGCA