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

GGACGTGAACGAGGCTCTGGAGGTGGTCCGCTTCGACATCCAGTACTGCGACTGGAGGGCGCGCCAGGATCTCCTCACCATCATGCTTCTCCACAGCAAGgtagtaccataagcttcgattatcagttcagttttgctgaatcatcagacgctcgaggaacttgaaactgaaataatgcag

Basic information

species Zea mays
transcript GRMZM2G171390_T04
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171390_T04 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os10g41760.1 (Oryza sativa), 5'ss of exon 2
GGACGTGAACGAGGCTCTGGAGGTGGTCCGCTTCGACATCCAGTACTGCGACTGGAGGGCGCGCCAGGATCTCCTCACCATCATGCTTCTCCACAGCAAGgt----agtaccata-----agcttcgattat-cagttcagttttgctgaatcatcagacg-ctcgaggaacttgaaactgaaataatgcag--------
||| || ||| |||| || ||||||||||| |||| ||||||||||||||| ||||||||||| ||||| ||||||||||||||| |||| |||| ||||||    | ||  |||     |   | |   || |||     ||  | ||||   ||  | | |  |   |  ||||  |  ||| ||  |          
GGATGTTAACCAGGCCCTTGAGGTGGTCCGATTCGGCATCCAGTACTGCGATTGGAGGGCGCGGCAGGACCTCCTCACCATCATGGTTCTGCACAACAAGgtatgaaatagtatatatgaaatattggccatgcagaaagtttcagatgaaaggtctcagggcctgttcactttgatgccaaaaaaaaccttaccaaatt

upper sequence: GRMZM2G171390_T04 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os10g41780.1 (Oryza sativa), 5'ss of exon 2
GGACGTGAACGAGGCTCTGGAGGTGGTCCGCTTCGACATCCAGTACTGCGACTGGAGGGCGCGCCAGGATCTCCTCACCATCATGCTTCTCCACAGCAAGgtagta-------------ccataagcttcgattatcagttcagttttgctgaatc---atcagac-gctcgaggaacttgaaactgaaata-atgcag---------------------------------------------------------------------------
||| || ||| | ||||| ||||||||||| ||||| |||||||| ||||| ||||||||||| ||||| ||||||||||||||| |||| |||| |||||||| |              || ||| |  ||  |   ||  |   || |  | ||   ||   || | ||  || | |  ||| || | |  || | |                                                                           
GGATGTCAACCAAGCTCTTGAGGTGGTCCGGTTCGATATCCAGTATTGCGATTGGAGGGCGCGGCAGGACCTCCTCACCATCATGGTTCTTCACAACAAGgtaggaagcattggacaagtcacaagttcagagaagaggtcaaagctttcatagtctgaattttacagatcatgggattcaaaattggactgcatactgaataatgcttgaggttgaagtttcggatgactgacataggttaacttaaatgaatttttgaacattgaaatgcag
















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|71773513|gb|DR971413.1|DR971413
EST:     ACTGGAGGGCGCGCCAGGATCTCCTCACCATCATGCTTCTCCACAGCAAG                         GTGGTGGAGGTCCTCAACCCTCTGGCGAGGGAGTTCAAGTCCATCGGGACC
genomic: ACTGGAGGGCGCGCCAGGATCTCCTCACCATCATGCTTCTCCACAGCAAGgtagtaccat ... aataatgcagGTGGTGGAGGTCCTCAACCCTCTGGCGAGGGAGTTCAAGTCCATCGGGACC
EST: gi|71447084|gb|DR828134.1|DR828134
EST:     ACTGGAGGGCGCGCCAGGATCTCCTCACCATCATGCTTCTCCACAGCAAG                         GTGGTGGAGGTCCTCAACCCTCTGGCGAGGGAGTTCAAGTCCATCGGGACC
genomic: ACTGGAGGGCGCGCCAGGATCTCCTCACCATCATGCTTCTCCACAGCAAGgtagtaccat ... aataatgcagGTGGTGGAGGTCCTCAACCCTCTGGCGAGGGAGTTCAAGTCCATCGGGACC
EST: gi|71764822|gb|DR962759.1|DR962759
EST:     ACTGGAGGGCGCGCCAGGATCTCCTCACCATCATGCTTCTCCACAGCAAG                         GTGGTGGAGGTCCTCAACCCTCTGGCGAGGGAGTTCAAGTCCATCGGGACC
genomic: ACTGGAGGGCGCGCCAGGATCTCCTCACCATCATGCTTCTCCACAGCAAGgtagtaccat ... aataatgcagGTGGTGGAGGTCCTCAACCCTCTGGCGAGGGAGTTCAAGTCCATCGGGACC
EST: gi|211346611|gb|FL190888.1|FL190888
EST:     ACTGGAGGGCGCGCCAGGATCTCCTCACCATCATGCTTCTCCACAGCAAG                         GTGGTGGAGGTCCTCAACCCTCTGGCGAGGGAGTTCAAGTCCATCGGGACC
genomic: ACTGGAGGGCGCGCCAGGATCTCCTCACCATCATGCTTCTCCACAGCAAGgtagtaccat ... aataatgcagGTGGTGGAGGTCCTCAACCCTCTGGCGAGGGAGTTCAAGTCCATCGGGACC
EST: gi|76935489|gb|DV174344.1|DV174344
EST:     ACTGGAGGGCGCGCCAGGATCTCCTCACCATCATGCTTCTCCACAGCAAG                         GTGGTGGAGGTCCTCAACCCTCTGGCGAGGGAGTTCAAGTCCATCGGGACC
genomic: ACTGGAGGGCGCGCCAGGATCTCCTCACCATCATGCTTCTCCACAGCAAGgtagtaccat ... aataatgcagGTGGTGGAGGTCCTCAACCCTCTGGCGAGGGAGTTCAAGTCCATCGGGACC
EST: gi|101394335|gb|EB819102.1|EB819102
EST:     ACTGGAGGGCGCGCCAGGATCTCCTCACCATCATGCTTCTCCACAGCAAG                         GTGGTGGAGGTCCTCAACCCTCTGGCGAGGGAGTTCAAGTCCATCGGGACC
genomic: ACTGGAGGGCGCGCCAGGATCTCCTCACCATCATGCTTCTCCACAGCAAGgtagtaccat ... aataatgcagGTGGTGGAGGTCCTCAACCCTCTGGCGAGGGAGTTCAAGTCCATCGGGACC
EST: gi|78085618|gb|DV514011.1|DV514011
EST:     CTGGAGGGCGCGCCAGGATCTCCTCACCATCATGCTTTCTCCACAGCAAG                         GTGGTGGAGGTCCTCAACCCTCTGGCGAGGGAGTTCAAGTCCATCGGGACC
genomic: CTGGAGGGCGCGCCAGGATCTCCTCACCATCATGCTT-CTCCACAGCAAGgtagtaccat ... aataatgcagGTGGTGGAGGTCCTCAACCCTCTGGCGAGGGAGTTCAAGTCCATCGGGACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGACGTGAACGAGGCTCTGGAGGTGGTCCGCTTCGACATCCAGTACTGCGACTGGAGGGCGCGCCAGGATCTCCTCACCATCATGCTTCTCCACAGCAAGgtagtaccataagcttcgattatcagttcagttttgctgaatcatcagacgctcgaggaacttgaaactgaaataatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG