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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagcataattgtactgagacatcagtgttgctattctgtcagtaaatcttctgttaccttaacatgggcatacttgagaatttaacctagctagtttcaaattggattctcagctaaaactgatcagatgtttgcaatactgacagAGCTAAAAGGCGTTCCCCCAGAAGTCATCGATCGCCTTGTCCCAGAGCACTCAAGAAGGCAGAGTTTGTTCATGGCGCTAAGGACCTAGTTTTTGCCGTT

Basic information

species Zea mays
transcript GRMZM2G138676_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138676_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os03g62500.1 (Oryza sativa), 3'ss of exon 12
gtagcataattgtactgagacatcagtgttgctattctgtcagtaaatcttctgttaccttaacatgggcatacttgagaatttaacctagctagtttcaaattggattctcagctaaaactgatcagatgtttgcaatactgacagAGCTAAAAGGCGTTCCCCCAGAAGTCATCGATCGCCTTGTCCCAGAGCACTCAAGAAGGCAGAGTTTGTTCATGGCGCTAAGGACCTAGTTTTTGCCGTT
                                 ||| |  |  ||| | ||   |  ||| ||  |    ||            || |  |||  ||| || ||  || |||||||||| |||||   |  ||||||| | || |||||||||| ||| | || ||||||| |||||| || || || || |||||  | ||||||||||||||||||||||||||  | |||||||| |     | 
---------------------------------attgttccgttaattgtttgttcgcctcaatgtcaaaatg-----------aatcctgctgctttgaattt--atcctcagctaaa-ctgatacaacatttgcaacattggcagAGCTAAATGGCATCCCTCCAGAAGCCATCGAACGTCTGGTTCCCGAGCATGCGAGAAGGCAGAGTTTGTTCATGGCGCTGCGCACCTAGTTCTCTAGCTC
















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|29947291|gb|CB816579.1|CB816579
EST:     TCTACCCAATGGTCGGCCTCTGCCGCCTCTCTTCAACTTCAGATCTCAAG                         AGCTAAAAGGCGTTCCCCCAGAAGTCATCGATCGCCTTGTCCCAGAGCACT
genomic: TCTACCCAATGGTCGGCCTCTGCCGCCTCTCTTCAACTTCAGATCTCAAGgtagcataat ... atactgacagAGCTAAAAGGCGTTCCCCCAGAAGTCATCGATCGCCTTGTCCCAGAGCACT
EST: gi|76292959|gb|DV032527.1|DV032527
EST:     TCTACCCAATGGTCGGCCTCTGCCGCCTCTCTTCAACTTCAGATCTCAAG                         AGCTAAAAGGCGTTCCCCCAGAAGTCATCGATCGCCTTGTCCCAGAGCACT
genomic: TCTACCCAATGGTCGGCCTCTGCCGCCTCTCTTCAACTTCAGATCTCAAGgtagcataat ... atactgacagAGCTAAAAGGCGTTCCCCCAGAAGTCATCGATCGCCTTGTCCCAGAGCACT
EST: gi|31355062|gb|CD439419.1|CD439419
EST:     TCTACCCAATGGTCGGCCTCTGCCGCCTCTCTTCAACTTCAGATCTCAAG                         AGCTAAAAGGCGTTCCCCCAGAAGTCATCGATCGCCTTGTCCCAGAGCACT
genomic: TCTACCCAATGGTCGGCCTCTGCCGCCTCTCTTCAACTTCAGATCTCAAGgtagcataat ... atactgacagAGCTAAAAGGCGTTCCCCCAGAAGTCATCGATCGCCTTGTCCCAGAGCACT
EST: gi|38229772|gb|CF920085.1|CF920085
EST:     TCTACCCAATGGTCGGCCTCTGCCGCCTCTCTTCAACTTCAGATCTCAAG                         AGCTAAAAGGNGTTCCCCCAGAAGTCATCGATCGCCTTGTCCCA
genomic: TCTACCCAATGGTCGGCCTCTGCCGCCTCTCTTCAACTTCAGATCTCAAGgtagcataat ... atactgacagAGCTAAAAGGCGTTCCCCCAGAAGTCATCGATCGCCTTGTCCCA
EST: gi|78024451|gb|DV492838.1|DV492838
EST:     TCTACCCAATGGTCGGCCTCTGCCGCCTCTCTTCAACTTCAGATCTCAAG                         AGCTAAAAGGCGTTCCCCCAGAAGTCATCGATCGCCTTGTCCCAGAGCACT
genomic: TCTACCCAATGGTCGGCCTCTGCCGCCTCTCTTCAACTTCAGATCTCAAGgtagcataat ... atactgacagAGCTAAAAGGCGTTCCCCCAGAAGTCATCGATCGCCTTGTCCCAGAGCACT
EST: gi|71322556|gb|DR797955.1|DR797955
EST:     TCTACCCAATGGTCGGCCTCTGCCGCCTCTCTTCAACTTCAGATCTCAAG                         AGCTAAAAGGCGTTCCCCCAGAAGTCATCGATCGCCTTGTCCCAGAGCACT
genomic: TCTACCCAATGGTCGGCCTCTGCCGCCTCTCTTCAACTTCAGATCTCAAGgtagcataat ... atactgacagAGCTAAAAGGCGTTCCCCCAGAAGTCATCGATCGCCTTGTCCCAGAGCACT
EST: gi|71312506|gb|DR792786.1|DR792786
EST:     TCTACCCAATGGTCGGCCTCTGCCGCCTCTCTTCAACTTCAGATCTCAAG                         AGCTAAAAGGCGTTCCCCCAGAAGTCATCGATCGCCTTGTCCCAGAGCACT
genomic: TCTACCCAATGGTCGGCCTCTGCCGCCTCTCTTCAACTTCAGATCTCAAGgtagcataat ... atactgacagAGCTAAAAGGCGTTCCCCCAGAAGTCATCGATCGCCTTGTCCCAGAGCACT
EST: gi|32834795|gb|CD974473.1|CD974473
EST:     TCTACCCAATGGTCGGCCTCTGCCGCCTCTCTTCAACTTCAGATCTCAAG                         AGCTAAAAGGCGTTCCCCCAGAAGTCATCGATCGCCTTGTCCCAGAGCACT
genomic: TCTACCCAATGGTCGGCCTCTGCCGCCTCTCTTCAACTTCAGATCTCAAGgtagcataat ... atactgacagAGCTAAAAGGCGTTCCCCCAGAAGTCATCGATCGCCTTGTCCCAGAGCACT
EST: gi|32832205|gb|CD971883.1|CD971883
EST:     TCTACCCAATGGTCGGCCTCTGCCGCCTCTCTTCAACTTCAGATCTCAAG                         AGCTAAAAGGCGTTCCCCCAGAAGTCATCGATCGCCTTGTCCCAGAGCACT
genomic: TCTACCCAATGGTCGGCCTCTGCCGCCTCTCTTCAACTTCAGATCTCAAGgtagcataat ... atactgacagAGCTAAAAGGCGTTCCCCCAGAAGTCATCGATCGCCTTGTCCCAGAGCACT
EST: gi|6021801|gb|AW066729.1|AW066729
EST:     TCTACCCAATGGTCGGCCTCTGCCGCCTCTCTTCAACTTCAGATCTCAAG                         AGCTAAAAGGCGTTCCCCCAGAAGTCATCGATCGCCTTGTCCCAGAGCACT
genomic: TCTACCCAATGGTCGGCCTCTGCCGCCTCTCTTCAACTTCAGATCTCAAGgtagcataat ... atactgacagAGCTAAAAGGCGTTCCCCCAGAAGTCATCGATCGCCTTGTCCCAGAGCACT
EST: gi|32928721|gb|CF033533.1|CF033533
EST:     TCTACCCAATGGTCGGCCTCTGCCGCCTCTCTTCAACTTCAGATCTCAAG                         AGCTAAAAGGCGTTCCCCCAGAAGTCATCGATCGCCTTGTCCCAGAGCACT
genomic: TCTACCCAATGGTCGGCCTCTGCCGCCTCTCTTCAACTTCAGATCTCAAGgtagcataat ... atactgacagAGCTAAAAGGCGTTCCCCCAGAAGTCATCGATCGCCTTGTCCCAGAGCACT
EST: gi|76292960|gb|DV032528.1|DV032528
EST:     TCTACCCAATGGTCGGCCTCTGCCGCCTCTCTTCAACTTCAGATCTCAAG                         AGCTAAAAGGCGTTCCCCCAGAAGTCATCGATCGCCTTGTCCCAGAGCACT
genomic: TCTACCCAATGGTCGGCCTCTGCCGCCTCTCTTCAACTTCAGATCTCAAGgtagcataat ... atactgacagAGCTAAAAGGCGTTCCCCCAGAAGTCATCGATCGCCTTGTCCCAGAGCACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtttcaaattggattctcagctaaaactgatcagatgtttgcaatactgacagAGCTAAAAGGCGTTCCCCCAGAAGTCATCGATCGCCTTGTCCCAGAGCACTCAAGAAGGCAGAGTTTGTTCATGGCGCTAAGGACCTAGTTTTTGCCGTT
                          aactgat  putative branch site (score: 3)
     tcaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagcataattgtactgagacatcagtgttgctattctgtcagtaaatcttctgttaccttaacatgggcatacttgagaatttaacctagctagtttcaaattggattctcagctaaaactgatcagatgtttgcaatactgacagAGCTAAAAGGCGTTCCCCCAGAAGTCATCGATCGCCTTGTCCCAGAGCACTCAAGAAGGCAGAGTTTGTTCATGGCGCTAAGGACCTAGTTTTTGCCGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG