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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCGAGAGGCTTGCTGATCTTCTTTGCCTGACTTTGCAGgtttgtttgttttttcacctttgcatgatattgtatttcctttgtgatgccaaccgtggcatcttgtgtttaaacccactacatgacaatcacctgaattgttaggcattttatggctgcagcttgagatatcttaactgccccccctacacgttactctttcatttcag

Basic information

species Zea mays
transcript GRMZM2G014116_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014116_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os03g63430.1 (Oryza sativa), 5'ss of exon 10
AATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCGAGAGGCTTGCTGATCTTCTTTGCCTGACTTTGCAGgtttgtttgttttttcacctttgcatgatattgtatttcctttgtgatgccaaccgtggcatcttgtgtttaaacccactacatgacaatcacctgaattgttaggcattttatggctgcagcttgagatatcttaactgccccccctacacgttactctttcatttcag
|||||||||||||| || ||||||||| ||||| |||||||  ||||||| || |||||||||||| |||  |||||||||||| |       |  | | |||| |  ||||||| |  |||| |        || || |     | |  |||   |  ||      || | |  |                                                                        
AATATCTTGGTTGTTTCGAAGTACTATTCAAGGATTACCCTGAAGAGGCTCGCAGATCTTCTTTGCTTGAGCTTGCAGgtttgtgttcccagccttcctagcatcac-ttgtattcctcttgttacttt----gtagcctaccaagatctaacatgccccacatttttctcattcag-----------------------------------------------------------------------

upper sequence: GRMZM2G014116_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os03g63430.2 (Oryza sativa), 5'ss of exon 10
AATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCGAGAGGCTTGCTGATCTTCTTTGCCTGACTTTGCAGgtttgtttgttttttcacctttgcatgatattgtatttcctttgtgatgccaaccgtggcatcttgtgtttaaacccactacatgacaatcacctgaattgttaggcattttatggctgcagcttgagatatcttaactgccccccctacacgttactctttcatttcag
|||||||||||||| || ||||||||| ||||| |||||||  ||||||| || |||||||||||| |||  |||||||||||| |       |  | | |||| |  ||||||| |  |||| |        || || |     | |  |||   |  ||   || |   || | |    ||                                                                 
AATATCTTGGTTGTTTCGAAGTACTATTCAAGGATTACCCTGAAGAGGCTCGCAGATCTTCTTTGCTTGAGCTTGCAGgtttgtgttcccagccttcctagcatcac-ttgtattcctcttgttacttt----gtagcctaccaagatctaacatgcccca---catttttctcattcaggag-----------------------------------------------------------------
















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|31910182|gb|CD651296.1|CD651296
EST:     CAAGGGTTACCCTCGAGAGGCTTGCTGATCTTCTTTGCCTGACTTTGCAG                         GAGGCAGAGAAGCATCTCTCAGACATGGTTAACTCGAAATCTCTAGTGGCA
genomic: CAAGGGTTACCCTCGAGAGGCTTGCTGATCTTCTTTGCCTGACTTTGCAGgtttgtttgt ... ttcatttcagGAGGCAGAGAAGCATCTCTCAGACATGGTTAACTCGAAATCTCTAGTGGCA
EST: gi|113701567|gb|EE679071.1|EE679071
EST:     CAAGGGTTACCCTCGAGAGGCTTGCTGATCTTCTTTGCCTGACTTTGCAG                         GAGGCAGAGAAGCATCTCTCAGACATGGTTAACTCGAAATCTCTAGTGGCA
genomic: CAAGGGTTACCCTCGAGAGGCTTGCTGATCTTCTTTGCCTGACTTTGCAGgtttgtttgt ... ttcatttcagGAGGCAGAGAAGCATCTCTCAGACATGGTTAACTCGAAATCTCTAGTGGCA
EST: gi|24769954|gb|CA405083.1|CA405083
EST:     CAAGGGTTACCCTCGAGAGGCTTGCTGATCTTCTTTGCCTGACTTTGCAG                         GAGGCAGAGAAGCATCTCTCAGACATGGTTAACTCGAAATCTCTAGTGGCA
genomic: CAAGGGTTACCCTCGAGAGGCTTGCTGATCTTCTTTGCCTGACTTTGCAGgtttgtttgt ... ttcatttcagGAGGCAGAGAAGCATCTCTCAGACATGGTTAACTCGAAATCTCTAGTGGCA
EST: gi|60672488|gb|DN475194.1|DN475194
EST:     CAAGGGTTACCCTCAAGAGGCTTGCCGATCTTCTTTGCCTGACTTTGCAG                         GAGGCAGAGAAGCATCTCTCAGACATGGTTAACTCGAAATCTCTAGTGGCA
genomic: CAAGGGTTACCCTCGAGAGGCTTGCTGATCTTCTTTGCCTGACTTTGCAGgtttgtttgt ... ttcatttcagGAGGCAGAGAAGCATCTCTCAGACATGGTTAACTCGAAATCTCTAGTGGCA
EST: gi|453340|gb|T15314.1|T15314
EST:     CAAGGGTTACCCTCGAGAGGCTTGCTGATCTTCTTTGCCTGACTTTGCAG                         GAGGCAGAGAAGCATCTCTCAGACATGGTTA-CTCGAAATCTCTAGTGGCA
genomic: CAAGGGTTACCCTCGAGAGGCTTGCTGATCTTCTTTGCCTGACTTTGCAGgtttgtttgt ... ttcatttcagGAGGCAGAGAAGCATCTCTCAGACATGGTTAACTCGAAATCTCTAGTGGCA
EST: gi|60343636|gb|DN210609.1|DN210609
EST:     CAAGGGTTACCCTCGAGAGGCTTGCTGATCTTCTTTGCCTGACTTTGCAG                         GAGGCAGAGAAGCATCTCTCAGACATGGTTAACTCGAAATCTCTAGTGGCA
genomic: CAAGGGTTACCCTCGAGAGGCTTGCTGATCTTCTTTGCCTGACTTTGCAGgtttgtttgt ... ttcatttcagGAGGCAGAGAAGCATCTCTCAGACATGGTTAACTCGAAATCTCTAGTGGCA
EST: gi|60341988|gb|DN208961.1|DN208961
EST:     CAAGGGTTACCCTCGAGAGGCTTGCTGATCTTCTTTGCCTGACTTTGCAG                         GAGGCAGAGAAGCATCTCTCAGACATGGTTAACTCGAAATCTCTAGTGGCA
genomic: CAAGGGTTACCCTCGAGAGGCTTGCTGATCTTCTTTGCCTGACTTTGCAGgtttgtttgt ... ttcatttcagGAGGCAGAGAAGCATCTCTCAGACATGGTTAACTCGAAATCTCTAGTGGCA
EST: gi|60344719|gb|DN211692.1|DN211692
EST:     CAAGGGTTACCCTCGAGAGGCTTGCTGATCTTCTTTGCCTGACTTTGCAG                         GAGGCAGAGAAGCATCTCTCAGACATGGTTAACTCGAAATCTCTAGTGGCA
genomic: CAAGGGTTACCCTCGAGAGGCTTGCTGATCTTCTTTGCCTGACTTTGCAGgtttgtttgt ... ttcatttcagGAGGCAGAGAAGCATCTCTCAGACATGGTTAACTCGAAATCTCTAGTGGCA
EST: gi|211150173|gb|FL276378.1|FL276378
EST:     CAAGGGTTACCCTCAAGAGGCTTGCCGATCTTCTTTGCCTGACTTTGCAG                         GAGGCAGAGAAGCATCTCTCAGACATGGTTAACTCGAAATCTCTAGTGGCA
genomic: CAAGGGTTACCCTCGAGAGGCTTGCTGATCTTCTTTGCCTGACTTTGCAGgtttgtttgt ... ttcatttcagGAGGCAGAGAAGCATCTCTCAGACATGGTTAACTCGAAATCTCTAGTGGCA
EST: gi|24766335|gb|CA401489.1|CA401489
EST:     CAAGGGTTACCCTCGAGAGGCTTGCTGATCTTCTTTGCCTGACTTTGCAG                         GAGGCAGAGAAGCATCTCTCAGACATGGTTAACTCGAAATCTCTAGTGGCA
genomic: CAAGGGTTACCCTCGAGAGGCTTGCTGATCTTCTTTGCCTGACTTTGCAGgtttgtttgt ... ttcatttcagGAGGCAGAGAAGCATCTCTCAGACATGGTTAACTCGAAATCTCTAGTGGCA
EST: gi|32907838|gb|CF012651.1|CF012651
EST:     CAAGGGTTACCCTCAAGAGGCTTGCCGATCTTCTTTGCCTGACTTTGCAG                         GAGGCAGAGAAGCATCTCTCAGACATGGTTAACTCGAAATCTCTAGTGGCA
genomic: CAAGGGTTACCCTCGAGAGGCTTGCTGATCTTCTTTGCCTGACTTTGCAGgtttgtttgt ... ttcatttcagGAGGCAGAGAAGCATCTCTCAGACATGGTTAACTCGAAATCTCTAGTGGCA
EST: gi|16379510|gb|BI992995.1|BI992995
EST:     CAAGGGTTACCCTCGAGAGGCTTGCTGATCTTCTTTGCCTGACTTTGCAG                         GAGGCAGAGAAGCATCTCTCAGACATGGTTAACTCGAAATCTCTAGTGGCA
genomic: CAAGGGTTACCCTCGAGAGGCTTGCTGATCTTCTTTGCCTGACTTTGCAGgtttgtttgt ... ttcatttcagGAGGCAGAGAAGCATCTCTCAGACATGGTTAACTCGAAATCTCTAGTGGCA
EST: gi|44681826|gb|CK786874.1|CK786874
EST:     CAAGGGTTACCCTCAAGAGGCTTGCCGATCTTCTTTGCCTGACTTTGCAG                         GAGGCAGAGAAGCATCTCTCAGACATGGTTAACTCGAAATCTCTAGTGGCA
genomic: CAAGGGTTACCCTCGAGAGGCTTGCTGATCTTCTTTGCCTGACTTTGCAGgtttgtttgt ... ttcatttcagGAGGCAGAGAAGCATCTCTCAGACATGGTTAACTCGAAATCTCTAGTGGCA
EST: gi|71762659|gb|DR960596.1|DR960596
EST:     CAAGGGTTACCCTCGAGAGGCTTGCTGATCTTTTTTGCCTGACTTTGCAG                         GAGGCAGAGAAGCATCTTTCAGACATGGTTAACTCGAAATCTCTAGTGGCA
genomic: CAAGGGTTACCCTCGAGAGGCTTGCTGATCTTCTTTGCCTGACTTTGCAGgtttgtttgt ... ttcatttcagGAGGCAGAGAAGCATCTCTCAGACATGGTTAACTCGAAATCTCTAGTGGCA
EST: gi|60346799|gb|DN213772.1|DN213772
EST:     CAAGGGTTACCCTCGAGAGGCTTGCTGATCTTCTTTGCCTGACTTTGCAG                         GAGGCAGAGAAGCATCTCTCAGACATGGTTAACTCGAAATCTCTAGTGGCA
genomic: CAAGGGTTACCCTCGAGAGGCTTGCTGATCTTCTTTGCCTGACTTTGCAGgtttgtttgt ... ttcatttcagGAGGCAGAGAAGCATCTCTCAGACATGGTTAACTCGAAATCTCTAGTGGCA
EST: gi|16926500|gb|BM079573.1|BM079573
EST:     CAAGGGTTACCCTCGAGAGGCTTGCTGATCTTCTTTGCCTGACTTTGCAG                         GAGGCAGAGAAGCATCTCTCAGACATGGTTAACTCGAAATCTCTAGTGGCA
genomic: CAAGGGTTACCCTCGAGAGGCTTGCTGATCTTCTTTGCCTGACTTTGCAGgtttgtttgt ... ttcatttcagGAGGCAGAGAAGCATCTCTCAGACATGGTTAACTCGAAATCTCTAGTGGCA
EST: gi|24764505|gb|CA399669.1|CA399669
EST:     CAAGGGTTACCCTCGAGAGGCTTGCTGATCTTCTTTGCCTGACTTTGCAG                         GAGGCAGAGAAGCATCTCTCAGACATGGTTAACTCGAAATCTCTAGTGGCA
genomic: CAAGGGTTACCCTCGAGAGGCTTGCTGATCTTCTTTGCCTGACTTTGCAGgtttgtttgt ... ttcatttcagGAGGCAGAGAAGCATCTCTCAGACATGGTTAACTCGAAATCTCTAGTGGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCGAGAGGCTTGCTGATCTTCTTTGCCTGACTTTGCAGgtttgtttgttttttcacctttgcatgatattgtatttcctttgtgatgccaaccgtggcatcttgtgtttaaacccactacatgacaatcacctgaattgttaggcattttatggctgcagcttgagatatcttaactgccccccctacacgttactctttcatttcag

- - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT