Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagagccggccgagctggagtctccatttgcgtgactgaaaaagctccgcactgcacgcatgacaccaaagctgaccgtgcacttctttcatcgttccctcttgcagACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATGAAGAAG

Basic information

species Zea mays
transcript GRMZM2G116185_T07
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116185_T07 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g50900.1 (Oryza sativa), 3'ss of exon 5
gtagagccggccgagctggagtctccatttgcgtgactgaaaaagctccgcactgcacgcatgacaccaaagctgaccgtgcacttctttcatcgttccctcttgcagACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATGAAGAAG
                       | ||  | ||   |  |   | |     |  |   |    |  ||||||||||   |       ||| |   |    | | ||||||||| |||||||||||||||||||||||||| || ||| | |||||||||||||||
----------------------gtacacgtacgcctcgtacctaccaagaaagagtttgtg-aatgccaaagctgatgat-----ctttttactctcttttttggcagACCATTGCTCTGATCGCCGTCAGAGAAGGCGTTGTACAGTTAGGCTCCATGAAGAAG
















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|71441211|gb|DR822261.1|DR822261
EST:     CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG                         ACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
genomic: CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAGgtagagccgg ... cctcttgcagACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
EST: gi|50330624|gb|CO525750.1|CO525750
EST:     CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG                         ACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
genomic: CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAGgtagagccgg ... cctcttgcagACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
EST: gi|93015353|gb|EB640873.1|EB640873
EST:     CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG                         ACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
genomic: CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAGgtagagccgg ... cctcttgcagACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
EST: gi|88754599|gb|DY538740.1|DY538740
EST:     CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG                         ACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCACG
genomic: CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAGgtagagccgg ... cctcttgcagACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
EST: gi|76291868|gb|DV031436.1|DV031436
EST:     CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG                         ACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
genomic: CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAGgtagagccgg ... cctcttgcagACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
EST: gi|93016819|gb|EB642339.1|EB642339
EST:     CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG                         ACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
genomic: CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAGgtagagccgg ... cctcttgcagACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
EST: gi|78092357|gb|DV520731.1|DV520731
EST:     CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG                         ACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
genomic: CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAGgtagagccgg ... cctcttgcagACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
EST: gi|71299044|gb|DR785510.1|DR785510
EST:     CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG                         ACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
genomic: CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAGgtagagccgg ... cctcttgcagACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
EST: gi|94474694|gb|EB703652.1|EB703652
EST:     CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG                         ACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
genomic: CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAGgtagagccgg ... cctcttgcagACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
EST: gi|86473098|gb|DY239468.1|DY239468
EST:     CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG                         ACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
genomic: CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAGgtagagccgg ... cctcttgcagACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
EST: gi|101393157|gb|EB818509.1|EB818509
EST:     CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG                         ACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
genomic: CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAGgtagagccgg ... cctcttgcagACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
EST: gi|78084496|gb|DV512889.1|DV512889
EST:     CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG                         ACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
genomic: CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAGgtagagccgg ... cctcttgcagACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
EST: gi|74244543|gb|DT652457.1|DT652457
EST:     CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG                         ACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
genomic: CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAGgtagagccgg ... cctcttgcagACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
EST: gi|76011281|gb|DT938451.1|DT938451
EST:     CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG                         ACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
genomic: CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAGgtagagccgg ... cctcttgcagACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
EST: gi|149058752|gb|EE156770.2|EE156770
EST:     CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG                         ACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
genomic: CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAGgtagagccgg ... cctcttgcagACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
EST: gi|50336433|gb|CO531559.1|CO531559
EST:     CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG                         ACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
genomic: CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAGgtagagccgg ... cctcttgcagACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
EST: gi|88751941|gb|DY536082.1|DY536082
EST:     CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG                         ACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
genomic: CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAGgtagagccgg ... cctcttgcagACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
EST: gi|76910706|gb|DV163993.1|DV163993
EST:     CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG                         ACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
genomic: CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAGgtagagccgg ... cctcttgcagACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
EST: gi|71316516|gb|DR794932.1|DR794932
EST:     CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG                         ACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
genomic: CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAGgtagagccgg ... cctcttgcagACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
EST: gi|89251137|gb|DY622923.1|DY622923
EST:     CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG                         ACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
genomic: CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAGgtagagccgg ... cctcttgcagACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
EST: gi|74244764|gb|DT652678.1|DT652678
EST:     CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG                         ACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
genomic: CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAGgtagagccgg ... cctcttgcagACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
EST: gi|148933880|gb|EC877854.2|EC877854
EST:     CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG                         ACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
genomic: CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAGgtagagccgg ... cctcttgcagACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
EST: gi|71442161|gb|DR823211.1|DR823211
EST:     CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG                         ACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
genomic: CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAGgtagagccgg ... cctcttgcagACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
EST: gi|71323162|gb|DR798249.1|DR798249
EST:     CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG                         ACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG
genomic: CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAGgtagagccgg ... cctcttgcagACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcacgcatgacaccaaagctgaccgtgcacttctttcatcgttccctcttgcagACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATGAAGAAG
                 agctgac  putative branch site (score: 3)
                            cacttctttcatcgtt  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagagccggccgagctggagtctccatttgcgtgactgaaaaagctccgcactgcacgcatgacaccaaagctgaccgtgcacttctttcatcgttccctcttgcagACCATCGCTCTGATCGCCGTCAGAGAAGGCGTCGTGCAGCTTGGCTCCATGAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG