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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttcctcgtatctcattcctcaaatccatccatcgcacacgatttcttccatctcctccgatcctactaaagctcttcggtcttcaccaccaatggcagGTTCCCTATTGGGCAGTGCGGCAACAACGTGGGGCTGCTTCTGCTGCTCGACAAGGCTCCTAGGGCAGGCCACGGGCACCAGAGGCCTCCCAAGAGGATC

Basic information

species Zea mays
transcript GRMZM2G035839_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G035839_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g30500.1 (Oryza sativa), 3'ss of exon 2
gtgagttcctcgt----atctcattcc--tcaaatccatccatcgcacacgatttcttccatctcctccgatcctactaaagctctt-cggtcttcaccaccaatggcagGTTCCCTATTGGGCAGTGCGGCAACAACGTGGGGCTGCTTCTGCTGCTCGACAAGGCTCCTAGGGCAGGCCACGGGCACCAGAGGCCTCCCAAGAGGATC
|||||||| ||      |||| ||  |  | |||| | | | |  || | ||   || |  |    ||      | ||     || |    | ||   | ||  | |||||| ||| ||||| ||||| ||||||||||| ||  |||| |||||||||||||||||||| ||| |||| ||||| ||||||| |   |||||||  || 
gtgagttcatccccatcatcttatctccgtaaaattcctgcgttccaaaggagacctacatttctatcgcgcattcctccttttcatatattttttttcgccttttgcagGTACCCAATTGGTCAGTGTGGCAACAACGTCGGCTTGCTGCTGCTGCTCGACAAGGCTCCCAGGCCAGGGCACGGCCACCAGAAGATGCCCAAGAAAATT
















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|76015764|gb|DT942934.1|DT942934
EST:     TGGGTTACATCAATCATGTGGTGGCGAAGGAAATCATCTCGCGTAAA                         GTTCCCTATTGGGCAGTGCGGCAACAACGTGGGGCTGCTTCTGCTGCTCGA
genomic: TGGGTTACATCAATCATGTGGTGGCGAAGGAAATCATCTCGCGTAAAgtgagttcct ... ccaatggcagGTTCCCTATTGGGCAGTGCGGCAACAACGTGGGGCTGCTTCTGCTGCTCGA
EST: gi|76016393|gb|DT943563.1|DT943563
EST:     TGGGTTACATCAATCATGTGGTGGCGAAGGAAATCATCTCGCGTAAA                         GTTCCCTATTGGGCAGTGCGGCAACAACGTGGGGCTGCTTTTGCTGCTCGA
genomic: TGGGTTACATCAATCATGTGGTGGCGAAGGAAATCATCTCGCGTAAAgtgagttcct ... ccaatggcagGTTCCCTATTGGGCAGTGCGGCAACAACGTGGGGCTGCTTCTGCTGCTCGA
EST: gi|71758789|gb|DR956726.1|DR956726
EST:     TGGGTTACATCAATCATGTGGTGGCGAAGGAAATCATCTCGCGTAAA                         GTTCCCTATTGGGCAGTGCGGCAACAACGTGGGGCTGCTTCTGCTGCTCGA
genomic: TGGGTTACATCAATCATGTGGTGGCGAAGGAAATCATCTCGCGTAAAgtgagttcct ... ccaatggcagGTTCCCTATTGGGCAGTGCGGCAACAACGTGGGGCTGCTTCTGCTGCTCGA
EST: gi|87155089|gb|DY399878.1|DY399878
EST:     TGGGTTACATCAATCATGTGGTGGCGAAGGAAATCATCTCGCGTAAA                         GTTCCCTATTGGGCAGTGCGGCAACAACGTGGGGCTGCTTCTGCTGCTCGA
genomic: TGGGTTACATCAATCATGTGGTGGCGAAGGAAATCATCTCGCGTAAAgtgagttcct ... ccaatggcagGTTCCCTATTGGGCAGTGCGGCAACAACGTGGGGCTGCTTCTGCTGCTCGA
EST: gi|74243447|gb|DT651361.1|DT651361
EST:     TGGGTTACATCAATCATGTGGTGGCGAAGGAAATCATCTCGCGTAAA                         GTTCCCTATTGGGCAGTGCGGCAACAACGTGGGGCTGCTTTTGCTGCTCGA
genomic: TGGGTTACATCAATCATGTGGTGGCGAAGGAAATCATCTCGCGTAAAgtgagttcct ... ccaatggcagGTTCCCTATTGGGCAGTGCGGCAACAACGTGGGGCTGCTTCTGCTGCTCGA
EST: gi|71758840|gb|DR956777.1|DR956777
EST:     TGGGTTACATCAATCATGTGGTGGCGAAGGAAATCATCTCGCGTAAA                         GTTCCCTATTGGGCAGTGCGGCAACAACGTGGGGCTGCTTCTGCTGCTCGA
genomic: TGGGTTACATCAATCATGTGGTGGCGAAGGAAATCATCTCGCGTAAAgtgagttcct ... ccaatggcagGTTCCCTATTGGGCAGTGCGGCAACAACGTGGGGCTGCTTCTGCTGCTCGA
EST: gi|93017243|gb|EB642763.1|EB642763
EST:     TGGGTTACATCAATCATGTGGTGGCGAAGGAAATCATCTCGCGTAAA                         GTTCCCTATTGGGCAGTGCGGCAACAACGTGGGGCTGCTTCTGCTGCTCGA
genomic: TGGGTTACATCAATCATGTGGTGGCGAAGGAAATCATCTCGCGTAAAgtgagttcct ... ccaatggcagGTTCCCTATTGGGCAGTGCGGCAACAACGTGGGGCTGCTTCTGCTGCTCGA
EST: gi|86467261|gb|DY233631.1|DY233631
EST:     TGGGTTACATCAATCATGTGGTGGCGAAGGAAATCATCTCGCGTAAA                         GTTCCCTATTGGGCAGTGCGGCAACAACGTGGGGCTGCTTCTGCTGCTCGA
genomic: TGGGTTACATCAATCATGTGGTGGCGAAGGAAATCATCTCGCGTAAAgtgagttcct ... ccaatggcagGTTCCCTATTGGGCAGTGCGGCAACAACGTGGGGCTGCTTCTGCTGCTCGA
EST: gi|71435302|gb|DR816352.1|DR816352
EST:     TGGGTTACATCAATCATGTGGTGGCGAAGGAAATCATCTCGCGTAAA                         GTTCCCTATTGGGCAGTGCGGCAACAACGTGGGGCTGCTTCTGCTGCTCGA
genomic: TGGGTTACATCAATCATGTGGTGGCGAAGGAAATCATCTCGCGTAAAgtgagttcct ... ccaatggcagGTTCCCTATTGGGCAGTGCGGCAACAACGTGGGGCTGCTTCTGCTGCTCGA
EST: gi|12047065|gb|BF729204.1|BF729204
EST:     TGGGTTACATCAATCATGTGGTGGCGAAGGAAATCATCCCGCGTCAA                         GTTCCCTATTGGGCAGTGCGGCAACAACGTGGGGCTGCTTCTGCTGCTCGA
genomic: TGGGTTACATCAATCATGTGGTGGCGAAGGAAATCATCTCGCGTAAAgtgagttcct ... ccaatggcagGTTCCCTATTGGGCAGTGCGGCAACAACGTGGGGCTGCTTCTGCTGCTCGA
EST: gi|71421397|gb|DR805409.1|DR805409
EST:     TGGGTTACATCAATCATGTGGTGGCGAAGGAAATCATCTCGCGTAAA                         GTTCCCTATTGGGCAGTGCGGCAACAACGTGGGGCTGCTTCTGCTGCTCGA
genomic: TGGGTTACATCAATCATGTGGTGGCGAAGGAAATCATCTCGCGTAAAgtgagttcct ... ccaatggcagGTTCCCTATTGGGCAGTGCGGCAACAACGTGGGGCTGCTTCTGCTGCTCGA
EST: gi|21330834|gb|BQ486215.1|BQ486215
EST:     TGGGTTACATCAATCATGTGGTGGCGAAGGAAATCATCTCGCGTAAA                         GTTCCCTATTGGGCAGTGCGGCAACAACGTGGGGCTGCTTCTGCTGCTCGA
genomic: TGGGTTACATCAATCATGTGGTGGCGAAGGAAATCATCTCGCGTAAAgtgagttcct ... ccaatggcagGTTCCCTATTGGGCAGTGCGGCAACAACGTGGGGCTGCTTCTGCTGCTCGA
EST: gi|78179427|gb|DV549800.1|DV549800
EST:     TGGGTTACATCAATCATGTGGTGGCGAAGGAAATCATCCCGCGTCAA                         GTTCCCTATTGGGCAGTGCGGCAACAACGTGGGGCTGCTTCTGCTGCTCGA
genomic: TGGGTTACATCAATCATGTGGTGGCGAAGGAAATCATCTCGCGTAAAgtgagttcct ... ccaatggcagGTTCCCTATTGGGCAGTGCGGCAACAACGTGGGGCTGCTTCTGCTGCTCGA
EST: gi|71759952|gb|DR957889.1|DR957889
EST:     TGGGTTACATCAATCATGTGGTGGCGAAGGAAATCATCTCGCGTAAA                         GTTCCCTATTGGGCAGTGCGGCAACAACGTGGGGCTGCTTCTGCTGCTCGA
genomic: TGGGTTACATCAATCATGTGGTGGCGAAGGAAATCATCTCGCGTAAAgtgagttcct ... ccaatggcagGTTCCCTATTGGGCAGTGCGGCAACAACGTGGGGCTGCTTCTGCTGCTCGA
EST: gi|50331161|gb|CO526287.1|CO526287
EST:     TGGGTTACATCAATCATGTGGTGGCGAAGGAAATCATCTCGCGTAAA                         GTTCCCTATTGGGCAGTGCGGCAACAACGTGGGGCTGCTTCTGCTGCTCGA
genomic: TGGGTTACATCAATCATGTGGTGGCGAAGGAAATCATCTCGCGTAAAgtgagttcct ... ccaatggcagGTTCCCTATTGGGCAGTGCGGCAACAACGTGGGGCTGCTTCTGCTGCTCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttccatctcctccgatcctactaaagctcttcggtcttcaccaccaatggcagGTTCCCTATTGGGCAGTGCGGCAACAACGTGGGGCTGCTTCTGCTGCTCGACAAGGCTCCTAGGGCAGGCCACGGGCACCAGAGGCCTCCCAAGAGGATC
                    tactaaa  putative branch site (score: 1)
                    tactaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttcctcgtatctcattcctcaaatccatccatcgcacacgatttcttccatctcctccgatcctactaaagctcttcggtcttcaccaccaatggcagGTTCCCTATTGGGCAGTGCGGCAACAACGTGGGGCTGCTTCTGCTGCTCGACAAGGCTCCTAGGGCAGGCCACGGGCACCAGAGGCCTCCCAAGAGGATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT