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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtacagcgtcctcccatttccagctccagtcagatcagctagttgatttgccttttattatctctgcttaactcgtgctggtagataacttttgcatgtggcctgctaatttctgctttcagGATGAAGTTGTCAAGTATTCGCCTCACGCGCGTGCCATCCGTGATGTGGAGGATGAGGAGCTTCGCAGCTTCTTCTGTGGCATGTCACCATGGCAG

Basic information

species Zea mays
transcript GRMZM2G005859_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005859_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g01014.1 (Oryza sativa), 3'ss of exon 2
gtatgtacagcgtcctcccatttccagctccagtcagatcagctagttgatttgccttttattatctctgcttaactcgtgctggtagataacttttgcatgtggcctgctaatttctgctttcagGATGAAGTTGTCAAGTATTCGCCTCACGCGCGTGCCATCCGTGATGTGGAGGATGAGGAGCTTCGCAGCTTCTTCTGTGGCATGTCACCATGGCAG
                                                  |  |  |||   |||   |  |||     | || |       || ||  || ||      |||| ||||| | ||||||||||||||||| ||||| ||||| || || |||||| | ||||| |||||||||||||||||||||||||||| |||||||||||||||||||
-------------------------------------------------gtacgtatttatatataaatatttactaattacttgctctcttctcttcgatttgat----taatctctgcctgcagGATGAAGTTGTCAAATATTCACCTCATGCTCGCGCCATCAGGGATGTCGAGGATGAGGAGCTTCGCAGCTTCTTCTATGGCATGTCACCATGGCAG
















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|50335119|gb|CO530245.1|CO530245
EST:     GTCTTGGCTATGCAGCTCCACCAATCATGGCTCTGCTCTTCATCCTCGAT                         GATGAAGTTGTCAAGTATTCGCCTCACGCGCGTGCCATCCGTGATGTGGAG
genomic: GTCTTGGCTATGCAGCTCCACCAATCATGGCTCTGCTCTTCATCCTCGATgtatgtacag ... ctgctttcagGATGAAGTTGTCAAGTATTCGCCTCACGCGCGTGCCATCCGTGATGTGGAG
EST: gi|9028720|gb|BE238760.1|BE238760
EST:     CTATGCAGCTCCACCAATCATGGCTCTGCTCTTCATCCTCGAT                         GATGAAGTTGTCAAGTATTCGCCTCACGCGCGTGCCATCCGTGATGTGGAG
genomic: CTATGCAGCTCCACCAATCATGGCTCTGCTCTTCATCCTCGATgtatgtacag ... ctgctttcagGATGAAGTTGTCAAGTATTCGCCTCACGCGCGTGCCATCCGTGATGTGGAG
EST: gi|101392576|gb|EB818218.1|EB818218
EST:     GTCTTGGCTATGCAGCTCCACCAATCATGGCTCTGCTCTTCATCCTCGAT                         GATGAAGTTGTCAAGTATTCGCCTCACGCGCGTG
genomic: GTCTTGGCTATGCAGCTCCACCAATCATGGCTCTGCTCTTCATCCTCGATgtatgtacag ... ctgctttcagGATGAAGTTGTCAAGTATTCGCCTCACGCGCGTG
EST: gi|211010141|gb|FL113888.1|FL113888
EST:     GTCTTGGCTATGCAGCTCCACCAATCATGGCTCTGCTCTTCATCCTCGAT                         GATGAAGTTGTCAAGTATTCGCCTCACGCGCGTGCCATCCGTGATGTGGAG
genomic: GTCTTGGCTATGCAGCTCCACCAATCATGGCTCTGCTCTTCATCCTCGATgtatgtacag ... ctgctttcagGATGAAGTTGTCAAGTATTCGCCTCACGCGCGTGCCATCCGTGATGTGGAG
EST: gi|71445181|gb|DR826231.1|DR826231
EST:     GTCTTGGCTATGCAGCTCCACCAATCATGGCTCTGCTCTTCATCCTCGAT                         GATGAAGTTGTCAAGTATTCGCCTCACGCGCGTGCCATCCGTGATGTGGAG
genomic: GTCTTGGCTATGCAGCTCCACCAATCATGGCTCTGCTCTTCATCCTCGATgtatgtacag ... ctgctttcagGATGAAGTTGTCAAGTATTCGCCTCACGCGCGTGCCATCCGTGATGTGGAG
EST: gi|9953868|gb|BE640451.1|BE640451
EST:     CTTGGCTATGCAGCTCCACCAATCATGGCTCTGCTCTTCATCCTCGAT                         GATGAAGTTGTCAAGTATTCGCCTCACGCGCGTGCCATCCGTGATGTGGAG
genomic: CTTGGCTATGCAGCTCCACCAATCATGGCTCTGCTCTTCATCCTCGATgtatgtacag ... ctgctttcagGATGAAGTTGTCAAGTATTCGCCTCACGCGCGTGCCATCCGTGATGTGGAG
EST: gi|5525259|gb|AI861098.1|AI861098
EST:     GCTCCACCAATCATGGCTCTGCTCTTCATCCTCGAT                         GATGAAGTTGTCAAGTATTCGCCTCACGCGCGTGCCATCCGTGATGTGGAG
genomic: GCTCCACCAATCATGGCTCTGCTCTTCATCCTCGATgtatgtacag ... ctgctttcagGATGAAGTTGTCAAGTATTCGCCTCACGCGCGTGCCATCCGTGATGTGGAG
EST: gi|78109220|gb|DV527636.1|DV527636
EST:     GTCTTGGCTATGCAGCTCCACCAATCATGGCTCTGCTCTTCATCCTCGAT                         GATGAAGTTGTCAAGTATTCGCCTCACGCGCGTGCCATCCGTGATGTGGAG
genomic: GTCTTGGCTATGCAGCTCCACCAATCATGGCTCTGCTCTTCATCCTCGATgtatgtacag ... ctgctttcagGATGAAGTTGTCAAGTATTCGCCTCACGCGCGTGCCATCCGTGATGTGGAG
EST: gi|50338466|gb|CO533592.1|CO533592
EST:     GTCTTGGCTATGCAGCTCCACCAATCATGGCTCTGCTCTTCATCCTCGAT                         GATGAAGTTGTCAAGTATTCGCCTCACGCGCGTGCCATCCG
genomic: GTCTTGGCTATGCAGCTCCACCAATCATGGCTCTGCTCTTCATCCTCGATgtatgtacag ... ctgctttcagGATGAAGTTGTCAAGTATTCGCCTCACGCGCGTGCCATCCG
EST: gi|78022617|gb|DV491004.1|DV491004
EST:     GCTCCACCAATCATGGCTCTGCTCTTCATCCTCGAT                         GATGAAGTTGTCAAGTATTCGCCTCACGCGCGTGCCATCCGTGATGTGGAG
genomic: GCTCCACCAATCATGGCTCTGCTCTTCATCCTCGATgtatgtacag ... ctgctttcagGATGAAGTTGTCAAGTATTCGCCTCACGCGCGTGCCATCCGTGATGTGGAG
EST: gi|9028504|gb|BE238499.1|BE238499
EST:     GTCTTGGCTATGCAGCTCCACCAATCATGGCTCTGCTCTTCATCCTCGAT                         GATGAAGTTGTCAAGTATTCGCCTCACGCGCGTGCCATCCGTGATGTGGAG
genomic: GTCTTGGCTATGCAGCTCCACCAATCATGGCTCTGCTCTTCATCCTCGATgtatgtacag ... ctgctttcagGATGAAGTTGTCAAGTATTCGCCTCACGCGCGTGCCATCCGTGATGTGGAG
EST: gi|211423764|gb|FL057577.1|FL057577
EST:     GTCTTGGCTATGCAGCTCCACCAATCATGGCTCTGCTCTTCATCCTCGAT                         GATGAAGTTGTCAAGTATTCGCCTCACGCGCGTGCCATCCGTGATGTGGAG
genomic: GTCTTGGCTATGCAGCTCCACCAATCATGGCTCTGCTCTTCATCCTCGATgtatgtacag ... ctgctttcagGATGAAGTTGTCAAGTATTCGCCTCACGCGCGTGCCATCCGTGATGTGGAG
EST: gi|76290855|gb|DV030423.1|DV030423
EST:     GTCTTGGCTATGCAGCTCCACCAATCATGGCTCTGCTCTTCATCCTCGAT                         GATGAAGTTGTCAAGTATTCGCCTCACGCGCGTGCCATCCGTGATGTGGAG
genomic: GTCTTGGCTATGCAGCTCCACCAATCATGGCTCTGCTCTTCATCCTCGATgtatgtacag ... ctgctttcagGATGAAGTTGTCAAGTATTCGCCTCACGCGCGTGCCATCCGTGATGTGGAG
EST: gi|78091085|gb|DV519459.1|DV519459
EST:     GTCTTGGCTATGCAGCTCCACCAATCATGGCTCTGCTCTTCATCCTCGAT                         GATGAAGTTGTCAAGTATTCGCCTCACGCGCGTGCCATCCGTGATGTGGAG
genomic: GTCTTGGCTATGCAGCTCCACCAATCATGGCTCTGCTCTTCATCCTCGATgtatgtacag ... ctgctttcagGATGAAGTTGTCAAGTATTCGCCTCACGCGCGTGCCATCCGTGATGTGGAG
EST: gi|148964395|gb|EC905771.2|EC905771
EST:     GTCTTGGCTATGCAGCTCCACCAATCATGGCTCTGCTCTTCATCCTCGAT                         GATGAAGTTGTCAAGTATTCGCCTCACGCGCGTGCCATCCGTGATGTGGAG
genomic: GTCTTGGCTATGCAGCTCCACCAATCATGGCTCTGCTCTTCATCCTCGATgtatgtacag ... ctgctttcagGATGAAGTTGTCAAGTATTCGCCTCACGCGCGTGCCATCCGTGATGTGGAG
EST: gi|149074609|gb|EE163014.2|EE163014
EST:     GTCTTGGCTATGCAGCTCCACCAATCATGGCTCTGCTCTTCATCCTCGAT                         GATGAAGTTGTCAAGTATTCGCCTCACGCGCGTGCCATCCGTGATGTGGAG
genomic: GTCTTGGCTATGCAGCTCCACCAATCATGGCTCTGCTCTTCATCCTCGATgtatgtacag ... ctgctttcagGATGAAGTTGTCAAGTATTCGCCTCACGCGCGTGCCATCCGTGATGTGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaactcgtgctggtagataacttttgcatgtggcctgctaatttctgctttcagGATGAAGTTGTCAAGTATTCGCCTCACGCGCGTGCCATCCGTGATGTGGAGGATGAGGAGCTTCGCAGCTTCTTCTGTGGCATGTCACCATGGCAG
                                    tgctaat  putative branch site (score: 2)
                                          tttctgctttc  CT-rich tract
                 ataactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtacagcgtcctcccatttccagctccagtcagatcagctagttgatttgccttttattatctctgcttaactcgtgctggtagataacttttgcatgtggcctgctaatttctgctttcagGATGAAGTTGTCAAGTATTCGCCTCACGCGCGTGCCATCCGTGATGTGGAGGATGAGGAGCTTCGCAGCTTCTTCTGTGGCATGTCACCATGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT