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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAGgtacatttcttaacctgaaccagtttatattgctatgcaaggtctctacaatggtcagttatatacataaagaataccttaactattgatagctggttaattattaccttttccttgcag

Basic information

species Zea mays
transcript GRMZM2G087692_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G087692_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os12g10200.1 (Oryza sativa), 5'ss of exon 3
CTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAGgtacatttcttaacctgaaccagtttatattgctatgcaaggtctctacaatggtcagttatataca--taaagaataccttaactattgatagctggttaattattaccttttccttgcag
||| ||||||  |||||| || |||||||| |||||||||||||||||||||||||||||||||||||||||  |||| ||    |       ||    |||||| |||  || |   ||||   ||  |||   ||  | ||  |     | |   ||||| || |  ||                     
CTCGCAGGATACGATAATAAGTTGTCTTGGGCTTCATTGGACAAATGATCTACCTGGAGCAATGATACAGgtgaatttttt--tttagtttgattc---ttgcta-gcatagttt--gcaatatacaactattctcagttgaatgaactggttatacttgatggcagtgtag--------------------

upper sequence: GRMZM2G087692_T03 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA04G43650.2 (Glycine max), 5'ss of exon 5
CTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAGgtacatttcttaacctgaaccagtttatattgctatgcaaggtct-ctacaatggtcagttatatacataaagaataccttaactattgatagctggttaattattaccttttccttgcag
|||   ||||||| |  | || ||  | ||||| || ||||| |||||||| ||||||||||||||||||||   |  |||   ||        | || |||      ||  ||  | | | |  | ||   || | ||     |   |   | |||  | |  | | |   |                  
CTCTGTGGATTTGGTTGTTAGTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAGgttactgcctt---ctttcttttctaatgttgtcccttaaattcaaccatacttattaggcttaaatatgttttaggtccctaatataaaaaaattgatgcat------------------

upper sequence: GRMZM2G087692_T03 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA12G37130.2 (Glycine max), 5'ss of exon 5
CTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAGgtacatttcttaacctgaaccagtttatattgctatgcaaggtct-ctacaatggtcagttatatacataaagaataccttaactattgatagctggttaattattaccttttccttgcag
|||   ||||||| |  | || ||  | ||||| || ||||| |||||||| ||||||||||||||||||||   |  |||   ||        | || |||      ||  ||  | | | |  | ||   || | ||     |   |   | |||  | |  | |||   |                  
CTCTGTGGATTTGGTTGTTAGTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAGgttactgcctt---ctttcttttctaatgttgtcccttaaattcaaccatacttattaggcttaaatatgttttaggtccctaatataaaaaaattgttgcat------------------

upper sequence: GRMZM2G087692_T03 (Zea mays), 5'ss of exon 3
lower sequence: AT1G22800.1 (Arabidopsis thaliana), 5'ss of exon 5
CTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAGgtacatttcttaacctgaaccagtttatattgctatgcaaggtctctacaatggtcagttatatacataaagaataccttaactattgatagctggttaattattaccttttccttgcag
 ||    |||||||| || || |   | || ||||| |||||||||||||| |||||| | |||||||||||    ||  |    |       ||| | ||| | |          |  | ||||  ||  |||  | |||  ||   | |  | ||| |   ||| |  | || ||             
TTCGGTTGATTTGATCATTAGTTCGTTGGGGCTTCACTGGACAAATGATCTTCCTGGATCCATGATACAGgt----tttctcgttttcgttgctttttgttggtgtatg-------tgaattggtttgtcctatg-agaaaatatttataatgtgttggtt-ttggattgtaataactgcag--------

upper sequence: GRMZM2G087692_T03 (Zea mays), 5'ss of exon 3
lower sequence: Vv18s0001g06830.t01 (Vitis vinifera), 5'ss of exon 5
CTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAGgtacatttctt--aacctgaaccagttt---atattgctatgcaaggtctctacaatggtcagttatatacataaagaataccttaactattgatagctggttaattattaccttttccttgcag
 || |  ||| || |||| |||||  | ||||| |||||||| |||||||| |||||||| ||||||||||||   |||||   |  ||     ||||    ||||| ||| | | ||||| | | |    ||| ||   | |   |  |||  ||  | ||   |  ||                         
TTCTCTAGATCTGGTAATCAGCTGCTTGGGACTCCATTGGACGAATGATCTTCCTGGAGCCATGATACAGgtaagcttctttagagttgttatggttttaagtattgttat-cgatgtctcaaaactcaaaagtgatgggcctggtgc-tacgctatgtcttctgaagtgca-----------------------

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|89762249|gb|DY689931.1|DY689931
EST:     GCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAG                         TGTAGGCTGGCGTTGCAACCTGATGGCCTTTTTCTGGCAGCAATTCTTGGT
genomic: GCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAGgtacatttct ... ttccttgcagTGTAGGCTGGCGTTGCAACCTGATGGCCTTTTTCTGGCAGCAATTCTTGGT
EST: gi|78078319|gb|DV506734.1|DV506734
EST:     GCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAG                         -G----CTGGCGTTGCAACCTGATGGCCTTTTTCTGGCAGCAATTCTTGGT
genomic: GCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAGgtacatttct ... ttccttgcagTGTAGGCTGGCGTTGCAACCTGATGGCCTTTTTCTGGCAGCAATTCTTGGT
EST: gi|101393422|gb|EB818643.1|EB818643
EST:     GCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAG                         TGTAGGCTGGCGTTGCAACCTGATGGCCTTTTTCTGGCAGCAATTCTTGGT
genomic: GCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAGgtacatttct ... ttccttgcagTGTAGGCTGGCGTTGCAACCTGATGGCCTTTTTCTGGCAGCAATTCTTGGT
EST: gi|71440891|gb|DR821941.1|DR821941
EST:     CCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAG                         TGTAGGCTGGCGTTGCAACCTGATGGCCTTTTTCTGGCACCAATTCTTGGT
genomic: C-TGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAGgtacatttct ... ttccttgcagTGTAGGCTGGCGTTGCAACCTGATGGCCTTTTTCTGGCAGCAATTCTTGGT
EST: gi|26456098|gb|CA827681.1|CA827681
EST:     GCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAG                         TGTAGGCTGGCGTTGCAACCTGATGGCCTTTTTCTGTCAGCAATTCTTGGT
genomic: GCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAGgtacatttct ... ttccttgcagTGTAGGCTGGCGTTGCAACCTGATGGCCTTTTTCTGGCAGCAATTCTTGGT
EST: gi|26560078|gb|CA832313.1|CA832313
EST:     GCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAG                         TGTAGGCTGGCGTTGCAACCTGATGGC
genomic: GCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAGgtacatttct ... ttccttgcagTGTAGGCTGGCGTTGCAACCTGATGGC
EST: gi|50328095|gb|CO523221.1|CO523221
EST:     GCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAG                         TGTAGGCTGGCGTTGCAACCTGATGGCCTTTTTCTGGCAGCAATTCTTGGT
genomic: GCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAGgtacatttct ... ttccttgcagTGTAGGCTGGCGTTGCAACCTGATGGCCTTTTTCTGGCAGCAATTCTTGGT
EST: gi|74241982|gb|DT649896.1|DT649896
EST:     GCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAG                         TGTAGGCTGGCGTTGCAACCTGATGGCCTTTTTCTGGCAGCAATTCTTGGT
genomic: GCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAGgtacatttct ... ttccttgcagTGTAGGCTGGCGTTGCAACCTGATGGCCTTTTTCTGGCAGCAATTCTTGGT
EST: gi|20208228|gb|BQ134317.1|BQ134317
EST:     GCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAG                         TGTAGGCTGGCGTTGCAACCTGATGGCCTTTTTCTGTCAGCAATT
genomic: GCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAGgtacatttct ... ttccttgcagTGTAGGCTGGCGTTGCAACCTGATGGCCTTTTTCTGGCAGCAATT
EST: gi|87157627|gb|DY402416.1|DY402416
EST:     GCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAG                         TGTAGGCTGGCGTTGCAACCTGATGGCCTTTTTCTGTCAGCAATTC
genomic: GCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAGgtacatttct ... ttccttgcagTGTAGGCTGGCGTTGCAACCTGATGGCCTTTTTCTGGCAGCAATTC
EST: gi|22819976|gb|BU500066.1|BU500066
EST:     GCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAG                         TGTAGGCTGGCGTTGCAACCTGATGGCCTTTTTCTGTCAGCAATTCTTGGT
genomic: GCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAGgtacatttct ... ttccttgcagTGTAGGCTGGCGTTGCAACCTGATGGCCTTTTTCTGGCAGCAATTCTTGGT
EST: gi|93282992|gb|EB675256.1|EB675256
EST:     GCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAG                         TGTAGGCTGGCGTTGCAACCTGATGGCCTTTTTCTGGCAGCAATTCTTGGT
genomic: GCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAGgtacatttct ... ttccttgcagTGTAGGCTGGCGTTGCAACCTGATGGCCTTTTTCTGGCAGCAATTCTTGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAGgtacatttcttaacctgaaccagtttatattgctatgcaaggtctctacaatggtcagttatatacataaagaataccttaactattgatagctggttaattattaccttttccttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA