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'   		11  
 5'  3'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCATTATTGCTTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCGGAGAAGTATCCTGATATGATTATTAAGgttaagtgccctaatattattttgggctcagtgtttggctctgttgtgttccatatttacatgatacttctctaaattgtgttacttatgtttaaatttaatttatgggaataccag

Basic information

species Zea mays
transcript GRMZM2G064695_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064695_T03 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g40830.1 (Oryza sativa), 5'ss of exon 6
CTCATTATTGCTTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCGGAGAAGTATCCTGATATGATTATTAAGgttaagtgccctaatattattttgggctcagtgtt--tggctctgttgtg---ttccatatttacatgatacttctctaaattgtgttacttatgtttaaatttaatttatgggaataccag
|||||||| || ||||||||||||||||||||||||||||||||||| |||||||| ||||||||||| || ||||| ||         | | ||      | |  ||||     |    |||||   |||   ||||   | ||  ||    |     |    | ||  || ||||  |||     ||| | ||||
CTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAGAAGTACCCTGATATGATCATCAAGgtaaatctattgcctctaatcaatatccctctgttggcaacagcattgtgtgcttctgcatttttttaattgtttctaatgaaatcgatcatacattgaaatgcaatgctctggattgccag

upper sequence: GRMZM2G064695_T03 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA13G18730.1 (Glycine max), 5'ss of exon 6
CTCATTATTGCTTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCGGAGAAGTATCCTGATATGATTATTAAGgttaagtgccct-aatattattttg---ggctcagtgtttggctctgttgtgttccatatttacatgatacttctctaaattgtgttacttatgtttaaatttaatttatgggaataccag
 | || |||||||| || |||||||||||||| |||||||| || || ||||| | ||| || |||||||| |||||| | |  |||  | |||  | |    || | ||  |||  | |||   || ||  | |||||| |||||  ||      ||   |  |||| | ||                       
ATTATAATTGCTTGTAGTAAGGGAGGAACCAGCATTGAAGACCTAGCAGAGAAATTTCCGGACATGATTATAAAGgtttattatccttgacatttctcttcgtggtttagattttcac-ctgagctggtct-tctttacaagatacacct----gatgcactctttatttctagtag-------------------

upper sequence: GRMZM2G064695_T03 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA10G04480.1 (Glycine max), 5'ss of exon 6
CTCATTATTGCTTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCGGAGAAGTATCCTGATATGATTATTAAGgttaagtgccctaatattattttgggctcagtgtttggctctgttgtgttccatatttacatgatacttctctaaattgtgttacttatgtttaaatttaatttatgggaataccag
 | || |||||||| || |||||||||||||| |||||||| ||||| ||||| | ||| || |||||||| ||||||   || |||  |   ||||     |||  |||| | | | |          |  |      | ||||| |  |   | |  || ||||  |   ||  ||| | | |       
ATTATAATTGCTTGTAGTAAGGGAGGAACCAGCATTGAAGACCTTGCAGAGAAATTTCCGGACATGATTATAAAGgtttgttgtcct--tggcatttctca-tcatggtttagttttttc---------acctgagcagt-cttctttgcaagatatacctgatgt--actctttctttctagtag------

upper sequence: GRMZM2G064695_T03 (Zea mays), 5'ss of exon 6
lower sequence: AT2G20420.1 (Arabidopsis thaliana), 5'ss of exon 6
CTCATTATTGCTTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCGGAGAAGTATCCTGATATGATTATTAAGgttaagtgccctaatattattttgggctcagtgtttggctctgttgtgttccatatttacatgatacttctctaaattgtgttacttatgtttaaattta-atttatgggaataccag
 | || ||||| || |  ||||| || |||||||||||||||||||| |||||||  ||||| ||||| || ||||||   | |  |    ||  || |   |  ||| |  | |||   ||     ||  ||    ||| ||| ||| |   | |||  | |    | || | |   || || | |      
TTGATCATTGCCTGTAAAAAGGGTGGTACCAGTATTGAAGATCTTGCTGAGAAGTTCCCTGACATGATCATCAAGgttgt-tactgt----ttgattcgtatttggtggtctgatctccagtaaat-atcattctgagattctt-tctcatgcgggtttttgacacctcaagtcatggttttgcgtag-----

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|71760334|gb|DR958271.1|DR958271
EST:     GAACCAGTATTGAAGATCTTGCGGAGAAGTATCCTGATATGATTATTAAG                         GTTCCTATTGATGTATTTAAAGGAATCACAGATGAGGATGCAGCTA
genomic: GAACCAGTATTGAAGATCTTGCGGAGAAGTATCCTGATATGATTATTAAGgttaagtgcc ... ggaataccagGTTCCTATTGATGTATTTAAAGGAATCACAGATGAGGATGCAGCTA
EST: gi|149076126|gb|EE164711.2|EE164711
EST:     GAACCAGTATTGAAGATCTTGCGGAGAAGTATCCTGATATGATTATTAAG                         GTTCCTATTGATGTATTTAAAGGAATCACAGATGAGGATGCAGCTAAAGTT
genomic: GAACCAGTATTGAAGATCTTGCGGAGAAGTATCCTGATATGATTATTAAGgttaagtgcc ... ggaataccagGTTCCTATTGATGTATTTAAAGGAATCACAGATGAGGATGCAGCTAAAGTT
EST: gi|149094704|gb|EE180255.2|EE180255
EST:     GAACCAGTATTGAAGATCTTGCGGAGAAGTATCCTGATATGATTATTAAG                         GTTCCTATTGATGTATTTAAAGGAATCACAGATGAGGATGCAGCTAAAGTT
genomic: GAACCAGTATTGAAGATCTTGCGGAGAAGTATCCTGATATGATTATTAAGgttaagtgcc ... ggaataccagGTTCCTATTGATGTATTTAAAGGAATCACAGATGAGGATGCAGCTAAAGTT
EST: gi|148935326|gb|EC879367.2|EC879367
EST:     GAACCAGTATTGAAGATCTTGCGGAGAAGTATCCTGATATGATTATTAAG                         GTTCCTATTGATGTATTTAAAAGGA-TCACAGATGAGGATGCAGCTAAAGT
genomic: GAACCAGTATTGAAGATCTTGCGGAGAAGTATCCTGATATGATTATTAAGgttaagtgcc ... ggaataccagGTTCCTATTGATGTATTTAAA-GGAATCACAGATGAGGATGCAGCTAAAGT
EST: gi|13382325|gb|BG459000.1|BG459000
EST:     GAACCAGTATTGAAGATCTTGCGGAGAAGTATCCTGATATGATTATTAAG                         GTTCCTATTGATGTATTTAAAGGAATCACAGATGAGGATGCAGCTAAAGTT
genomic: GAACCAGTATTGAAGATCTTGCGGAGAAGTATCCTGATATGATTATTAAGgttaagtgcc ... ggaataccagGTTCCTATTGATGTATTTAAAGGAATCACAGATGAGGATGCAGCTAAAGTT
EST: gi|67017499|gb|CO446248.1|CO446248
EST:     GAACCAGTATTGAAGATCTTGCGGAGAAGTATCCTGATATGATTATTAAG                         GTTCCTATTGATGTATTTAAAGGAATCACAGATGAGGATGCAGCTAAAGTT
genomic: GAACCAGTATTGAAGATCTTGCGGAGAAGTATCCTGATATGATTATTAAGgttaagtgcc ... ggaataccagGTTCCTATTGATGTATTTAAAGGAATCACAGATGAGGATGCAGCTAAAGTT
EST: gi|91872808|gb|EB402765.1|EB402765
EST:     GAACCAGTATTGAAGATCTTGCGGAGAAGTATCCTGATATGATTATTAAG                         GTTCCTATTGATGTATTTAAAGGAATCACAGATGAGGATGCAGCTAAAGTT
genomic: GAACCAGTATTGAAGATCTTGCGGAGAAGTATCCTGATATGATTATTAAGgttaagtgcc ... ggaataccagGTTCCTATTGATGTATTTAAAGGAATCACAGATGAGGATGCAGCTAAAGTT
EST: gi|149017003|gb|EE154318.2|EE154318
EST:     GAACCAGTATTGAAGATCTTGCGGAGAAGTATCCTGATATGATTATTAAG                         GTTCCTATTGATGTATTTAAAGGAATCACAGATGAGGATGCAGCTAAAGTT
genomic: GAACCAGTATTGAAGATCTTGCGGAGAAGTATCCTGATATGATTATTAAGgttaagtgcc ... ggaataccagGTTCCTATTGATGTATTTAAAGGAATCACAGATGAGGATGCAGCTAAAGTT
EST: gi|76282776|gb|DV022344.1|DV022344
EST:     GAACCAGTATTGAAGATCTTGCGGAGAAGTATCCTGATATGATTATTAAG                         GTTCCTATTGATGTATTTAAAGGAATCACAGATGAGGATGCAGCTAAAGTT
genomic: GAACCAGTATTGAAGATCTTGCGGAGAAGTATCCTGATATGATTATTAAGgttaagtgcc ... ggaataccagGTTCCTATTGATGTATTTAAAGGAATCACAGATGAGGATGCAGCTAAAGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCATTATTGCTTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCGGAGAAGTATCCTGATATGATTATTAAGgttaagtgccctaatattattttgggctcagtgtttggctctgttgtgttccatatttacatgatacttctctaaattgtgttacttatgtttaaatttaatttatgggaataccag

- - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT