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

GACTTCAGATGATAGAGTGAAGGCAATTCTAGTGAACATTTTTGGTGGCATTATGAAATGTGATGTGATAGCAAGTGGAATTGTTAATGCTGCCAAACAGgtacatttttagcctttcttagctttatgtataacataggttcctgacaatgttggcataccccccacccccctccccccccaacaacaacaacagaatc...

Basic information

species Zea mays
transcript GRMZM2G064695_T04
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064695_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os02g40830.1 (Oryza sativa), 5'ss of exon 10
GACTTCAGATGATAGAGTGAAGGCAATTCTAGTGAACATTTTTGGTGGCATTATGAAATGTGATGTGATAGCAAGTGGAATTGTTAATGCTGCCAAACAGgtacatttttagcctttcttagctttatgtataacataggttcctgacaatgttggcataccccccacccccctccccccccaacaacaacaacagaatc-
|||||| ||||||||||||||||| ||||||||||||||||||||||| || ||||||||||||||||||||||||||||| || ||||| || ||||||||   | || |   ||| |  |   | |  ||   ||   |     |   | |||   | ||| |    |  |         ||  |||| |     ||  
GACTTCCGATGATAGAGTGAAGGCTATTCTAGTGAACATTTTTGGTGGTATCATGAAATGTGATGTGATAGCAAGTGGAATAGTGAATGCAGCAAAACAGgtttgtcttcaaattttgtatgtagttttcatttaatgactaaagcagcttattgtggttccctct-tgcttcaaattaataaattacaatatacctattg

upper sequence: GRMZM2G064695_T02 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA13G18730.1 (Glycine max), 5'ss of exon 10
GACTTCAGATGATAGAGTGAAGGCAATTCTAGTGAACATTTTTGGTGGCATTATGAAATGTGATGTGATAGCAAGTGGAATTGTTAATGCTGCCAAACAGgtacatttttagcctttcttagctttatgtataacataggttcctgacaatgttggcata------ccccccacccccctccccccccaacaacaacaacagaatc
|||| | ||||| | ||||||||||||| | || ||||||||||| || || ||||| |||||||| |||||||||||||| || |||||||| ||| ||||   |||   |||| |     | |     | || |||  |   ||| ||    |  ||       |    || ||   |  |  ||      |||| | | |   
GACTGCTGATGACAAAGTGAAGGCAATTTTGGTTAACATTTTTGGGGGTATAATGAAGTGTGATGTTATAGCAAGTGGAATAGTGAATGCTGCAAAAGAGgttagttt---gcctattcccccctcccacaaaaaataaataaatgaaaaaacagaaatcttatgtctttacaaccagttttcttcctttgtccaaccatata---

upper sequence: GRMZM2G064695_T02 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA10G04480.1 (Glycine max), 5'ss of exon 10
GACTTCAGATGATAGAGTGAAGGCAATTCTAGTGAACATTTTTGGTGGCATTATGAAATGTGATGTGATAGCAAGTGGAATTGTTAATGCTGCCAAACAGgt---------acatttttagccttt---cttagctttatgtataacataggttcctg---acaatgttggcataccccccacccccctccccccccaacaacaacaacagaatc
|||| | ||||| | ||||||||||||| | || |||||||||||||| || ||||| |||||||| |||||||||||||| || |||||||| ||| ||||         |||| |  |  ||||    ||      |||||  |  |   ||  ||   || ||||||   ||                   |  ||                
GACTGCTGATGACAAAGTGAAGGCAATTTTGGTTAACATTTTTGGTGGTATAATGAAGTGTGATGTTATAGCAAGTGGAATAGTGAATGCTGCAAAAGAGgttagtcaagaacatgtaaattctttatatttgatcccatgtaagatttcaatttttgtttacgatgttgatgtaattgttgatattacaatttctgaaa---------------

upper sequence: GRMZM2G064695_T02 (Zea mays), 5'ss of exon 10
lower sequence: AT2G20420.1 (Arabidopsis thaliana), 5'ss of exon 10
GACTTCAGATGATAGAGTGAAGGCAATTCTAGTGAACATTTTTGGTGGCATTATGAAATGTGATGTGATAGCAAGTGGAATTGTTAATGCTGCCAAACAGgtacatttttagc--ctttcttagctttatgtataacataggttcctgacaatgttggcataccccccacccccctccccccccaacaacaacaacagaatc
||| || || |||| |||||| |||||  | |||||||| |||||||| || ||||||||||||||||| || |||||||| || || ||||| ||| ||||   |    | |  | || ||| | | || | |  ||||  ||| |||     |    |||   || |      |        ||   | |  ||||    
GACATCGGACGATAAAGTGAAAGCAATCTTGGTGAACATATTTGGTGGGATAATGAAATGTGATGTGATTGCTAGTGGAATCGTGAACGCTGCAAAAGAGgtgagtgagaaacaaccttgttaccataatattt--catatattcatgat----tgaaaataaatccgagt---gtttgtgtggaatggcgaggacag----

upper sequence: GRMZM2G064695_T02 (Zea mays), 5'ss of exon 10
lower sequence: Vv07s0005g03790.t01 (Vitis vinifera), 5'ss of exon 10
GACTTCAGATGATAGAGTGAAGGCAATTCTAGTGAACATTTTTGGTGGCATTATGAAATGTGATGTGATAGCAAGTGGAATTGTTAATGCTGCCAAACAGgtacatttttagcctttcttagct----ttatgtataacataggttcctgacaatgttggcataccccccacccccctccccccccaacaacaacaacagaatc
|||| | |||||||  || || |||||| |||||||||||||||| || || |||||||||||  | |||||||||||||||||||||||||| ||| |||||   | |    |    || | |    || |||  |  |     |  ||   ||  ||||  |       |    |   | | | ||  |   |  |      
GACTGCTGATGATAAGGTCAAAGCAATTTTAGTGAACATTTTTGGAGGAATAATGAAATGTGACATAATAGCAAGTGGAATTGTTAATGCTGCTAAAGAGgtaagatctgcatcaagattggttcagattctgttgattacctacttttgctcatagtggc-cattaaat-cttgtcatgctctctaattatgtcttctagt--

upper sequence: GRMZM2G064695_T02 (Zea mays), 5'ss of exon 10
lower sequence: PP1S9_103V6.1 (Physcomitrella patens), 5'ss of exon 10
GACTTCAGATGATAGAGTGAAGGCAATTCTAGTGAACATTTTTGGTGGCATTATGAAATGTGATGTGATAGCAAGTGGAATTGTTAATGCTGCCAAACAGgtacattt-ttagcctttcttagctttatgtataacataggttc---ctgacaatgttggcataccccccacccccctccccccccaacaacaacaacagaatc
|||||| ||    |||||||| || ||||| ||||||||||||||||| || ||||| |||||||| || ||   |||||||||   |||||| ||||||||| | || |     | |   ||    |||| |  |  || ||    |   ||||  | | |     |  |         |    ||  | ||    ||     
GACTTCCGACACGAGAGTGAAAGCTATTCTGGTGAACATTTTTGGTGGGATCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgtctaagtgtggcagaagaatgttttgctgagttttgttccttcaatactcgtaacattctgatatggaagtctatacataagcatgttcat----

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|18162086|gb|BM331925.1|BM331925
EST:     TTATGAAATGTGATGTGATAGCAAGTGGAATTGTTAATGCTGCCAAACAG                         GTTGACCTGAAAGTTCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTAGAC
genomic: TTATGAAATGTGATGTGATAGCAAGTGGAATTGTTAATGCTGCCAAACAGgtacattttt ... ccgttgtcagGTTGACCTGAAAGTTCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTAGAC
EST: gi|113831703|gb|DW948357.1|DW948357
EST:     GAATTGTTAATGCTAGCCAAACAG                         GTTGACCTGAAAGTTCCTGTTAGTTGTTCGGTTGGAAGGCACCAATGTAG
genomic: GAATTGTTAATGCT-GCCAAACAGgtacattttt ... ccgttgtcagGTTGACCTGAAAGTTCCTGTT-GTTGTTCGGTTGGAAGGCACCAATGTAG
EST: gi|211240439|gb|FL261946.1|FL261946
EST:     TT-TAAAATGTGATGTGATAGCAAGTGGAATTGTTAATGCTGCCAAACAG                         GTTGACCTGAAAGTTCCTGTTGTT
genomic: TTATGAAATGTGATGTGATAGCAAGTGGAATTGTTAATGCTGCCAAACAGgtacattttt ... ccgttgtcagGTTGACCTGAAAGTTCCTGTTGTT
EST: gi|211240437|gb|FL261944.1|FL261944
EST:     TTATGAAATGTGATGTGATAGCAAGTGGAATTGTTAATGCTGCCAAACAG                         GTTGACCTGAAAGTTCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTAGAC
genomic: TTATGAAATGTGATGTGATAGCAAGTGGAATTGTTAATGCTGCCAAACAGgtacattttt ... ccgttgtcagGTTGACCTGAAAGTTCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTAGAC
EST: gi|60354613|gb|DN221586.1|DN221586
EST:     TTATGAAATGTGATGTGATAGCAAGTGGAATTCTTAATGCTGCCAAACAT                         CTTGACCTGAAAGTTCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTAGAC
genomic: TTATGAAATGTGATGTGATAGCAAGTGGAATTGTTAATGCTGCCAAACAGgtacattttt ... ccgttgtcagGTTGACCTGAAAGTTCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTAGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACTTCAGATGATAGAGTGAAGGCAATTCTAGTGAACATTTTTGGTGGCATTATGAAATGTGATGTGATAGCAAGTGGAATTGTTAATGCTGCCAAACAGgtacatttttagcctttcttagctttatgtataacataggttcctgacaatgttggcataccccccacccccctccccccccaacaacaacaacagaatc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC