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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGGCTGATGTGTTTCATATACTTTCAGGCATGTGGAAGACACCTGCTGAAAGGTGCTTCCTATGGCTTGGGGGTTTTCGTCCATCTGAGCTTTTAAAGgtgagcattgtcaggcttcgttttttttctgtgtcctcactggaaatgcaaggttgctgatttgtctgcataatggaaaatatcag

Basic information

species Zea mays
transcript GRMZM2G361847_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G361847_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os07g48820.2 (Oryza sativa), 5'ss of exon 8
AAAGGCTGATGTGTTTCATATACTTTCAGGCATGTGGAAGACACCTGCTGAAAGGTGCTTCCTATGGCTTGGGGGTTTTCGTCCATCTGAGCTTTTAAAGgtgagcattg-tcaggcttcgttttttttctgtgt----------cctcactggaaatgcaaggt-tgctgatttgtctgcataatggaaaatatcag
|||||| |||||||||||||||||||||||||||||||||||||| || ||||| |||||||| |||||||| ||||| ||||||||||||||| ||||||||| |   | | |    ||  | ||||  | | |          |||  ||||   || ||  | | |||||||  |   ||  |  ||||| ||||
AAAGGCCGATGTGTTTCATATACTTTCAGGCATGTGGAAGACACCCGCAGAAAGATGCTTCCTGTGGCTTGGTGGTTTCCGTCCATCTGAGCTTCTAAAGgtgaccgcagattaaatctcaatattttcttatttgtctgatgcccctttctggtcctgtaatttatactgatttcaccatatggtacaaaatttcag

upper sequence: GRMZM2G361847_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA20G39050.2 (Glycine max), 5'ss of exon 8
AAAGGCTGATGTGTTTCATATACTTTCAGGCATGTGGAAGACACCTGCTGAAAGGTGCTTCCTATGGCTTGGGGGTTTTCGTCCATCTGAGCTTTTAAAGgtgagca---ttgtcaggcttcgttttttt-tctgtgtcctcactggaaatgcaaggttgctgatttgtctgcataatggaaaatatcag--------------
 ||||||||||| || ||| |  | || || |||||||||||||| || || ||||| || ||||||||||| ||||||||  ||||||| ||  | |||||||||    |||| |  ||||| |||  | |  |  |  |   | ||||   |   ||| ||| || |||  | | | |    | |  |              
TAAGGCTGATGTCTTCCATTTGTTGTCTGGAATGTGGAAGACACCAGCAGAGAGGTGTTTTCTATGGCTTGGTGGTTTTCGGTCATCTGAACTCCTCAAGgtgagctgatttgtgacccttcgatttgctgttcgcatggtttgttgaaagata---ttg-tgacttttctaaaaagtagtttttcttggtaacatacagagta

upper sequence: GRMZM2G361847_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA10G44270.1 (Glycine max), 5'ss of exon 8
AAAGGCTGATGTGTTTCATATACTTTCAGGCATGTGGAAGACACCTGCTGAAAGGTGCTTCCTATGGCTTGGGGGTTTTCGTCCATCTGAGCTTTTAAAGgtgagcattgtcaggctt----cgttttttttctgtgtcctcactggaaatgcaaggttgctgatttgtctgcataatggaaaatatcag----------
 ||||||||||| || ||| | || || || |||||||||||||| || || ||||| || ||||||||||| ||||||||  ||||||| ||  | |||||||||    |   | ||    |  ||   ||   ||  ||||  |    |  || |    ||     | |  | || | |   |    |          
TAAGGCTGATGTCTTCCATTTGCTGTCTGGAATGTGGAAGACACCAGCAGAGAGGTGTTTTCTATGGCTTGGTGGTTTTCGGTCATCTGAACTCCTCAAGgtgagctgatttgtgattgtaacccttcagtttgctgctctcaaggtttgttgaaagacattgtggcttttctaaaaagtagttttcttggtaacataca

upper sequence: GRMZM2G361847_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA13G26280.1 (Glycine max), 5'ss of exon 10
AAAGGCTGATGTGTTTCATATACTTTCAGGCATGTGGAAGACACCTGCTGAAAGGTGCTTCCTATGGCTTGGGGGTTTTCGTCCATCTGAGCTTTTAAAGgtgagcattgtcaggcttcgttttttttctgtgtcctcactggaaatgcaaggttgctgatttgtctgcataatggaaaatatcag--------------------
 ||||||||||| || ||| | || || ||||||||||| ||||||||||| ||||| ||  | |||||||| ||||||||  ||||||| ||| | ||||||||  || |   | | | |||  ||   || || |   |   ||  |  | ||  |   ||       ||||||| | | |                       
TAAGGCTGATGTTTTCCATTTGCTGTCTGGCATGTGGAAAACACCTGCTGAGAGGTGTTTTTTGTGGCTTGGTGGTTTTCGGTCATCTGAACTTCTCAAGgtgag-gttatgctgatccttttcattctagtttcatggtttagaaaacgggttttgtagatta-----gtaatggacagttttgtttaaattttttaaaaagaag

upper sequence: GRMZM2G361847_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv08s0007g05170.t01 (Vitis vinifera), 5'ss of exon 9
AAAGGCTGATGTGTTTCATATACTTTCAGGCATGTGGAAGACACCTGCTGAAAGGTGCTTCCTATGGCTTGGGGGTTTTCGTCCATCTGAGCTTTTAAAGgtgagcattgtc-----aggcttcgttttttttctgtgtcctcactggaaatgcaaggttgctgatttgtctgcataatggaa----aatatcag-------
 ||||||||||| || || || || ||||| ||||||||||||||||| ||| |||| ||  | ||| |||| ||||| ||| |||||||  |  | |||||||| |||||      | | |||  | | |||   |||  | ||   |||  |||  |     || |||   |   ||  ||     || |  |       
CAAGGCTGATGTCTTCCACATCCTGTCAGGAATGTGGAAGACACCTGCAGAACGGTGTTTTATGTGGATTGGCGGTTTCCGTTCATCTGAAGTCCTCAAGgtgagaattgtttcctgatgattccatctattttactgt--ttaccttaaaaacaacatctactatatgttccctggattaaattgggattttggttgaatg

upper sequence: GRMZM2G361847_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv13s0084g00660.t01 (Vitis vinifera), 5'ss of exon 10
AAAGGCTGATGTGTTTCATATACTTTCAGGCATGTGGAAGACACCTGCTGAAAGGTGCTTCCTATGGCTTGGGGGTTTTCGTCCATCTGAGCTTTTAAAGgtgagcattgtcaggcttcgttttttttctgtgtcctcactggaaatgcaaggttgctgatttgtctgcataat-ggaaaatatcag-----------------
 ||||||||||| || ||| || | |||||||||||||| |||||||| || ||||| ||  | |||||||| ||||| ||| ||||||| ||  |||||||    ||   |    | |  ||||  |   |  | ||  | |   |     |   || |         ||||| |||| |  |||                  
CAAGGCTGATGTTTTCCATTTATTATCAGGCATGTGGAAAACACCTGCAGAGAGGTGTTTTTTGTGGCTTGGTGGTTTCCGTTCATCTGAACTCCTAAAGgt----atgacccttttaccattttgatggtttccttctgttggggtattcagaccctcaccctgacaaataataggaagacttcatctccatatccatttctt

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|67010792|gb|CO439541.1|CO439541
EST:     AAAGGTGCTTCCTATGGCTTGGGGGTTTTCGTCCATCTGAGCTTTTAAAG                         CTCCTAGCGAATCACCTCGAGTCTCTAACTGAGCAGCAAATGCTGGGTTTG
genomic: AAAGGTGCTTCCTATGGCTTGGGGGTTTTCGTCCATCTGAGCTTTTAAAGgtgagcattg ... aaaatatcagCTCCTAGCGAATCACCTCGAGCCTCTAACTGAGCAGCAAATGCTGGGTTTG
EST: gi|71761438|gb|DR959375.1|DR959375
EST:     GAGCTTTTAAAG                         CTCCTAGCGAATCACCTCGAGCCTCTAACTGAGCAGCAAATGCTGGGTTTG
genomic: GAGCTTTTAAAGgtgagcattg ... aaaatatcagCTCCTAGCGAATCACCTCGAGCCTCTAACTGAGCAGCAAATGCTGGGTTTG
EST: gi|18659659|gb|BM500456.1|BM500456
EST:     TGGGGGTTTTCGTCCATCTGAGCTTTTAAAG                         CTCCTAGCGAATCACCTCGAGCCTCTAACTGAGCAGCAAATGCTGGGTTTG
genomic: TGGGGGTTTTCGTCCATCTGAGCTTTTAAAGgtgagcattg ... aaaatatcagCTCCTAGCGAATCACCTCGAGCCTCTAACTGAGCAGCAAATGCTGGGTTTG
EST: gi|211297091|gb|FL187053.1|FL187053
EST:     AAAGGTGCTTCCTATGGCTTGGGGGTTTTCGTCCATCTGAGCTTTTAAAG                         CTCCTAGCGAATCACCTCGAGCCTCTAACTGAGCAGCAAATGCTGGGTTTG
genomic: AAAGGTGCTTCCTATGGCTTGGGGGTTTTCGTCCATCTGAGCTTTTAAAGgtgagcattg ... aaaatatcagCTCCTAGCGAATCACCTCGAGCCTCTAACTGAGCAGCAAATGCTGGGTTTG
EST: gi|211475615|gb|FL459206.1|FL459206
EST:     AAAGGTGCTTCCTATGGCTTGGGGGTTTTCGTCCATCTGAGCTTTTAAAG                         CTCCTAGCGAATCACCTCGAGCCTCTAACTGAGCAGCAAATGCTGGGTTTG
genomic: AAAGGTGCTTCCTATGGCTTGGGGGTTTTCGTCCATCTGAGCTTTTAAAGgtgagcattg ... aaaatatcagCTCCTAGCGAATCACCTCGAGCCTCTAACTGAGCAGCAAATGCTGGGTTTG
EST: gi|44901587|gb|CK828132.1|CK828132
EST:     AAAGGTGCTTCNTATGGCTT-GGGGTTTTCGTCCATCTGAGC-TTTAAAG                         CTCCTAGCGAATCACCTCGAGCCTCTAACTGAGCAGCAAATGCTGGGTTTG
genomic: AAAGGTGCTTCCTATGGCTTGGGGGTTTTCGTCCATCTGAGCTTTTAAAGgtgagcattg ... aaaatatcagCTCCTAGCGAATCACCTCGAGCCTCTAACTGAGCAGCAAATGCTGGGTTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGGCTGATGTGTTTCATATACTTTCAGGCATGTGGAAGACACCTGCTGAAAGGTGCTTCCTATGGCTTGGGGGTTTTCGTCCATCTGAGCTTTTAAAGgtgagcattgtcaggcttcgttttttttctgtgtcctcactggaaatgcaaggttgctgatttgtctgcataatggaaaatatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT