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'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACGCATGGGTCTTGGAAAGTCATCCTCAAATGTTGAGCCTCCTGAATTTGGTGCTGCAGCTGATGGAGATGCTGACCGCAACATGATTCTTGGTAAAAGgtatgatctgtttgagtatcttattttctacaaaatttgttacagattctagaaaagcgcaaggaattcatgacactcccctttgccttgctatag

Basic information

species Zea mays
transcript GRMZM2G109383_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G109383_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os03g50480.1 (Oryza sativa), 5'ss of exon 10
---AACGCATGGGTCTTGGAAAGTCATCCTCAAATGTTGAGCCTCCTGAATTTGGTGCTGCAGCTGATGGAGATGCTGACCGCAACATGATTCTTGGTAAAAGgtatgatct-gtttgagtatcttattttctacaaaatttgttacagattctagaaaagcgcaaggaattcatgacactcccctttgccttgctatag
   | || ||||| ||||||||   ||||||||||| ||| || || ||||||||||||||||||||||| |||||||| |||||||||||||| ||||||||||||  |   |  |   || |||         ||  |||  || | | ||   |        || |||| ||||   |  |||||||||| |||   
TTGACCGGATGGGCCTTGGAAA---ATCCTCAAATGCTGAACCCCCAGAATTTGGTGCTGCAGCTGATGGTGATGCTGATCGCAACATGATTCTGGGTAAAAGgtattcttcagcctagatagcttg--------aagtttttgtatatactcataagtgctatgagaaatttatgatg-tgtcctttgcctt-ctag--

upper sequence: GRMZM2G109383_T02 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA05G34790.1 (Glycine max), 5'ss of exon 10
AACGCATGGGTCTTGGAAAGTCATCCTCAAATGTTGAGCCTCCTGAATTTGGTGCTGCAGCTGATGGAGATGCTGACCGCAACATGATTCTTGGTAAAAGgtatgatctgtttgagtatcttattttctacaaaatttgttacagattctagaaaagcgcaaggaattcatgacactcccctttgccttgctatag
  || |||||  | || || ||     || | | ||| || || || |||||||||||  ||||||| ||||| || ||||||||||| ||||||||||||||   |     | | | | |  |    |   |||| |  | ||  || | |      |      ||   ||   | ||  ||||           
CTCGTATGGGATTGGGCAAATCCGAACCACAAGATGATCCCCCAGAGTTTGGTGCTGCTTCTGATGGTGATGCAGATCGCAACATGATACTTGGTAAAAGgtagtgttgcccttaatttgtggtgaatt--taaatattctccaactttttg-----tgtgtaatatctgtgtatcccctgtttgttag-------

upper sequence: GRMZM2G109383_T02 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA08G04890.1 (Glycine max), 5'ss of exon 10
AACGCATGGGTCTTGGAAAGTCATCCTCAAATGTTGAGCCTCCTGAATTTGGTGCTGCAGCTGATGGAGATGCTGACCGCAACATGATTCTTGGTAAAAGgtatgatctgtttgagtatcttattttctacaaaatttgttacagattctagaaaagcgcaaggaattcatgacactcccctttgccttgctatag
  || |||||  | || || ||     |  | |  ||||| || || |||||||||||  ||||||| ||||| || ||||||||| ||||||||||||||||   |     | | | | | ||    |  || |||   ||    || |      | | ||   ||   ||   | ||  ||||           
CTCGTATGGGATTGGGCAAATCCGAACCCCAAGAAGAGCCCCCAGAGTTTGGTGCTGCTTCTGATGGTGATGCAGATCGCAACATGGTTCTTGGTAAAAGgtagtgttgtccttaatttgtgatgaatttaaatattctctaactttttt------gtgtaat--atctgtgtatcccctgtttgttag-------

upper sequence: GRMZM2G109383_T02 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA03G05150.1 (Glycine max), 5'ss of exon 3
AACGCATGGGTCTTGGAAAGTCATCCTCAAATGTTGAGCCTCCTGAATTTGGTGCTGCAGCTGATGGAGATGCTGACCGCAACATGATTCTTGGTAAAAGgtatgatctgtttgagtatcttattttctacaaaatttgttacagattctagaaaagcgcaaggaattcatgacactcccctttgccttgctatag
  || |||||  | || || ||     |  | | |||||| || || |||||||||||  ||||||| ||||| || ||||||||| ||||||||||||||||   |     | | | | | ||    |  || |||   ||    || |      | | ||   ||   ||   | |   ||||           
CTCGTATGGGATTGGGCAAATCTGAACCCCAAGATGAGCCCCCAGAGTTTGGTGCTGCTTCTGATGGTGATGCAGATCGCAACATGGTTCTTGGTAAAAGgtagtgttgtccttaatttgtgatgaatttaaatattctctaactttttt------gtgtaat--atctgtgtatcccttgtttgttag-------

upper sequence: GRMZM2G109383_T02 (Zea mays), 5'ss of exon 10
lower sequence: AT1G23190.1 (Arabidopsis thaliana), 5'ss of exon 10
AACGCATGGGTCTTGGAAAGTCATCCTCAAATGTTGAGCCTCCTGAATTTGGTGCTGCAGCTGATGGAGATGCTGACCGCAACATGATTCTTGGTAAAAGgtatgatctgtttgagtatcttattttctacaaaatttgttacagattctagaaaagcgcaaggaattcatgacactcccctttgccttgct-atag
 ||| |||||  | || || ||   | |    | ||| ||||| || ||||| || || |||||||| ||||| ||||| |||||||| ||||||||||||||     |  |   ||      |||      | ||   |    |   |||| | |   |||| | ||    ||        |  | |   |  |||
CACGAATGGGATTAGGTAAATCCGACACTGGAGGTGAACCTCCAGAGTTTGGCGCCGCTGCTGATGGTGATGCAGACCGTAACATGATCCTTGGTAAAAGgta--gcttactgacgt------tttcaagagagatacatccatggaactagtatac--caagtacttttaaacttaaagtatctcttcatttgtag

upper sequence: GRMZM2G109383_T02 (Zea mays), 5'ss of exon 10
lower sequence: AT1G70730.1 (Arabidopsis thaliana), 5'ss of exon 10
AACGCATGGGTCTTGG--AAAGTCATCCT-CAAATGTTGAGCCTCCTGAATTTGGTGCTGCAGCTGATGGAGATGCTGACCGCAACATGATTCTTGGTAAAAGgtatgatctgtttgagtatcttattttctacaaaatttgttacagattctagaaaagcgcaaggaattcatgacactcccctttgccttgctatag-------------
   |||||||  |  |  ||| | ||  | |   ||  |||||||| || ||||| || || |||||||| ||||| ||||| |||||||| || |||||||||||  |         |   || ||| |||   || |       ||||   ||| | | | |  | ||  |  || |||||| ||  |     |||              
---GCATGGGATTGAGTAAAACTGATGATGCTGGTGGCGAGCCTCCAGAGTTTGGCGCCGCTGCTGATGGTGATGCAGACCGAAACATGATCCTCGGTAAAAGgtagca---------gagactaattctcttttaagtg------agatcacagagatgtggagcggatataccactctccccgttaaccaaaaatatctcttctccgcag

upper sequence: GRMZM2G109383_T02 (Zea mays), 5'ss of exon 10
lower sequence: PP1S4_12V6.2 (Physcomitrella patens), 5'ss of exon 11
---AACGCATGGGTCTTGGAAAGTCATCCTCAAATGTTGAGCCTCCTGAATTTGGTGCTGCAGCTGATGGAGATGCTGACCGCAACATGATTCTTGGTAAAAGgtatgatctgtttgagtatcttattttctacaaaatttgttacagattctagaaaagcgcaaggaattcatgacact---cccctttgccttgctatag----
   ||   |||||  | || |||    |   |  ||  |||  ||| ||||| ||||| || |||||||| ||||||||||| ||||||||| | || || | |||||   || |   |  ||  || | | ||    | | |||     ||| |||        |   |   |    ||   |||  |     ||   |||    
TGCAAGTTATGGGATTGGGCAAGA---CTCAACCTGACGAGATTCCGGAATTCGGTGCCGCTGCTGATGGTGATGCTGACCGAAACATGATTTTGGGCAAGAAgtatg---tgatcagggctcccatctacgactccttgtcttaatctatctggaagttgatgtgatttctgtattcctgatcccgctaattctgtgttagcttt

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|32915471|gb|CF020283.1|CF020283
EST:     GGTGCTGCAGCTGATGGAGATGCTGACCGCAACATGATTCTTGGTAAAAG                         ATTCTTTGTGACACCGTCGGACTCTGTTGCCATTATCGCAGCAAATGCTGT
genomic: GGTGCTGCAGCTGATGGAGATGCTGACCGCAACATGATTCTTGGTAAAAGgtatgatctg ... cttgctatagATTCTTTGTGACACCGTCGGACTCTGTTGCCATTATCGCAGCCAATGCTGT
EST: gi|67018536|gb|CO447285.1|CO447285
EST:     GGTGCTGCAGCTGATGGAGATGCTGACCGCAACATGATTCTTGGTAAAAG                         ATTCTTTGTGACACCGTCGGACTCTGTTGCCATTATCGCAGCCAATGCTGT
genomic: GGTGCTGCAGCTGATGGAGATGCTGACCGCAACATGATTCTTGGTAAAAGgtatgatctg ... cttgctatagATTCTTTGTGACACCGTCGGACTCTGTTGCCATTATCGCAGCCAATGCTGT
EST: gi|31363628|gb|CD447985.1|CD447985
EST:     GGCGCTGCAGCTGATGGAGATGCTGACCGCAACATGATTCTTGGTAAAAG                         ATTCTTTGTGACACCGTCGGACTCTGTTGCCATTATCGCAGCCAATGCTGT
genomic: GGTGCTGCAGCTGATGGAGATGCTGACCGCAACATGATTCTTGGTAAAAGgtatgatctg ... cttgctatagATTCTTTGTGACACCGTCGGACTCTGTTGCCATTATCGCAGCCAATGCTGT
EST: gi|67025909|gb|CO454658.1|CO454658
EST:     GTGCTGCAACTGATGGAGATGCTGACCGCAACATGATTCTTTGGTAAAAG                         ATTCTTTGTGACACCGTC
genomic: GTGCTGCAGCTGATGGAGATGCTGACCGCAACATGATTCTT-GGTAAAAGgtatgatctg ... cttgctatagATTCTTTGTGACACCGTC
EST: gi|31353391|gb|CD437748.1|CD437748
EST:     GGCGCTGCAGCTGATGGAGATGCTGACCGCAACATGATTCTTGGTAAAAG                         ATTCTTTGTGACACCGTCGGACTCTGTTGCCATTATCGCAGCCAATGCTGT
genomic: GGTGCTGCAGCTGATGGAGATGCTGACCGCAACATGATTCTTGGTAAAAGgtatgatctg ... cttgctatagATTCTTTGTGACACCGTCGGACTCTGTTGCCATTATCGCAGCCAATGCTGT
EST: gi|32910896|gb|CF015708.1|CF015708
EST:     GGTGCTGCAGCTGATGGAGATGCTGACCGCAACATGATTCTTGGTAAAAG                         ATTCTTTGTGACACCGTCGGACTCTGTTGCCATTATCGCAGCAAATGCTGT
genomic: GGTGCTGCAGCTGATGGAGATGCTGACCGCAACATGATTCTTGGTAAAAGgtatgatctg ... cttgctatagATTCTTTGTGACACCGTCGGACTCTGTTGCCATTATCGCAGCCAATGCTGT
EST: gi|67022599|gb|CO451348.1|CO451348
EST:     GGTGCTGCAGCTGATGGAGATGCTGACCGCAACATGATTCTTGGTAAAAG                         ATTCTTTGTGACACCGTCGGACTCTGTTGCCATTATCGCAGCCAATGCTGT
genomic: GGTGCTGCAGCTGATGGAGATGCTGACCGCAACATGATTCTTGGTAAAAGgtatgatctg ... cttgctatagATTCTTTGTGACACCGTCGGACTCTGTTGCCATTATCGCAGCCAATGCTGT
EST: gi|31354675|gb|CD439032.1|CD439032
EST:     GGCGCTGCAGCTGATGGAGATGCTGACCGCAACATGATTCTTGGTAAAAG                         ATTCTTTGTGACACCGTCGGACTCTGTTGCCATTATCGCAGCCAATGCTGT
genomic: GGTGCTGCAGCTGATGGAGATGCTGACCGCAACATGATTCTTGGTAAAAGgtatgatctg ... cttgctatagATTCTTTGTGACACCGTCGGACTCTGTTGCCATTATCGCAGCCAATGCTGT
EST: gi|211541124|gb|FL006425.1|FL006425
EST:     GGTGCTGCAGCTGATGGAGATGCTGACCGCAACATGATTCTTGGTAAAAG                         ATTCTTTGTGACACCGTCGGACTCTGTTGCCATTATCGCAGCCAATGCTGT
genomic: GGTGCTGCAGCTGATGGAGATGCTGACCGCAACATGATTCTTGGTAAAAGgtatgatctg ... cttgctatagATTCTTTGTGACACCGTCGGACTCTGTTGCCATTATCGCAGCCAATGCTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACGCATGGGTCTTGGAAAGTCATCCTCAAATGTTGAGCCTCCTGAATTTGGTGCTGCAGCTGATGGAGATGCTGACCGCAACATGATTCTTGGTAAAAGgtatgatctgtttgagtatcttattttctacaaaatttgttacagattctagaaaagcgcaaggaattcatgacactcccctttgccttgctatag

- - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG