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

GAAGGGTAATGAAAAGGCTGTCGTTGCACGGCATGAAGTAGGTCATGCACTCGTGGGAACTGCTGTAGCGAACCTTCTTCCTGGACAGCCACGTGTTGAGgtttgaacttaagcaattactgatagaacaatctgagagaagatgtaatttgacttactttttcaatgctgaatttaacag

Basic information

species Zea mays
transcript GRMZM2G163193_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G163193_T03 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os02g43350.1 (Oryza sativa), 5'ss of exon 10
GAAGGGTAATGAAAAGGCTGTCGTTGCACGGCATGAAGTAGGTCATGCACTCGTGGGAACTGCTGTAGCGAACCTTCTTCCTGGACAGCCACGTGTTGAGgtttgaacttaagcaattactgatagaacaatctgagagaagatgtaatttgacttactttttcaatgctgaatttaacag------
||||||||||||||||||||| ||||||||||||||||| ||||||||  | ||||||||||||||||| |||||  | || || ||||||||||| |||||||||||  |||||| ||  ||||||||| | | ||| ||  |     |||   |    ||| | || ||   ||           
GAAGGGTAATGAAAAGGCTGTTGTTGCACGGCATGAAGTTGGTCATGCCGTTGTGGGAACTGCTGTAGCAAACCTATTGCCAGGGCAGCCACGTGTGGAGgtttgaacgcaagcaactatcgatagaacagtttaagaaaatgttcgtcttgggcttacattttagtgttgttcttttttccaccag

upper sequence: GRMZM2G163193_T03 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA0028S00210.1 (Glycine max), 5'ss of exon 10
GAAGGGTAATGAAAAGGCTGTCGTTGCACGGCATGAAGTAGGTCATGCACTCGTGGGAACTGCTGTAGCGAACCTTCTTCCTGGACAGCCACGTGTTGAGgt------ttgaacttaagcaattactgatag---aacaatctgagagaagatgtaatttgacttactttttcaatgctgaatttaacag----------
|   || | ||| |||||||| |||||||| ||||| |  ||||||||  | || || ||||| || ||||| |||||||||||||||||||||||||||||      |||||  |   | |||||||  |    || ||| | |  |    |  |  |   |  | |       |  |     ||   |          
GCGAGGAAGTGAGAAGGCTGTAGTTGCACGACATGAGGCTGGTCATGCTGTAGTAGGTACTGCAGTTGCGAAGCTTCTTCCTGGACAGCCACGTGTTGAGgtaaactgttgaagatgctctattactggaaactaaaaaatgtcactgccattacagatatgcagattgaacttgtattacgcatatttgcctattttga

upper sequence: GRMZM2G163193_T03 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA14G37090.1 (Glycine max), 5'ss of exon 11
GAAGGGTAATGAAAAGGCTGTCGTTGCACGGCATGAAGTAGGTCATGCACTCGTGGGAACTGCTGTAGCGAACCTTCTTCCTGGACAGCCACGTGTTGAGgtttgaacttaagcaattactga---tagaacaatctgagagaa--gatgtaatttgacttactttttcaatgct-gaatttaacag---------------
||| || | ||| |||||||| ||||||||||||||||  ||||||||  | || || ||||| || || |||||||||||||||||||||||||||||||  | |||    | || | ||     |    | || | |        |||  |||  |  ||  |     ||||| | |   |                   
GAAAGGAAGTGAGAAGGCTGTAGTTGCACGGCATGAAGCTGGTCATGCTGTGGTAGGTACTGCAGTTGCAAACCTTCTTCCTGGACAGCCACGTGTTGAGg--taaaccatggaaaatgctctatttttggccatttaaatatgtcaatgccattgcagatatgtagatgatgcttggaccaagttacttgcctgcttgaat

upper sequence: GRMZM2G163193_T03 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA18G07280.1 (Glycine max), 5'ss of exon 10
GAAGGGTAATGAAAAGGCTGTCGTTGCACGGCATGAAGTAGGTCATGCACTCGTGGGAACTGCTGTAGCGAACCTTCTTCCTGGACAGCCACGTGTTGAGgt------ttgaacttaagcaattactgatag---aacaatctgagagaagatgta---atttgacttactttttcaatgctgaatttaacag-------
|   || | ||| |||||||| |||||||| ||||| |  ||||||||  | || || ||||| || || || |||||||||||||||||||||||||||||      |||||  |     |||||||  |    || ||| | |  |   ||  |   ||     || |  ||  |       ||||  |         
GCGAGGAAGTGAGAAGGCTGTAGTTGCACGACATGAGGCTGGTCATGCTGTAGTAGGTACTGCAGTTGCAAAGCTTCTTCCTGGACAGCCACGTGTTGAGgtaaaccattgaagatgctatattactggcaactaaaaaatgtcactgccaatacagatatgcagattgcgcttgtatacacatatttgcctatttgaaa

upper sequence: GRMZM2G163193_T03 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA02G39040.1 (Glycine max), 5'ss of exon 11
GAAGGGTAATGAAAAGGCTGTCGTTGCACGGCATGAAGTAGGTCATGCACTCGTGGGAACTGCTGTAGCGAACCTTCTTCCTGGACAGCCACGTGTTGAGgtttgaacttaagcaattactgatagaacaatctgagagaag---atgtaatttgacttactttttcaatgct-gaatttaacag---------------
||| || | ||| |||||||| ||||||||||||||||  ||||||||  | || || ||||| || || ||||||||||||||||||||||||||||||||      |  || |    ||  |       | | | | | |   |||  |||  |  ||        ||||| | |    | |                
GAAAGGAAGTGAGAAGGCTGTAGTTGCACGGCATGAAGCTGGTCATGCTGTAGTAGGTACTGCAGTTGCAAACCTTCTTCCTGGACAGCCACGTGTTGAGgtaaaccatggagaatgctctattcttggccttttaaatatgtcaatgccattgcagatatgcagatgatgcttgtaccacatacttgcctgcttgaatt

upper sequence: GRMZM2G163193_T03 (Zea mays), 5'ss of exon 9
lower sequence: AT3G47060.1 (Arabidopsis thaliana), 5'ss of exon 10
GAAGGGTAATGAAAAGGCTGTCGTTGCACGGCATGAAGTAGGTCATGCACTCGTGGGAACTGCTGTAGCGAACCTTCTTCCTGGACAGCCACGTGTTGAGgtttgaacttaagcaattactgatagaacaatctgagagaagatgtaatttg--acttac---tttttcaa----tgctgaatttaacag---------
 || || ||||| ||||| || || ||| |||||||||  || |||||| | || || || ||||| || || |||||| ||||||||||||||||||||||   ||   ||  | ||  |        |  || |  |   ||||  |||   || | |   |  |||||    |||| |  ||    |         
AAAAGGCAATGAGAAGGCAGTGGTCGCAAGGCATGAAGCTGGGCATGCAGTGGTTGGTACCGCTGTTGCAAATCTTCTTACTGGACAGCCACGTGTTGAGgta-aaatgcaaaaactttgtctacatttacgctcattgtttatgttgtttagtacgtgcaaatgattcaagttttgctcatctttgtggtgttgtcag

upper sequence: GRMZM2G163193_T03 (Zea mays), 5'ss of exon 9
lower sequence: Vv06s0004g06120.t01 (Vitis vinifera), 5'ss of exon 10
GAAGGGTAATGAAAAGGCTGTCGTTGCACGGCATGAAGTAGGTCATGCACTCGTGGGAACTGCTGTAGCGAACCTTCTTCCTGGACAGCCACGTGTTGAGgtttgaacttaagcaattactgatag--aacaatctgagagaagatgtaa-----tttgacttactt--tttcaatgctgaatttaacag----------
| |||| | ||| |||||||| ||||||||||||||||  ||||||||| | |||||||||||||| || || |||||||||||||||||||||||||||||  |   ||| |   ||| | | |   || | | |     |     |||     ||  | ||| ||    ||  ||  ||||||   ||          
GCAGGGAAGTGAGAAGGCTGTTGTTGCACGGCATGAAGCTGGTCATGCAGTAGTGGGAACTGCTGTTGCTAATCTTCTTCCTGGACAGCCACGTGTTGAGgtaagttattaggaccttatttacaataaatattttcctttactgcttaacaagtttcaaattatttaacctccctggagaatttggaagacacgtgaga

upper sequence: GRMZM2G163193_T03 (Zea mays), 5'ss of exon 9
lower sequence: PP1S10_296V6.2 (Physcomitrella patens), 5'ss of exon 13
GAAGGGTAATGAAAAGGCTGTCGTTGCACGGCATGAAGTAGGTCATGCACTCGTGGGAACTGCTGTAGCGAACCTTCTTCCTGGACAGCCACGTGTTGAGgtttgaacttaagcaattactgatagaacaatctgagagaagatgtaatttgacttactttttcaatgctgaatttaacag------------------------------------------------------------------------------------------------
| | ||   |||||||| |||||| ||||||||||| | |||||||||| | || ||||| ||||| || ||  || | ||||| |   |||| ||  ||||   | ||    |  ||| |  | |     | ||        |||| |  |  | |  |  | ||| |  | || ||||                                                                                                 
GCATGGCTCTGAAAAGGGTGTCGTAGCACGGCATGAGGCAGGTCATGCAGTGGTTGGAACCGCTGTTGCCAAGTTTATACCTGGTCTTACACGAGTGCAGgtacaacctc---cttttagttcttggtttctttgtttct---tgtattcagcgtcagctcctaaatccgtatttgaacaaatgacttcatttccctcttatgcatggttgagtaggttacctccaccttctttagccgtgaaatttctcaaatgtggtgttctttttatcttgcag

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|67033989|gb|CO462738.1|CO462738
EST:     TCGTGGGAACTGCTGTAGCGAACCTTCTTCCTGGACAGCCACGTGTTGAG                         AAATTGAGTATATTGCCAAGGTCAGGAGGTGCATTAGGCTTTACATACACC
genomic: TCGTGGGAACTGCTGTAGCGAACCTTCTTCCTGGACAGCCACGTGTTGAGgtttgaactt ... aatttaacagAAATTGAGTATATTGCCAAGGTCAGGAGGTGCATTAGGCTTTACATACACC
EST: gi|211378707|gb|FL467950.1|FL467950
EST:     TCGTGGGAACTGCTGTATCGAACCTTCTTCCTGGACAGCCACGTGTTGAG                         AAATTGAGTATATTGCCAAGGTCAGGAGGTGCATTAGGCTTTACATACACC
genomic: TCGTGGGAACTGCTGTAGCGAACCTTCTTCCTGGACAGCCACGTGTTGAGgtttgaactt ... aatttaacagAAATTGAGTATATTGCCAAGGTCAGGAGGTGCATTAGGCTTTACATACACC
EST: gi|71329683|gb|DR801566.1|DR801566
EST:     TCGTGGGAACTGCTGTAGCGAACCTTCTTCCTGGACAGCCACGTGTTGAG                         AAATTGAGTATATTGCCAAGGTCAGGAGGTGCATTAGGCTTTACATACACC
genomic: TCGTGGGAACTGCTGTAGCGAACCTTCTTCCTGGACAGCCACGTGTTGAGgtttgaactt ... aatttaacagAAATTGAGTATATTGCCAAGGTCAGGAGGTGCATTAGGCTTTACATACACC
EST: gi|211271700|gb|FL183886.1|FL183886
EST:     TCGTGGGAACTGCTGTATCGAACCTTCTTCCTGGACAGCCACGTGTTGAG                         AAATTGAGTATATTGCCAAGGTCAGGAGGTGCATTAGGCTTTACATACACC
genomic: TCGTGGGAACTGCTGTAGCGAACCTTCTTCCTGGACAGCCACGTGTTGAGgtttgaactt ... aatttaacagAAATTGAGTATATTGCCAAGGTCAGGAGGTGCATTAGGCTTTACATACACC
EST: gi|211271701|gb|FL183887.1|FL183887
EST:     TCGTGGGAACTGCTGTATCGAACCTTCTTCCTGGACAGCCACGTGTTGAG                         AAATTGAGTATATTGCCAAGGTCAGGAGGTCCATTAGGCTTTACATACACC
genomic: TCGTGGGAACTGCTGTAGCGAACCTTCTTCCTGGACAGCCACGTGTTGAGgtttgaactt ... aatttaacagAAATTGAGTATATTGCCAAGGTCAGGAGGTGCATTAGGCTTTACATACACC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 90

GAAGGGTAATGAAAAGGCTGTCGTTGCACGGCATGAAGTAGGTCATGCACTCGTGGGAACTGCTGTAGCGAACCTTCTTCCTGGACAGCCACGTGTTGAGgtttgaactt ... aatttaacagAAATTGAGTATATTGCCAAGGTCAGGAGGTGCATTAGGCTTTACATACACCCCTCCCACCACAGAGGATAGATATTTACTCTTTGTTGATGAACTACGTG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 134

GAAGGGTAATGAAAAGGCTGTCGTTGCACGGCATGAAGTAGGTCATGCACTCGTGGGAACTGCTGTAGCGAACCTTCTTCCTGGACAGCCACGTGTTGAGgtttgaactt ... aatttaacagAAATTGAGTATATTGCCAAGGTCAGGAGGTGCATTAGGCTTTACATACACCCCTCCCACCACAGAGGATAGATATTTACTCTTTGTTGATGAACTACGTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 152

GAAGGGTAATGAAAAGGCTGTCGTTGCACGGCATGAAGTAGGTCATGCACTCGTGGGAACTGCTGTAGCGAACCTTCTTCCTGGACAGCCACGTGTTGAGgtttgaactt ... aatttaacagAAATTGAGTATATTGCCAAGGTCAGGAGGTGCATTAGGCTTTACATACACCCCTCCCACCACAGAGGATAGATATTTACTCTTTGTTGATGAACTACGTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 194

GAAGGGTAATGAAAAGGCTGTCGTTGCACGGCATGAAGTAGGTCATGCACTCGTGGGAACTGCTGTAGCGAACCTTCTTCCTGGACAGCCACGTGTTGAGgtttgaactt ... aatttaacagAAATTGAGTATATTGCCAAGGTCAGGAGGTGCATTAGGCTTTACATACACCCCTCCCACCACAGAGGATAGATATTTACTCTTTGTTGATGAACTACGTG