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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATCCATTACATTCTGACATCCTGGCTAGCGGAAGTTTGGATCATGAAGTTCGTCTATGGGATGCTAATACTTCAGACTGTATTGGGTCACAAGACTTCCgtaatttttctcagaagactgcttgcattctattcatagtcaattttgagaacaatgtaacttatttttgatgttcttggggcag

Basic information

species Zea mays
transcript GRMZM2G007229_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G007229_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g18820.1 (Oryza sativa), 5'ss of exon 6
CATCCATTACATTCTGACATCCTGGCTAGCGGAAGTTTGGATCATGAAGTTCGTCTATGGGATGCTAATACTTCAGACTGTATTGGGTCACAAGACTTCCgtaatttttctcagaagac-----tgcttgcat-tctattcatag-tcaattttgagaacaatgtaacttatttttgatgttcttggggcag----
|||||||||| | |||| ||||| |||||||| ||||||||||| ||||| ||||| ||||| ||||| || |||||||||||||| || || |||||||||||| | ||| || |||      ||  |   | ||  | ||| | | || | |||  || |   | ||| |   |||||||||       |    
CATCCATTACTTCCTGATATCCTTGCTAGCGGTAGTTTGGATCAGGAAGTCCGTCTTTGGGACGCTAAAACCTCAGACTGTATTGGATCTCAGGACTTCCgtaatatatctaagcagatcctaatgagtatgtctccttccatgggtgaaatctgaatacta---accttttcagtgatgttctcttatttgatag

upper sequence: GRMZM2G007229_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA03G32620.2 (Glycine max), 5'ss of exon 5
CATCCATTACATTCTGACATCCTGGCTAGCGGAAGTTTGGATCATGAAGTTCGTCTATGGGATGCTAATACTTCAGACTGTATTGGGTCACAAGACTTCCgtaatttttctca--gaagactgcttgcattctattcatagtcaattttgagaacaatgtaacttat--ttttgatgttcttggggcag------------------------------------------------
|||||||| ||| |  | || || ||||| || || |||||||| ||||||||| ||||||||||||| || ||||| || ||    || ||  | ||| |||  ||| || |  |   |   ||    |||| |||  | | | | |||  |    |   |  |||  ||||| |  | ||   |                                                   
CATCCATTGCATCCACATATACTTGCTAGTGGGAGCTTGGATCAAGAAGTTCGTTTATGGGATGCTAACACATCAGAGTGCATAATATCTCATCATTTCTgtatgtttacttactgtgaatctctccttttcttttctaaattactcttgtaacacttactatatatgtttttgttccttttcatgtgtatattggtttctctctctgatgaattcattggttgtttcttctcacag

upper sequence: GRMZM2G007229_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA19G35370.2 (Glycine max), 5'ss of exon 6
CATCCATTACATTCTGACATCCTGGCTAGCGGAAGTTTGGATCATGAAGTTCGTCTATGGGATGCTAATACTTCAGACTGTATTGGGTCACAAGACTTCCgtaatttttctca--gaagactgcttgcattctattcatagtcaattttgagaacaatgtaact--tatttttgatgttcttggggcag------------------------------------------------------------
|||||||| ||  |  | || || ||||| || || |||||||| ||||||||| ||||||||||||| || ||||| || ||    || ||  | ||| |||  ||| || |  |   |   ||    |||| |||  | | | | |||  ||   |||||||  || | |  ||||| |||   |                                                              
CATCCATTGCACCCACATATACTTGCTAGTGGGAGCTTGGATCAAGAAGTTCGTTTATGGGATGCTAACACATCAGAGTGCATAATATCTCATCATTTCTgtatgtttacttactgtgaatctctccttttcttttctaaattactcttgttaa-gttgtaactgttactatatatgtttttgttccttttcatgtgtatattggtttctcttctctctgatgaattcattgggtgtttcttctcacag

upper sequence: GRMZM2G007229_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv05s0077g00140.t01 (Vitis vinifera), 5'ss of exon 5
CATCCATTACATTCTGACATCCTGGCTAGCGGAAGTTTGGATCATGAAGTTCGTCTATGGGATGCTAATACTTCAGACTGTATTGGGTCACAAGACTTCCgtaatttttctcagaagactgcttgcattctatt-catagtcaattttgagaaca-atgtaacttatttttgatgttcttgg--ggcag--------------------
|||||| |  || |||| || || || || |||||||||||||||||||||||  | |||||||| | |||| |||| || || |||||||  |||||  |||||  ||   |     ||  ||   |   ||| || || |||| ||  |  || |||||   | || |  || |  |||   |  |                     
CATCCACTCTATCCTGAAATACTTGCAAGTGGAAGTTTGGATCATGAAGTTCGATTGTGGGATGCAAGTACTGCAGAGTGCATAGGGTCACGTGACTTTTgtaatgatttctatggacctctttttctaacatttcaaagacaatattacgctcagatgtatacttttgtgtatttgattgattgataatttccttttcctccatgcag

upper sequence: GRMZM2G007229_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv07s0005g04630.t01 (Vitis vinifera), 5'ss of exon 5
CATCCATTACATTCTGACATCCTGGCTAGCGGAAGTTTGGATCATGAAGTTCGTCTATGGGATGCTAATACTTCAGACTGTATTGGGTCACAAGACTTCCgtaattt---------ttctcagaa-gactgctt-------gcattctattcatagtcaattttgagaacaatgtaacttatttttgatgttct-tggggcag--------------------------
|| ||| | ||| |||| || || || || || ||||| ||||||||||||||| |||||||||| |||||| | || ||||| || || |  || ||| |||||||         ||||||    |  |||||       ||| || |  || |  |||     |  |||   |||    ||  | |||   | || ||                             
CACCCAGTGCATCCTGAAATACTTGCAAGTGGGAGTTTAGATCATGAAGTTCGTATATGGGATGCAAATACTGCGGAGTGTATAGGATCTCGTGATTTCTgtaatttctattttcattctcattccggttgctttgttgatgcaatccagacacacacaaacacaaacacacactaagcatttagttatgccttatgtggtgaatttgatctctatctgttttcaccag

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|94476551|gb|EB705509.1|EB705509
EST:     TCGTCTATGGGATGCTAATACTTCAGACTGTATTGGGTCACAAGACTTCC                         ATCGGCCAATTGCTTCCATTGCATTTCATGGGAGTGGGGAGATTTTGGCAG
genomic: TCGTCTATGGGATGCTAATACTTCAGACTGTATTGGGTCACAAGACTTCCgtaatttttc ... cttggggcagATCGGCCAATTGCTTCCATTGCATTTCATGGAAGTGGGGAGATTTTGGCAG
EST: gi|78122102|gb|DV540486.1|DV540486
EST:     TCGTCTATGGGATGCTAATACTTCAGACTGTATTGGGTCACAAGACTTCC                         ATCGGCCAATTGCTTCCATTGCATTTCATGGAAGTGGGGAGATTTTGGCAG
genomic: TCGTCTATGGGATGCTAATACTTCAGACTGTATTGGGTCACAAGACTTCCgtaatttttc ... cttggggcagATCGGCCAATTGCTTCCATTGCATTTCATGGAAGTGGGGAGATTTTGGCAG
EST: gi|93017682|gb|EB643202.1|EB643202
EST:     TCGTCTATGGGATGCTAATACTTCAGACTGTATTGGGTCACAAGACTTCC                         ATCGGCCAATTGCTTCCATTGCATTTCATGGAAGTGGGGAGATTTTGGCAG
genomic: TCGTCTATGGGATGCTAATACTTCAGACTGTATTGGGTCACAAGACTTCCgtaatttttc ... cttggggcagATCGGCCAATTGCTTCCATTGCATTTCATGGAAGTGGGGAGATTTTGGCAG
EST: gi|78120030|gb|DV538414.1|DV538414
EST:     TCGTCTATGGGATGCTAATACTTCAGACTGTATTGGGTCACAAGACTTCC                         ATCGGCCAATTGCTTCCATTGCATTTCATGGAAGTGGGGAGATTTTGGCAG
genomic: TCGTCTATGGGATGCTAATACTTCAGACTGTATTGGGTCACAAGACTTCCgtaatttttc ... cttggggcagATCGGCCAATTGCTTCCATTGCATTTCATGGAAGTGGGGAGATTTTGGCAG
EST: gi|31353753|gb|CD438110.1|CD438110
EST:     TCGTCTATGGGATGCTAATACTTCAGACTGTATTGGGTCACAAGACTTCC                         ATCGGCCAATTGCTTCCATTGCATTTCATGGAAGTGGGGAGATTTTGGCAG
genomic: TCGTCTATGGGATGCTAATACTTCAGACTGTATTGGGTCACAAGACTTCCgtaatttttc ... cttggggcagATCGGCCAATTGCTTCCATTGCATTTCATGGAAGTGGGGAGATTTTGGCAG

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: 49 (upstream exon), 49 (downstream exon)
Score: 203

CATCCATTACATTCTGACATCCTGGCTAGCGGAAGTTTGGATCATGAAGTTCGTCTATGGGATGCTAATACTTCAGACTGTATTGGGTCACAAGACTTCCgtaatttttc ... cttggggcagATCGGCCAATTGCTTCCATTGCATTTCATGGAAGTGGGGAGATTTTGGCAGTTGCATCAGGTCACAAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 146

CATCCATTACATTCTGACATCCTGGCTAGCGGAAGTTTGGATCATGAAGTTCGTCTATGGGATGCTAATACTTCAGACTGTATTGGGTCACAAGACTTCCgtaatttttc ... cttggggcagATCGGCCAATTGCTTCCATTGCATTTCATGGAAGTGGGGAGATTTTGGCAGTTGCATCAGGTCACAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 147

CATCCATTACATTCTGACATCCTGGCTAGCGGAAGTTTGGATCATGAAGTTCGTCTATGGGATGCTAATACTTCAGACTGTATTGGGTCACAAGACTTCCgtaatttttc ... cttggggcagATCGGCCAATTGCTTCCATTGCATTTCATGGAAGTGGGGAGATTTTGGCAGTTGCATCAGGTCACAAA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 108

CATCCATTACATTCTGACATCCTGGCTAGCGGAAGTTTGGATCATGAAGTTCGTCTATGGGATGCTAATACTTCAGACTGTATTGGGTCACAAGACTTCCgtaatttttc ... cttggggcagATCGGCCAATTGCTTCCATTGCATTTCATGGAAGTGGGGAGATTTTGGCAGTTGCATCAGGTCACAAA