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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTGAGGTTCTTGGTGACAACGACTCTCCTGTCATGCCCATAATGCTCTACAATCCGGCCAAGATTCCTGCGTTTTCTCGGGAGTGCTTTAGACAAAAGgttattagtgctagagtttgtcgacgaaacactctgaagatccgaatagcaattgacagaattttttgtgctagctgcag

Basic information

species Zea mays
transcript GRMZM2G030862_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030862_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os11g31640.1 (Oryza sativa), 5'ss of exon 10
CTTTGAGGTTCTTGGTGACAACGACTCTCCTGTCATGCCCATAATGCTCTACAATCCGGCCAAGATTCCTGCGTTTTCTCGGGAGTGCTTTAGACAAAAGgttattagtgctagagtttgtcgacgaaacactctgaagat-ccgaatagcaattgacag-aattttttgtg-----ctagctgcag----------------------------------
 ||||||||||| || ||||| |||||||| || ||||| ||||||||||||||||| ||||| ||||| || |||||  |||||||| ||||||||||||||| || || || ||  ||      |    |    | | | | |||||    ||      | ||||||||      |||||  |                                    
TTTTGAGGTTCTCGGAGACAATGACTCTCCAGTTATGCCAATAATGCTCTACAATCCAGCCAAAATTCCAGCTTTTTCCAGGGAGTGCCTTAGACAAAAGgttagtaatggtatagaatgctatttatcttcagaaatggtacagaataatggtttttgccagttttttgtcgttccctagcccctattaccgtgcgactgatgtggcactggcatttcag

upper sequence: GRMZM2G030862_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA02G07250.1 (Glycine max), 5'ss of exon 10
CTTTGAGGTTCTTGGTGACAACGACTCTCCTGTCATGCCCATAATGCTCTACAATCCGGCCAAGATTCCTGCGTTTTCTCGGGAGTGCTTTAGACAAAAGgttattagtgctagagtttgtcga-cgaaacactctgaagat-ccgaatagcaattgaca--gaattttttg--tgctagctgcag-------------
 |||||||||||||| || || || ||||| || ||||| || ||||| ||||| |||||||| || ||||| |||||  | |||||| | |  || || || |  |   | |   |    | | | |  | |  ||  ||| ||  | | ||  | | |  |||||| ||   |  |   | ||              
ATTTGAGGTTCTTGGGGATAATGATTCTCCAGTAATGCCAATCATGCTTTACAACCCGGCCAAAATCCCTGCCTTTTCAAGAGAGTGCCTCAAGCAGAATgtgagaacatcaaatatccaactatctatgctccttgttgataccctacatcatataagaatgaatttgttaattaatgtttacaattttttatttcag

upper sequence: GRMZM2G030862_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv17s0000g00500.t01 (Vitis vinifera), 5'ss of exon 11
CTTTGAGGTTCTTGGTGACAACGACTCTCCTGTCATGCCCATAATGCTCTACAATCCGGCCAAGATTCCTGCGTTTTCTCGGGAGTGCTTTAGACAAAAGgtta---ttagtgctagagtttgtcgacgaaacactctgaagatccgaatagcaattgacagaattttt-tgtgctagctgcag------------------------------------------------------------------------------------
||||||||||||||| || || || |||||||| ||||| |||||||| |||||||| ||||| |||||||| ||||| ||||||||  | | ||| || || |   |||    ||   | | |  |   | || ||      |   | |    ||| |   |  |    |        | ||                                                                                     
CTTTGAGGTTCTTGGAGATAATGATTCTCCTGTAATGCCAATAATGCTTTACAATCCAGCCAAAATTCCTGCCTTTTCGCGGGAGTGTCTCAAACAGAATgtaagctttatctttaatttctatacattcaccattcatgtcttttcattcttgattaaagtagctgcaatacagagattccaagtcattcatttgtatagcactgctcattaatctccagttcaagttcacttgtgtggctagtattgacaagttatgctgttccag

upper sequence: GRMZM2G030862_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv14s0068g01300.t01 (Vitis vinifera), 5'ss of exon 10
CTTTGAGGTTCTTGGTGACAACGACTCTCCTGTCATGCCCATAATGCTCTACAATCCGGCCAAGATTCCTGCGTTTTCTCGGGAGTGCTTTAGACAAAAGgttattagtgctagagtttgtcga--cgaaacactctgaagatccgaatagcaattgacagaattt-tttgtgctagctgcag---------------------------------------------------------------
 |||||||||||||| || || |||||||| || ||||| |||||||| || ||||| | ||| |||||||| || || || |||||| | |  ||||| || | |    | |||  |   ||   |  |  ||| |||  || | | |    | |   ||    | | | |   | |||                                                                  
TTTTGAGGTTCTTGGGGATAATGACTCTCCAGTGATGCCAATAATGCTTTATAATCCTGGCAAAATTCCTGCCTTCTCGCGAGAGTGCCTCAAGCAAAATgtgagtccatcaagacatgcacgtgtcctataactatgattattccattctggacttttagctcatgtctatatgacctgtccttcaaatggcacagtttattctcatttcatggctttttatcaaagtcaatggtgctgttacag

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|83279403|gb|DV943411.1|DV943411
EST:     ACAATCCGGCCAAGATTCCTGCGTTTTCTCGGGAGTGCTTTAGACAAAAG                         GTTGCCGTTATCACTGTGGCGTTTCCTGTGACTCCTCTCCTTCTCGCAAGA
genomic: ACAATCCGGCCAAGATTCCTGCGTTTTCTCGGGAGTGCTTTAGACAAAAGgttattagtg ... ctagctgcagGTTGCCGTTATCACTGTGGCGTTTCCTGTGACTCCTCTCCTTCTCGCAAGA
EST: gi|60344069|gb|DN211042.1|DN211042
EST:     ACAATCCGGCCAAGATTCCTGCGTTTTCTCGGGAGTGCTTTAGACAAAAG                         GTTGCCGTTATCACTGTGGCGTTTCCTGTGACTCCTCTCCTTCTCGCAAGA
genomic: ACAATCCGGCCAAGATTCCTGCGTTTTCTCGGGAGTGCTTTAGACAAAAGgttattagtg ... ctagctgcagGTTGCCGTTATCACTGTGGCGTTTCCTGTGACTCCTCTCCTTCTCGCAAGA
EST: gi|60343785|gb|DN210758.1|DN210758
EST:     ACAATCCGGCCAAGATTCCTGCGTTTTCTCGGGAGTGCTTTAGACAAAAG                         GTTGCCGTTATCACTGTGGCGTTTCCTGTGACTCCTCTCCTTCTCGCAAGA
genomic: ACAATCCGGCCAAGATTCCTGCGTTTTCTCGGGAGTGCTTTAGACAAAAGgttattagtg ... ctagctgcagGTTGCCGTTATCACTGTGGCGTTTCCTGTGACTCCTCTCCTTCTCGCAAGA

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 2 RNA-Seq libraries.


Block sizes: 26 (upstream exon), 42 (downstream exon)
Score: 6

CTTTGAGGTTCTTGGTGACAACGACTCTCCTGTCATGCCCATAATGCTCTACAATCCGGCCAAGATTCCTGCGTTTTCTCGGGAGTGCTTTAGACAAAAGgttattagtg ... ctagctgcagGTTGCCGTTATCACTGTGGCGTTTCCTGTGACTCCTCTCCTTCTCGCAAGAGCACGTTTCTGCATTTCAGCTTCGCACACTAGGGAGGACCTGACGAAAG


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 19

CTTTGAGGTTCTTGGTGACAACGACTCTCCTGTCATGCCCATAATGCTCTACAATCCGGCCAAGATTCCTGCGTTTTCTCGGGAGTGCTTTAGACAAAAGgttattagtg ... ctagctgcagGTTGCCGTTATCACTGTGGCGTTTCCTGTGACTCCTCTCCTTCTCGCAAGAGCACGTTTCTGCATTTCAGCTTCGCACACTAGGGAGGACCTGACGAAAG




<