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

TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCGgtaagtattgaatgtggcagaaatgacctgaaactttaaatctacatagcatggagttcagattgacaattgatgcatgccaagcatcctgttggctgga...

Basic information

species Zea mays
transcript GRMZM2G006428_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006428_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os04g41470.1 (Oryza sativa), 5'ss of exon 10
TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCGgtaagt-attgaatgtggcagaaatgacctgaa----actttaaatct-acatagcatggagttcagattgacaattgatgcatgccaagcatcctgttggctgga---------------------
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||| |||||||||||||||||||||||| ||||  |     | || | |||||||     | ||   | | |||||    | |    |||||  ||||  || |     ||| |   |  ||| |                        
TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCGgtaagttattgggtacaagaaaagttacctgaacaaagcattgtgttttacataagtagtaaaaaagatttccaatcaatactcaagaagaacttttctggtttcttaatatcttctcgttatgcag

upper sequence: GRMZM2G006428_T02 (Zea mays), 5'ss of exon 10
lower sequence: AT1G65430.1 (Arabidopsis thaliana), 5'ss of exon 10
TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCGgtaagta----ttgaatgtggcagaaatgacctgaaac-tttaaatctacatagcatggagttcagattgacaattgatgcatgccaagcatcctgttggctgga
||||||||  ||||||   |  |||| |||||||||||||| |||||||||||||| || || |||||  |||||||| ||||||| |||||| |||    || |       |||| | || ||     ||||  ||  | |     |||  |   |   | ||||       | |||   || | ||       
TATGATGAGACTGAAAAACGCCGAGAGATGGCAAAGAACTCTCTTGAGAGATATACCCACTACTATGAGAGATGGGCAACCAATCAATCGgtatgtaaatttttatccatttagaattcacatgttttatttagctcctcttgaaggggaaatttaagaaagaattttcagccgtcaaat-tcatattcct----

upper sequence: GRMZM2G006428_T02 (Zea mays), 5'ss of exon 10
lower sequence: Vv00s0207g00090.t01 (Vitis vinifera), 5'ss of exon 10
TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCGgtaagtattgaatgtggcagaaatgac-ctgaaactttaa-atctacatagcatggagttcagattgacaattgatgcatgccaagcatcctgttggctgga
||||||||  |||| |   |||| || ||||| ||||||||  | ||||||||||| ||||||||||||||||||||  |||| || || ||| || |||| | |  ||||     | ||    || ||| ||  ||||    |      |  |||        ||  |  |||||  |    |    ||  
TATGATGAGGCTGAGAAACGAAGGGATATGGCTAAGAACTCTTTGGAGAGATATACTCATTATTATGAACGATGGGCGACCAACCAATCTgtatgt-ttgacttttccagatcctcctcttttgctgtaatatggacattatttcagaaacccattatttcagaatttagtccaagattgtcctcatttgc-

upper sequence: GRMZM2G006428_T02 (Zea mays), 5'ss of exon 10
lower sequence: PP1S114_2V6.1 (Physcomitrella patens), 5'ss of exon 10
TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCGgtaagtattgaatg--tggcagaaatgacctgaaactttaaatctacatagcatggagttcagattgacaattgatgcatg----ccaagcatcctgttggctgga-------------------------------------------------------
||||||||| | ||  ||||||| |||||||| ||||||||||||||  | ||||||||||| |||||||| |||||  | ||  | || ||||||  || |      ||| |  |  ||       |||  | | | |    | |   |  ||||| ||  |  ||  |     |  | |   || |    |  |                                                       
TATGATGAAGCAGAGCGGAGAAGGGAAATGGCTAAGAACTCGCTTGAACGCTATACACATTACTATGAACGTTGGGCTACAAACGAATCTgtaagtggtgcagaatctgcacattttcccatctgaattaggttttcctcagttcgccatgggattg-cacctattgtttaggatcttaactctctctcaatttaaagacgtgatctgcgtttgtgttttcttgacttttgaaatctcctttgtttttcag

upper sequence: GRMZM2G006428_T02 (Zea mays), 5'ss of exon 10
lower sequence: EFJ15174 (Selaginella moellendorffii), 5'ss of exon 10
TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCGgt-aagtattgaatgtggcagaaatgacctgaaactttaaatctacatagcatggagttcagattgacaattgatgcatgccaagcatcctgttggctgga
|| |||||| |||| ||||| ||||||||||| ||||||||| | ||||||||||||||||| || || ||||||||  | ||  | || ||  ||| |  ||| ||    |  |||   |    | ||| |      |   |  ||                                            
TACGATGAAGCTGAGAGGAGGAGAGAAATGGCTAAGAACTCGTTAGAGAGATATACACATTACTACGAGCGATGGGCCACGAACGAATCAgttgagtttccaatttga-gtatctgataggcctttctaacttcgttcatggtacag--------------------------------------------

upper sequence: GRMZM2G006428_T02 (Zea mays), 5'ss of exon 10
lower sequence: EFJ08409 (Selaginella moellendorffii), 5'ss of exon 10
TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCGgt-aagtattgaatgtggcagaaatgacctgaaactttaaatctacatagcatggagttcagattgacaattgatgcatgccaagcatcctgttggctgga
|| |||||| |||| ||||| || |||||||| ||||||||| | ||||||||||||||||| || || ||||||||  | ||  | || ||  ||| |  ||| ||    |  |||   |    | ||| |   |  |   |  ||                                            
TACGATGAAGCTGAGAGGAGGAGGGAAATGGCTAAGAACTCGTTAGAGAGATATACACATTACTACGAGCGATGGGCCACGAACGAATCAgttgagtttccaatttga-gtatctgataggcctttctaacttcgctcatggtacag--------------------------------------------

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|76281609|gb|DV021177.1|DV021177
EST:     CGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCG                         TCGAGGCAAA-GGCACTGGGG
genomic: CGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCGgtaagtattg ... catggcgcagTCGAGGCAAAAGGCACTGGGG
EST: gi|211292139|gb|FL375498.1|FL375498
EST:     CGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCG                         TCGAGGCAAAAGGCACTGGNGGGACCTTCAAAGCCTACAGAACGACAAG
genomic: CGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCGgtaagtattg ... catggcgcagTCGAGGCAAAAGGCACTGG-GGGACCTTCAAAGCCTACAGAACGACAAG
EST: gi|78080365|gb|DV508777.1|DV508777
EST:     CGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCG                         TCGAGGCAAAAGGCACTGGGGGACCTTCAAAGCCTACAGAACGACAAG
genomic: CGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCGgtaagtattg ... catggcgcagTCGAGGCAAAAGGCACTGGGGGACCTTCAAAGCCTACAGAACGACAAG

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), 48 (downstream exon)
Score: 327

TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCGgtaagtattg ... catggcgcagTCGAGGCAAAAGGCACTGGGGGACCTTCAAAGCCTACAGAACGACAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 306

TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCGgtaagtattg ... catggcgcagTCGAGGCAAAAGGCACTGGGGGACCTTCAAAGCCTACAGAACGACAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 323

TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCGgtaagtattg ... catggcgcagTCGAGGCAAAAGGCACTGGGGGACCTTCAAAGCCTACAGAACGACAAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 221

TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCGgtaagtattg ... catggcgcagTCGAGGCAAAAGGCACTGGGGGACCTTCAAAGCCTACAGAACGACAAG