Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATAATTCTCGTAGGGACAAAGCTTGgtaagtatgattatgtcctttttttggaaatccagccttctgtgcttgtaagcttcacgatgctagttttcgatagatacaatacaattattagagtttt...

Basic information

species Zea mays
transcript GRMZM5G803949_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G803949_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g02840.1 (Oryza sativa), 5'ss of exon 4
TGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATAATTCTCGTAGGGACAAAGCTTGgtaagtatgatt--atgtcctttttttggaaatccagccttctgtgcttgtaagcttcacgatgctagttttcgatagatacaatacaattattagagtttt-
||||||||||| |||||||||||||||||||||||||| || || || || || ||||||||||||||| |   |   | |  || ||||  |||||| |  ||| ||| | ||| |      || |  |  |||| ||| ||   | |      ||  || |||| 
TGGATACCTGAGCTGAAGCATTATGCACCTGGTGTGCCTATCATCCTTGTGGGAACAAAGCTTGgtaagaaccgtgcaaggctctattttgagaaatctaatcttttgtacctgtcacaagttcggttttgattttggatggaagtagtgg---catgggattttta

upper sequence: GRMZM5G803949_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA11G08380.1 (Glycine max), 5'ss of exon 5
TGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATAATTCTCGTAGGGACAAAGCTTGgtaag--tatgattatgtcctttttt-tggaaatccagccttctgtgcttgtaagcttcacgatgctagttttcgatagatacaatacaattattagagtttt
||||| || ||  |||||||||||||||||||||| || || ||||| || || |||||||||||||||  |||   |   |  | |  |   || ||  ||     ||   |  | || | |      || | ||    |  ||  |||  | | | |   | || 
TGGATTCCAGAGTTGAAGCATTATGCACCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTGgtaagcttattgctgcataatgtgatactgatattgagtaccatgcattcattagatgcttccctctggctt---gtttatttaatttagtcaatgtggcttg

upper sequence: GRMZM5G803949_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA01G36880.1 (Glycine max), 5'ss of exon 5
TGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATAATTCTCGTAGGGACAAAGCTTGgtaag--tatgattatgtcctttttt-tggaaatccagccttctgtgcttgtaagcttcacgatgctagttttcgatagatacaatacaattattagagtttt
||||| || ||  ||||||||||||| |||||||| || || ||||| || || |||||||||||||||  |||   |   |  | |  |   || ||  ||     ||   |  | || | |    | || | ||    |  ||  |||  | | |||   | || 
TGGATTCCGGAGTTGAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTGgtaagcttattgctgcataatgtgatactgatattgagtaccatgcattcattagatactgccttctggctt---gtttatttaatttattcattgtggcttg

upper sequence: GRMZM5G803949_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA04G02540.2 (Glycine max), 5'ss of exon 4
TGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATAATTCTCGTAGGGACAAAGCTTGgtaag--tatgattatgtcctttttt---tggaa----atccagccttctgtgcttgtaagcttcacgatgctagttttcgatagatacaatacaattattagagtttt
||||| |||||||| | ||||||||| |||||||| |||||||||||||| || |||||| | ||||||  | |     | |||||  ||   |||||    | | | ||   ||  | ||| ||     |  |||  | ||| | |   |  |||    || ||        
TGGATCCCTGAACTAAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAGgtaagcctttacccctttccttcattgaatggaatggaaccaatccagatgatcctgttagagcttcc-tgcctggttttggttattgaaatggttttctt--------

upper sequence: GRMZM5G803949_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA04G02530.3 (Glycine max), 5'ss of exon 4
TGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATAATTCTCGTAGGGACAAAGCTTGgtaagtatgattatgtcctttttttggaa--atccagccttctgtgcttgtaagct----tcacgatgctagttttcgatagatacaatacaattattagagtttt
||||| |||||||| | ||||||||| |||||||| |||||||||||||| || |||||| | |||| || |      |  |  ||  | |||   |   || |    |  ||   | |     | || | | ||        |   |||  |  | |||||  |     
TGGATCCCTGAACTAAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAGgtaggtgtttacccgcacccttcattgaattgtttggcatatgctatttactaacccatatgaccacgttatagccttgtgcttacc-tttagttatttaa-----

upper sequence: GRMZM5G803949_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA06G02580.2 (Glycine max), 5'ss of exon 4
TGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATAATTCTCGTAGGGACAAAGCTTGgtaag--tatgattatgtcctttttt---tggaa----atccagccttctgtgcttgtaagcttcacgatgctagttttcgatagatacaatacaattattagagtttt
||||| |||||||| | ||||||||| |||||||| |||||||||||||| || |||||| | ||||||  | |     | |||||  ||   |||||    | | | |||   |  | ||| ||     |  |||| |  || | |   |  |||    || ||        
TGGATCCCTGAACTAAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAGgtaagcctttacccctttccttcattgaatggaatggaaccaatcctgacgatcctgttagagcttcc-tgcttggctttggttattgaaatggttttctt--------

upper sequence: GRMZM5G803949_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv18s0001g14670.t01 (Vitis vinifera), 5'ss of exon 4
TGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATAATTCTCGTAGGGACAAAGCTTGgtaagtatgattatgtcctttttttggaaatc-cagccttctgt-gct--tgtaagcttcacgatgctagttttcgatagatacaatacaa-ttattagagtttt
||||| |||||||||| |||||||||||||||||| ||||||||||| || || || ||||||||||||  |   | | || | |  |||  ||||  |   || ||| |||  ||| |  |||        || | |   |   || | |  || || |  ||     
TGGATTCCTGAACTGAGGCATTATGCACCTGGTGTTCCAATAATTCTTGTTGGAACCAAGCTTGgtaagattatctctatcatatgcttgttaatcataattttgtgttgctgttgttattttcttatcatcagctgtgagtttgtaaattgaaagttctctga-----

upper sequence: GRMZM5G803949_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv04s0023g03860.t01 (Vitis vinifera), 5'ss of exon 5
TGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATAATTCTCGTAGGGACAAAGCTTGgtaagtatgattatgtcctttttttggaaatccagccttctgtgcttgtaagcttcacga-tgctagttttcgatagatacaatacaattattagagtttt-------
||||| || ||| |||||||||||||||||||||| || ||| |||| || || || ||||||||| ||    |||   |      |||     |||   ||||| | || |||  || ||    ||||  |||   ||    |  |      | | |||    |       
TGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTTGGCACTAAGCTTGgttag----atttcctttcagctttatggttcc--tcttct-tact-gtagactccatagctgctcttttcttatgttcatgaagatggtttcagatccatgtccaac

upper sequence: GRMZM5G803949_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv03s0038g02380.t01 (Vitis vinifera), 5'ss of exon 5
TGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATAATTCTCGTAGGGACAAAGCTTGgtaagtatgattatgtcctttttttggaaatccagccttctgtgcttgtaagcttcacgatgctagttttcgatagatacaatacaattattagagtttt--
||||| |||||  ||| |||||||||||| ||||| ||||||||||| || ||||||||||||||| ||  |       |||  |||||  || | |       | |  || |    ||  |    | |||   | | | ||  |||    |||| |   || |  
TGGATTCCTGAGTTGAGGCATTATGCACCCGGTGTTCCAATAATTCTTGTCGGGACAAAGCTTGgttagattctcctaatccaatttttttaagtgctattaatttttttttttcaattaccagaacaagtgagctacaaatgtaatgt--ttataatttttctct

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|211356952|gb|FL222516.1|FL222516
EST:     GAAGCATTATGCACCTGGTGTGCCAATAATTCTCGTARGGACAAAGCTTG                         ATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCCN
genomic: GAAGCATTATGCACCTGGTGTGCCAATAATTCTCGTAGGGACAAAGCTTGgtaagtatga ... ttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCC--




















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), 49 (downstream exon)
Score: 368

TGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATAATTCTCGTAGGGACAAAGCTTGgtaagtatga ... ttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 216

TGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATAATTCTCGTAGGGACAAAGCTTGgtaagtatga ... ttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 274

TGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATAATTCTCGTAGGGACAAAGCTTGgtaagtatga ... ttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 984

TGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATAATTCTCGTAGGGACAAAGCTTGgtaagtatga ... ttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG