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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGCATTGCGACAACAAAGATTTGTCCGTGAAGTGACAATACAGTACAACCTCTGCAACGAGCCATGgtgcctttctgtcctgcatcctaagatctcttgattgtattagttcactaaggcttatccagtaccagtattgtcatctctagtttatttttcagtctgt...

Basic information

species Zea mays
transcript GRMZM2G464000_T03
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G464000_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os07g29450.1 (Oryza sativa), 5'ss of exon 9
AATGCATTGCGACAACAAAGATTTGTCCGTGAAGTGACAATACAGTACAACCTCTGCAACGAGCCATGgtgcctttctgtcctgcatcctaagatctcttgattgtattagttcactaaggctt-atccagtac-cagtattgtcatctctagtttatttttcagtctgt------------------------------------------------------------------------------------------------------
||||| || || |||||||||||||| || ||||| |||||||||||||| ||||||||||||||||||| | ||  || ||| | | || |     ||       ||| | |||  || | |  |||||| ||  | |   | | | |||  |  || |    |  |||                                                                                                      
AATGCGTTACGTCAACAAAGATTTGTTCGGGAAGTCACAATACAGTACAATCTCTGCAACGAGCCATGgtactttcttgacctaccttctgatgctactc------atttgctcatgaaagttccatccagcacgtactgcagccttttctgttgcatatgagtgcttgtttgtttcagcgctcaactcctcagcttttagaagcctttgtctaggtctttgttgagctaaggttgctcctactaaccttgtacctgattactttacttcag

upper sequence: GRMZM2G464000_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA10G31960.1 (Glycine max), 5'ss of exon 9
AATGCATTGCGACAACAAAGATTTGTCCGTGAAGTGACAATACAGTACAACCTCTGCAACGAGCCATGgtgcctttctgtcctgcatcctaagatctcttgattgtattagttcactaaggcttatccagtaccagtattgtcatctctagtttatttttcagtctgt-
||||||||||| |||||||||||||| || ||||| |||||||||||||| |||||||| |||||||||| |     | |  |   |   ||  |  ||    || ||   || |  ||    |   | |  | | |||||| || | |  ||| |           | 
AATGCATTGCGGCAACAAAGATTTGTTCGAGAAGTCACAATACAGTACAATCTCTGCAATGAGCCATGgtacgcaagttttttttttggcaaagtgactaatctg-atatttttataaacaagttgactgatctaatattgtaatgtgtgttttgtgcaaagaataatt

upper sequence: GRMZM2G464000_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA16G33300.1 (Glycine max), 5'ss of exon 8
AATGCATTGCGACAACAAAGATTTGTCCGTGAAGTGACAATACAGTACAACCTCTGCAACGAGCCATGgtgcctttctgtcctgcatcctaagatctcttgattgtattagttcactaaggcttatccagtaccagtat-tgtcatctctagtttatttttcagtctgt--
||||||||||| || ||||||||||| |||||||| ||||||||||||||||||||||| || || ||||    |  | |     ||    | |   |  | |  ||  |   || |  |  |||    | | ||| |  | ||   || |  ||  |  |   | |||  
AATGCATTGCGGCAGCAAAGATTTGTACGTGAAGTTACAATACAGTACAACCTCTGCAATGAACCTTGgtatgctagtatt---aattggcaaagtacaggctaatacaatagcattgtgttttaagatggagcagaaaatatctaatccaagtttgtggtatttttgtaa

upper sequence: GRMZM2G464000_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA20G35720.1 (Glycine max), 5'ss of exon 8
AATGCATTGCGACAACAAAGATTTGTCCGTGAAGTGACAATACAGTACAACCTCTGCAACGAGCCATGgtgcctttctgtcctgcatcctaagatctcttgattgtat-tagttcactaaggcttatccagtaccagtattgtcatctctagtttatttttcagtctgt--
||||||||||| |||||||||||||| || ||||| |||||||||||||| |||||||| ||||| ||||       | |  |   |||    |     ||| |  || || |    |||    | |   || | |  ||  |     ||| ||| || ||  |    |  
AATGCATTGCGGCAACAAAGATTTGTTCGAGAAGTCACAATACAGTACAATCTCTGCAATGAGCCTTGgtatgcaagttttttttttccgggaaaag--tgactaaatctaatattgtaatatgtgttt-gtgcaaaaataatagaaactaatttgttattttggtaatat

upper sequence: GRMZM2G464000_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA09G28530.1 (Glycine max), 5'ss of exon 7
AATGCATTGCGACAACAAAGATTTGTCCGTGAAGTGACAATACAGTACAACCTCTGCAACGAGCCATGgtgcctttctgtcctgcatcctaagatctcttgattgtattagttcactaaggcttatccagtaccagtat-tgtcatctctagtttatttttcagtctgt--
||||||||||| || ||||||||||| || ||||| ||||||||||||||||||||||| || |||||||    || | |       |  |  |     | ||   || |   || |  |  |||    | | ||| |  | |||  || |  ||  |  |   | |||  
AATGCATTGCGGCAGCAAAGATTTGTACGCGAAGTTACAATACAGTACAACCTCTGCAATGAACCATGgtatgcttgtattaattggcaaagtacagtctaatacaataa---cattgtgttttaagatggagcagaaaatatcaaatccaagtttgtggtatttttgtaa

upper sequence: GRMZM2G464000_T02 (Zea mays), 5'ss of exon 8
lower sequence: Vv07s0130g00270.t01 (Vitis vinifera), 5'ss of exon 8
AATGCATTGCGACAACAAAGATTTGTCCGTGAAGTGACAATACAGTACAACCTCTGCAACGAGCCATGgtgcctttctgtcctgcatcctaagatctct--tgattgtattagttcactaaggcttatccagtaccagtatt-gtcatctctagtttatttttcagtctgt
||||| ||||| |||||||||||||| || ||||| ||||||||||||||| | || || || || ||||    |||     |   |    || |   |  |  ||  ||| ||      ||  || |      | | |    | |||    ||| | |    ||      
AATGCGTTGCGGCAACAAAGATTTGTACGAGAAGTCACAATACAGTACAACTTATGTAATGAACCTTGgtatgcttcaaatttctttgggtagcttattgctcctttaattcgtaagtagagaatttttggaagcaaatggaaggcattgagagtgtttccaccaaat---

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|211146181|gb|FK958445.1|FK958445
EST:     AGATTTGTCCGTGAAGTGACAATACAGTACAACCTCTGCAACGAGCCATG                         GTTAAAATATAGTATAAGCATTGTGGCAGACAAGGGATTGAAAAAGTCACT
genomic: AGATTTGTCCGTGAAGTGACAATACAGTACAACCTCTGCAACGAGCCATGgtgcctttct ... cttccttcagGTTAAAATATAGTATAAGCATTGTGGCAGACAAGGGATTGAAAAAGTCACT
EST: gi|58029867|gb|CX725294.1|CX725294
EST:     AGATTTGTCCGTGAAGTGACAATACAGTACAATCTCTGCAACGAGCCATG                         GTTAAAATATAGTATAAGCATTGTGGCAGACAAGGGATTGAAAAAGTCACT
genomic: AGATTTGTCCGTGAAGTGACAATACAGTACAACCTCTGCAACGAGCCATGgtgcctttct ... cttccttcagGTTAAAATATAGTATAAGCATTGTGGCAGACAAGGGATTGAAAAAGTCACT
EST: gi|211146180|gb|FK958444.1|FK958444
EST:     AGATTTGTCCGTGAAGTGACAATACAGTACAATCTCTGCAACGAGCCATG                         GTTAATATATAGTATAAGCWTTGTGGCAGACAAGGGATTGATAAAGTCACT
genomic: AGATTTGTCCGTGAAGTGACAATACAGTACAACCTCTGCAACGAGCCATGgtgcctttct ... cttccttcagGTTAAAATATAGTATAAGCATTGTGGCAGACAAGGGATTGAAAAAGTCACT
EST: gi|78077940|gb|DV506360.1|DV506360
EST:     AGATTTGTCCGTGAAGTGACAATACAGTACAACCTCTGCAACGAGCCATG                         GTTAAAATATAGTATAAGCATTGTGGCAGACAAGGGATTGAAAAAGTCACT
genomic: AGATTTGTCCGTGAAGTGACAATACAGTACAACCTCTGCAACGAGCCATGgtgcctttct ... cttccttcagGTTAAAATATAGTATAAGCATTGTGGCAGACAAGGGATTGAAAAAGTCACT

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), 8 (downstream exon)
Score: 217

AATGCATTGCGACAACAAAGATTTGTCCGTGAAGTGACAATACAGTACAACCTCTGCAACGAGCCATGgtgcctttct ... cttccttcagGTTAAAATATAGTATAAGCATTGTGGCAGACAAGGGATTGAAAAAGTCACTTTATACTTCTGCTAGACTGAAGAAAGGAGAAGTAATATATTTGGAGACA


Block sizes: 49 (upstream exon), 8 (downstream exon)
Score: 131

AATGCATTGCGACAACAAAGATTTGTCCGTGAAGTGACAATACAGTACAACCTCTGCAACGAGCCATGgtgcctttct ... cttccttcagGTTAAAATATAGTATAAGCATTGTGGCAGACAAGGGATTGAAAAAGTCACTTTATACTTCTGCTAGACTGAAGAAAGGAGAAGTAATATATTTGGAGACA


Block sizes: 49 (upstream exon), 8 (downstream exon)
Score: 150

AATGCATTGCGACAACAAAGATTTGTCCGTGAAGTGACAATACAGTACAACCTCTGCAACGAGCCATGgtgcctttct ... cttccttcagGTTAAAATATAGTATAAGCATTGTGGCAGACAAGGGATTGAAAAAGTCACTTTATACTTCTGCTAGACTGAAGAAAGGAGAAGTAATATATTTGGAGACA


Block sizes: 49 (upstream exon), 8 (downstream exon)
Score: 147

AATGCATTGCGACAACAAAGATTTGTCCGTGAAGTGACAATACAGTACAACCTCTGCAACGAGCCATGgtgcctttct ... cttccttcagGTTAAAATATAGTATAAGCATTGTGGCAGACAAGGGATTGAAAAAGTCACTTTATACTTCTGCTAGACTGAAGAAAGGAGAAGTAATATATTTGGAGACA