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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCAAAATACAACAGCATTCAAAGAAGTAGCAATCATTAGTCATCCCCGTGTTGGTGAATATGCATTTGGATTCATAACATCAACCATGGTTCTTCAGgtactttttcatgcacactgcagctgtgtatggctttgaccggcagatgtaatcttttaatgatggatattttcctagttaatatgctgtccatagattt...

Basic information

species Zea mays
transcript GRMZM2G052855_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052855_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os05g36110.2 (Oryza sativa), 5'ss of exon 5
ATCAAAATACAACAGCATTCAAAGAAGTAGCAATCATTAGTCATCCCCGTGTTGGTGAATATGCATTTGGATTCATAACATCAACCATGGTTCTTCAGgtactttttcatgcacactgca-gctgt-gtatggctttgacc--ggcagatgtaatcttttaatga-tggatattttcctagttaatatgctgtccatagattt
||||||||||||| ||||| |||||||| ||||| ||||||||||||||| ||||||||||||||||||||||||||||||| || ||| | ||||||||| || || || || |      ||| | | |||  |   | |  |   | |  |  ||     ||  | |||  || |||     ||      | |||      
ATCAAAATACAACGGCATTTAAAGAAGTTGCAATAATTAGTCATCCCCGTATTGGTGAATATGCATTTGGATTCATAACATCGACGATGATCCTTCAGgtatttgtttatacatatcatgtgctctagaatgaatagaatcttgatggtttcagcctacacctgcctagatgattacctc-cagatgcctcattcatgt----

upper sequence: GRMZM2G052855_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA06G15360.2 (Glycine max), 5'ss of exon 5
ATCAAAATACAACAGCATTCAAAGAAGTAGCAATCATTAGTCATCCCCGTGTTGGTGAATATGCATTTGGATTCATAACATCAACCATGGTTCTTCAGgtactttttcatgcacactgcagctgtgtatggctttgaccggcagatgtaatcttttaatgatggatattttcctagttaatatgctgtccatagattt--
|||||||||| || || || ||||| |||||||| ||  |||| || ||||||||||||||||| |||||||| || ||||||||  |   ||| |||||||  | |  ||  | ||  |  | ||| || |        |  | | |  | | || ||  || |||      ||  |   |   | || ||   | |  
ATCAAAATACCACTGCCTTTAAAGAGGTAGCAATTATCCGTCACCCGCGTGTTGGTGAATATGCGTTTGGATTTATTACATCAACTGTTACTCTACAGgtaccctgtactgt-cgctataaatttgtttgccaaccttgtgatggtttcctttctttattttg-ataacaaattaacttcaacaatttctattattattt

upper sequence: GRMZM2G052855_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA04G39490.1 (Glycine max), 5'ss of exon 5
ATCAAAATACAACAGCATTCAAAGAAGTAGCAATCATTAGTCATCCCCGTGTTGGTGAATATGCATTTGGATTCATAACATCAACCATGGTTCTTCAGgtactttttcatg-cacactgcagctgtgtatgg--ctttgaccggcagatgtaatcttttaatgatggatattttcctagttaatatgctgtccatagattt
|||||||||| || || || ||||| |||||||| ||  |||| || ||||||||||||||||||||||| || || ||||||||  |  |||| |||||||| | |  || |||  |  |  ||| ||     || | |     |    | |  | |   |||||   |    | ||    | |   || |   | | | 
ATCAAAATACCACTGCCTTTAAAGAGGTAGCAATTATCCGTCACCCGCGTGTTGGTGAATATGCATTTGGCTTTATTACATCAACTGTTATTCTACAGgtactgtgtagtgtcactataaatttgtttaccaacctcttatttatattgattaaatatgtgtgatgagcaaccacataa--gagaacttgacatcacact-

upper sequence: GRMZM2G052855_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT1G43130.1 (Arabidopsis thaliana), 5'ss of exon 5
ATCAAAATACAACAGCATTCAAAGAAGTAGCAATCATTAGTCATCCCCGTGTTGGTGAATATGCATTTGGATTCATAACATCAACCATGGTTCTTCAGgt-actttttcatgcacactgcagctgtgtatggctttgaccggcagatgtaatcttttaatgatggatattttcctagttaatatgctgtccatagattt
| ||||| || || || || ||||| |||||||||||  |||| || ||| |||||||||| ||||||||||| || |||||| |  ||   |||||||| | || ||||    ||    | ||| |||   |        ||| || || |   ||  |        ||||  | |||   |                
ACCAAAACACTACTGCCTTTAAAGAGGTAGCAATCATCCGTCACCCTCGTATTGGTGAATACGCATTTGGATTTATTACATCATCGGTGACACTTCAGgtcagttattca---gcaacaaaactg-gtaaaacccaagtaagcaaat-tagttacttgctctcatgctttttttttgttgtaacag-------------

upper sequence: GRMZM2G052855_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv07s0031g02010.t01 (Vitis vinifera), 5'ss of exon 5
ATCAAAATACAACAGCATTCAAAGAAGTAGCAATCATTAGTCATCCCCGTGTTGGTGAATATGCATTTGGATTCATAACATCAACCATGGTTCTTCAGgtactttttcatgcacactgcagctgtgtatggc-tttgaccggcagatgtaatcttttaatgatggatattttcctagttaatatgctgtccatagattt
| |||||||| || || || ||||| ||||| |||||  ||||||| ||||||||||||||||||||||| || || ||||||||  |  | ||||||||||||||  ||  | |      || |   ||   ||||  |      | |  ||   | |   ||      ||  |  |   | |  | | ||||  |  
ACCAAAATACCACTGCTTTTAAAGAGGTAGCTATCATCCGTCATCCACGTGTTGGTGAATATGCATTTGGTTTTATTACATCAACAGTAATCCTTCAGgtacttttagata-atatgatttctcttcttgaaatttgttcaagctttttgctcaagtcagtttgagaggatttttgttcctttttttattcatatgtga

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|93283406|gb|EB675670.1|EB675670
EST:     GTGTTGGTGAATATGCATTTGGATTCATAACATCAACCATGGTTCTTCAG                         ACAGACAAAGGTGATGAAGAATTGTGTAGTGTTTATGTGCCAACCAATCAT
genomic: GTGTTGGTGAATATGCATTTGGATTCATAACATCAACCATGGTTCTTCAGgtactttttc ... tgcattgcagACAGACAAAGGTGATGAAGAATTGTGTAGTGTTTATGTGCCAACCAATCAT
EST: gi|88752753|gb|DY536894.1|DY536894
EST:     GTGTTGGTGAATATGCATTTGGATTCATAACATCAACCATGGTTCTTCAG                         ACAGACAAAGGTGATGAAGAATTGTGTAGTGTTTATGTGCCAACCAATCAT
genomic: GTGTTGGTGAATATGCATTTGGATTCATAACATCAACCATGGTTCTTCAGgtactttttc ... tgcattgcagACAGACAAAGGTGATGAAGAATTGTGTAGTGTTTATGTGCCAACCAATCAT
EST: gi|60397295|gb|DN230111.1|DN230111
EST:     GTGTTGGTGAATATGCATTTGGATTCATAACATCAACCATGGTTCTTCAG                         ACAGACAAAGGTGATGAAGAATTGTGTAGTGTTTATGTGCCAACCAATCAT
genomic: GTGTTGGTGAATATGCATTTGGATTCATAACATCAACCATGGTTCTTCAGgtactttttc ... tgcattgcagACAGACAAAGGTGATGAAGAATTGTGTAGTGTTTATGTGCCAACCAATCAT
EST: gi|32935666|gb|CF040478.1|CF040478
EST:     GTGTTGGTGAATATGCATTTGGATTCATAACATCAACCGTGGTTCTTCAG                         ACAGACAAAGGTGATGAAGAATTGTGTAGTGTTTATGTGCCAACCAATCAT
genomic: GTGTTGGTGAATATGCATTTGGATTCATAACATCAACCATGGTTCTTCAGgtactttttc ... tgcattgcagACAGACAAAGGTGATGAAGAATTGTGTAGTGTTTATGTGCCAACCAATCAT
EST: gi|148995086|gb|EE034390.2|EE034390
EST:     GTGTTGGTGAATATGCATTTGGATTCATAACATCAACCATGGTTCTTCAG                         ACAGACAAAGGTGATGAAGAATTGTGTAGTGTTTATGTGCCAACCAATCAT
genomic: GTGTTGGTGAATATGCATTTGGATTCATAACATCAACCATGGTTCTTCAGgtactttttc ... tgcattgcagACAGACAAAGGTGATGAAGAATTGTGTAGTGTTTATGTGCCAACCAATCAT
EST: gi|71319563|gb|DR796526.1|DR796526
EST:     GTGTTGGTGAATATGCATTTGGATTCATAACATCAACCATGGTTCTTCAG                         ACAGACAAAGGTGATGAAGAATTGTGTAGTGTTTATGTGCCAACCAATCAT
genomic: GTGTTGGTGAATATGCATTTGGATTCATAACATCAACCATGGTTCTTCAGgtactttttc ... tgcattgcagACAGACAAAGGTGATGAAGAATTGTGTAGTGTTTATGTGCCAACCAATCAT
EST: gi|148985826|gb|EE029793.2|EE029793
EST:     GTGTTGGTGAATATGCATTTGGATTCATAACATCAACCATGGTTCTTCAG                         ACAGACAAAGGTGATGAAGAATTGTGTAGTGTTTATGTGCCAACCAATCAT
genomic: GTGTTGGTGAATATGCATTTGGATTCATAACATCAACCATGGTTCTTCAGgtactttttc ... tgcattgcagACAGACAAAGGTGATGAAGAATTGTGTAGTGTTTATGTGCCAACCAATCAT
EST: gi|14245263|gb|BG873845.1|BG873845
EST:     GTGTTGGTGAATATGCATTTGGATTCATAACATCAACCATGGTTCTTCAG                         ACAGACAAAGGTGATGAAGAATTGTGTAGTGTTTATGTGCCAACCAATCAT
genomic: GTGTTGGTGAATATGCATTTGGATTCATAACATCAACCATGGTTCTTCAGgtactttttc ... tgcattgcagACAGACAAAGGTGATGAAGAATTGTGTAGTGTTTATGTGCCAACCAATCAT
EST: gi|91049872|gb|EB160290.1|EB160290
EST:     GTGTTGGTGAATATGCATTTGGATTCATAACATCAACCATGGTTCTTCAG                         ACAGACCAGGGTGATGAAGAATTGTGTAGTGTTTAT
genomic: GTGTTGGTGAATATGCATTTGGATTCATAACATCAACCATGGTTCTTCAGgtactttttc ... tgcattgcagACAGACAAAGGTGATGAAGAATTGTGTAGTGTTTAT
EST: gi|78109866|gb|DV528282.1|DV528282
EST:     GTGTTGGTGAATATGCATTTGGATTCATAACATCAACCATGGTTCTTCAG                         ACAGACAAAGGTGATGAAGAATTGTGTAGTGTTTATGTGCCAACCAATCAT
genomic: GTGTTGGTGAATATGCATTTGGATTCATAACATCAACCATGGTTCTTCAGgtactttttc ... tgcattgcagACAGACAAAGGTGATGAAGAATTGTGTAGTGTTTATGTGCCAACCAATCAT
EST: gi|89249400|gb|DY621186.1|DY621186
EST:     GTGTTGGTGAATATGCATTTGGATTCATAACATCAACCATGGTTCTTCAG                         ACAGACAAAGGTGATGAAGAATTGTGTAGTGTTTATGTGCCACCCAATCAT
genomic: GTGTTGGTGAATATGCATTTGGATTCATAACATCAACCATGGTTCTTCAGgtactttttc ... tgcattgcagACAGACAAAGGTGATGAAGAATTGTGTAGTGTTTATGTGCCAACCAATCAT

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: 58

ATCAAAATACAACAGCATTCAAAGAAGTAGCAATCATTAGTCATCCCCGTGTTGGTGAATATGCATTTGGATTCATAACATCAACCATGGTTCTTCAGgtactttttc ... tgcattgcagACAGACAAAGGTGATGAAGAATTGTGTAGTGTTTATGTGCCAACCAATCATTTATATATTGGTGACATCTTTTTGGTAAACTCCGCCGAAATTATAAGGC


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 41

ATCAAAATACAACAGCATTCAAAGAAGTAGCAATCATTAGTCATCCCCGTGTTGGTGAATATGCATTTGGATTCATAACATCAACCATGGTTCTTCAGgtactttttc ... tgcattgcagACAGACAAAGGTGATGAAGAATTGTGTAGTGTTTATGTGCCAACCAATCATTTATATATTGGTGACATCTTTTTGGTAAACTCCGCCGAAATTATAAGGC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 47

ATCAAAATACAACAGCATTCAAAGAAGTAGCAATCATTAGTCATCCCCGTGTTGGTGAATATGCATTTGGATTCATAACATCAACCATGGTTCTTCAGgtactttttc ... tgcattgcagACAGACAAAGGTGATGAAGAATTGTGTAGTGTTTATGTGCCAACCAATCATTTATATATTGGTGACATCTTTTTGGTAAACTCCGCCGAAATTATAAGGC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 88

ATCAAAATACAACAGCATTCAAAGAAGTAGCAATCATTAGTCATCCCCGTGTTGGTGAATATGCATTTGGATTCATAACATCAACCATGGTTCTTCAGgtactttttc ... tgcattgcagACAGACAAAGGTGATGAAGAATTGTGTAGTGTTTATGTGCCAACCAATCATTTATATATTGGTGACATCTTTTTGGTAAACTCCGCCGAAATTATAAGGC