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'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGATATTTCTGTTGTCGGTGTCACCAGCTTCAGTGGACCCGAAGGCCCCTTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAAgtaagtaacttgttatttcgtgtttttttccattgaagtgagaatatcgatgctttatatcattacatgttacttggatcatgttatgttcacaagggaatctaatgatttaattactgacatcaattccag

Basic information

species Zea mays
transcript GRMZM2G109383_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G109383_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g50480.1 (Oryza sativa), 5'ss of exon 7
TTGATATTTCTGTTGTCGGTGTCACCAGCTTCAGTGGACCCGAAGGCCCCTTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAAgtaagtaacttgttatttcgtgttttt---ttccattgaagtgagaat--atcgatgctttat-----atcattacatgttacttggatcatgttatgttcacaagggaatctaatgatttaattactgacat-----caattccag
| |||||||||||||| |||||||| | |||||||||||| |||||||| |||||||| |||||||||||||||| | ||||||||||||||||||||||||||||  |||   ||||    ||  |   | | |||    |  | ||   |||||| ||| |     || | |  || || |||| | | |  || |  |    |  ||     ||||||||||  | |  |      ||||||||
TCGATATTTCTGTTGTAGGTGTCACTACCTTCAGTGGACCTGAAGGCCCTTTTGATGTTGATGTTTTTGACTCTACTATAGATTACATAAAGTTAATGAAgtaagttgctt-ccatttgaatttactgaatgctatttccatatgtattgttcgatgttttcttttcaataagtgaattttccttgtagcttcataagaacctgcgaaaaatgggtgatttaatttgtaatttgtatttaattccag
















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|211163859|gb|FL345453.1|FL345453
EST:     TTTGATGTGGATGTTTTTGACTCTAGTGTAGAATACATAAAGTTAATGGA                         GTTCA-TTTTTGACTTCGAA
genomic: TT-GATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAAgtaagtaact ... tcaattccagGA-CAATTTTTGACTTCGAA
EST: gi|31349456|gb|CD433813.1|CD433813
EST:     TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAA                         GTCAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTT
genomic: TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAAgtaagtaact ... tcaattccagGACAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTT
EST: gi|31355827|gb|CD440184.1|CD440184
EST:     TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAA                         GTCAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCC
genomic: TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAAgtaagtaact ... tcaattccagGACAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCC
EST: gi|211126281|gb|FL366445.1|FL366445
EST:     TTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGT-AATGGAA                         GACA-TTTTTGACTTCGAAGCAATAAAAA-GCTGCTGACCTCCCCAAAGT
genomic: TTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATG-AAgtaagtaact ... tcaattccagGACAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGT
EST: gi|211213801|gb|FL354211.1|FL354211
EST:     TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGT-AATGAA                         GACAGTTTTTGACTTCGAAAGCA-TAAAAAA
genomic: TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAAgtaagtaact ... tcaattccagGACAATTTTTGACTTCGAA-GCAATAAAAAA
EST: gi|67035308|gb|CO463841.1|CO463841
EST:     TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAA                         GACAATTTTTGACTTCGAAAGCA-TAAAAA-GCTGCTGACCTCCC-AA-GT
genomic: TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAAgtaagtaact ... tcaattccagGACAATTTTTGACTTCGAA-GCAATAAAAAAGCTGCTGACCTCCCCAAAGT
EST: gi|67024904|gb|CO453653.1|CO453653
EST:     ATAAAGTTAATGCC                         GACAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTT
genomic: ATAAAGTTAATGAAgtaagtaact ... tcaattccagGACAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTT
EST: gi|211446296|gb|FL306989.1|FL306989
EST:     TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTA-TGAA                         GTCAATTTTTGACTTCGAAGCA-TAAAAAAGCTGCTGACCTCCCCAAAGTT
genomic: TT-GATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAAgtaagtaact ... tcaattccagGACAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTT
EST: gi|60351626|gb|DN218599.1|DN218599
EST:     TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAA                         GACAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTT
genomic: TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAAgtaagtaact ... tcaattccagGACAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTT
EST: gi|149013083|gb|EE042782.2|EE042782
EST:     TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAA                         GACAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTT
genomic: TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAAgtaagtaact ... tcaattccagGACAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTT
EST: gi|211001599|gb|FL335869.1|FL335869
EST:     TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAA                         GACAATTTTTGACTTCGAAAGCA-TAAAAA-GCTGCTGACC
genomic: TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAAgtaagtaact ... tcaattccagGACAATTTTTGACTTCGAA-GCAATAAAAAAGCTGCTGACC
EST: gi|148945839|gb|EC891128.2|EC891128
EST:     TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAA                         GACAATTTTTGACTT
genomic: TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAAgtaagtaact ... tcaattccagGACAATTTTTGACTT
EST: gi|31353391|gb|CD437748.1|CD437748
EST:     TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAA                         GTCAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTT
genomic: TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAAgtaagtaact ... tcaattccagGACAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTT
EST: gi|211153939|gb|FL327667.1|FL327667
EST:     TTTGATGTGGATGTTTTTGACTCTAGTGTAGAATACATAAAGTTAATGAA                         GACAATTTTTGAC
genomic: TT-GATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAAgtaagtaact ... tcaattccagGACAATTTTTGAC
EST: gi|67041650|gb|CO467905.1|CO467905
EST:     TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAA                         GACAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTT
genomic: TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAAgtaagtaact ... tcaattccagGACAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTT
EST: gi|211258211|gb|FL352267.1|FL352267
EST:     TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAA                         GACAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAA
genomic: TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAAgtaagtaact ... tcaattccagGACAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAA
EST: gi|31353888|gb|CD438245.1|CD438245
EST:     TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAA                         GTCAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTT
genomic: TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAAgtaagtaact ... tcaattccagGACAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTT
EST: gi|149109221|gb|EE190083.2|EE190083
EST:     TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAA                         GACAATTTTTGACTTCGAAAGCA-TAAAAAAGCTGCTGACCTCCCCAA-GT
genomic: TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAAgtaagtaact ... tcaattccagGACAATTTTTGACTTCGAA-GCAATAAAAAAGCTGCTGACCTCCCCAAAGT
EST: gi|60351436|gb|DN218409.1|DN218409
EST:     TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAA                         GACAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTT
genomic: TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAAgtaagtaact ... tcaattccagGACAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTT
EST: gi|149017022|gb|EE045668.2|EE045668
EST:     TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAA                         GACAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTT
genomic: TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAAgtaagtaact ... tcaattccagGACAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTT
EST: gi|67025687|gb|CO454436.1|CO454436
EST:     TTTGATGTGGATGTATTTGACTCTAGTGTAGATTACATAAAGTTAATGAA                         GGACATTTTTT
genomic: TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAAgtaagtaact ... tcaattccagG-ACAATTTTT
EST: gi|31356494|gb|CD440851.1|CD440851
EST:     TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAA                         GTCAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTT
genomic: TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAAgtaagtaact ... tcaattccagGACAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTT
EST: gi|67025909|gb|CO454658.1|CO454658
EST:     TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAA                         GACAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTT
genomic: TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAAgtaagtaact ... tcaattccagGACAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTT
EST: gi|211040466|gb|FL323564.1|FL323564
EST:     TTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAAGT-AATGAA                         GACAATTTTTGACTTCGAAAGCA-TAAAAA
genomic: TTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAA-GTTAATGAAgtaagtaact ... tcaattccagGACAATTTTTGACTTCGAA-GCAATAAAAA
EST: gi|84980113|gb|DW530462.1|DW530462
EST:     TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAA                         GACAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTT
genomic: TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAAgtaagtaact ... tcaattccagGACAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTT
EST: gi|148945380|gb|EC890603.2|EC890603
EST:     TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAA                         GACAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTT
genomic: TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAAgtaagtaact ... tcaattccagGACAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTT
EST: gi|211101215|gb|FL335616.1|FL335616
EST:     TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAA                         GACAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAAGT
genomic: TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAAgtaagtaact ... tcaattccagGACAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAA-GT
EST: gi|149099504|gb|EE185542.2|EE185542
EST:     TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAA                         GACAATTTTTGACTTCGAAGCAATAAAAA-GCTGCTGACCCTCCCCAA-GT
genomic: TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAAgtaagtaact ... tcaattccagGACAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACC-TCCCCAAAGT
EST: gi|149014023|gb|EE043541.2|EE043541
EST:     TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAA                         GACAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTT
genomic: TTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAAgtaagtaact ... tcaattccagGACAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTT

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), 47 (downstream exon)
Score: 362

TTGATATTTCTGTTGTCGGTGTCACCAGCTTCAGTGGACCCGAAGGCCCCTTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAAgtaagtaact ... tcaattccagGACAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTTTACATTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 517

TTGATATTTCTGTTGTCGGTGTCACCAGCTTCAGTGGACCCGAAGGCCCCTTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAAgtaagtaact ... tcaattccagGACAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTTTACATTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 404

TTGATATTTCTGTTGTCGGTGTCACCAGCTTCAGTGGACCCGAAGGCCCCTTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAAgtaagtaact ... tcaattccagGACAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTTTACATTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 921

TTGATATTTCTGTTGTCGGTGTCACCAGCTTCAGTGGACCCGAAGGCCCCTTTGATGTGGATGTTTTTGACTCTAGTGTAGATTACATAAAGTTAATGAAgtaagtaact ... tcaattccagGACAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTTTACATTCTG