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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCATATCCTTACAAATCCCCGTCCATCGGCTTCATCAACAAGATTTATCACCCAAATGTCGATGAGATgtgagcattatggtcttaaactatttttcttattttattgaagttcatgcatggagttaacatttccttacctgttcttatttgactgcaaaatgcag

Basic information

species Zea mays
transcript GRMZM2G053764_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G053764_T03 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA18G46940.1 (Glycine max), 5'ss of exon 3
GTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCATATCCTTACAAATCCCCGTCCATCGGCTTCATCAACAAGATTTATCACCCAAATGTCGATGAGATgtgagcattatggtcttaa-actatttttcttattt-tattga--agttcatgcatggagttaacatttccttacctgttcttatttgactgcaaaatgcag------------------------
 ||| ||||| || || || ||  |||| ||||| |||||||||||||| || ||||| ||||| ||||||||||| |||||||||||||| |||||||||| ||||  || ||  |||  || |     || | | ||||||  |||| |    || | |  | ||     ||  |||   |   ||  |   |  ||                           
-TGTGTGGAAAGTAAGAGTTGAGTTGCCGGATGCTTATCCTTACAAATCTCCTTCCATTGGCTTTATCAACAAGATCTATCACCCAAATGTTGATGAGATGtaagcac-atagtagtaatgctctgaaaattgtctgtattgagtagtttacatgtgtattagatataagaataattgtgtgtcggtgcgtctgatctgatcatcttggataacattaatttcagg

upper sequence: GRMZM2G053764_T03 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA09G39370.1 (Glycine max), 5'ss of exon 2
GTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCATATCCTTACAAATCCCCGTCCATCGGCTTCATCAACAAGATTTATCACCCAAATGTCGATGAGATgtgagcattatggtcttaa-actatttttcttattt-tattgaa-gttcatgcatggagttaacatttccttacctgttcttatttgactgcaaaatgcag
|||| ||||| || || || ||  |||| ||||| |||||||||||||| || ||||| || || ||||||||||| |||||||| ||||| |||||||||| ||||  || ||  |||  || |     || | | ||||||    |   |  |  | |      |    ||  || |   || |   |  | |||  | 
GTGTGTGGAAAGTAAGAGTTGAGTTGCCGGATGCTTATCCTTACAAATCTCCTTCCATTGGATTTATCAACAAGATCTATCACCCGAATGTTGATGAGATgtaagcac-atagtagtaatgctctgaaaattgtctgtattgagtagttgcgtgtctattagctgatagaatatatgataagatatatttagataatatat

upper sequence: GRMZM2G053764_T03 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA16G03940.2 (Glycine max), 5'ss of exon 3
GTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCATATCCTTACAAATCCCCGTCCATCGGCTTCATCAACAAGATTTATCACCCAAATGTCGATGAGATgtgagcattatg-gtcttaaactattttt------cttattttattgaagttcatgcatggagttaacatttccttacctgt----tcttatttgactgcaaaa--tgcag
|||| ||||| || || || || ||||| ||||| |||||||| ||||| || ||||| ||||| ||||| ||||| |||||||||||||| |||||||||| |  ||  ||  | ||  | ||||  |      ||   |   ||||      ||| | | |||||  ||   |    |||    || |||| || |  || |  | |||
GTGTATGGAAAGTAAGAGTTGAGCTGCCAGATGCTTATCCTTATAAATCTCCTTCCATAGGCTTTATCAATAAGATCTATCACCCAAATGTTGATGAGATgtaaaaatattgtattttttaatattgctgcgaaactctatactttgagtagtttgccttgtgttaattttaagtattgtgtgcgatcatattggattataataatttcag

upper sequence: GRMZM2G053764_T03 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA07G07540.3 (Glycine max), 5'ss of exon 2
GTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCATATCCTTACAAATCCCCGTCCATCGGCTTCATCAACAAGATTTATCACCCAAATGTCGATGAGATgtgagcattatg-gtcttaaactattttt------cttattttattgaagttcatgcatggagttaacattt----ccttacctgttcttatttgactgcaaaatg----cag
|||| ||||| || ||||| || ||||| ||||| |||||||| ||||| || ||||| ||||| ||||| ||||| |||||||||||||| |||||||||| || ||  ||  |  |  | ||||  |      ||   |   ||||      ||| | | |||||  ||        |   || || |||| ||    | |||     |||
GTGTGTGGAAAGTGAGGGTTGAGCTGCCAGATGCTTATCCTTATAAATCTCCTTCCATAGGCTTTATCAATAAGATCTATCACCCAAATGTTGATGAGATgtaagaatcttgtattattgaatattgctgcgaaactctataccttgagtagtttgccttgtgttaattttaagaattgtgtgtgatcatattggatattataataatttcag

upper sequence: GRMZM2G053764_T03 (Zea mays), 5'ss of exon 3
lower sequence: Vv02s0025g00070.t01 (Vitis vinifera), 5'ss of exon 3
GTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCATATCCTTACAAATCCCCGTCCATCGGCTTCATCAACAAGATTTATCACCCAAATGTCGATGAGATgtgagc--attatggtcttaaactatttttcttattttattgaag--------ttcatgcatggagttaacatttcctt-acctgttcttatttgactgcaaaatgcag------------------
|||| |||| | | ||||| || || || ||||| |||||||| ||||| || || || || ||  |||||||||| || ||||||||||| |||||||||||||    |    || | ||||    |   | |  ||     ||        ||| |  ||      |||||       |  || | || |   |    | |||   |                  
GTGTGTGGAGGATAAGGGTGGAGCTACCAGATGCTTATCCTTATAAATCTCCATCTATTGGTTTTGTCAACAAGATCTACCACCCAAATGTTGATGAGATgtgagttagtggatgtttaaaacctagtacttcagcttgcatgagctgcatttttcttatatatgacaaacataaggaagaattggttttctcaaatatgacaatcttgtgggtctttgagtttcag

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|12968800|gb|BG265836.1|BG265836
EST:     CCGTCCATCGGCTTCATCATCAAGATTTATCACCCTAATGTCGATGAGAT                         GTCTGGCTCTGTCTGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTT
genomic: CCGTCCATCGGCTTCATCAACAAGATTTATCACCCAAATGTCGATGAGATgtgagcatta ... caaaatgcagGTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTT
EST: gi|5895766|gb|AW037012.1|AW037012
EST:     CCGTCCATCGGCTTCATCAACAAGATTTATCACCCTAATGTCGATGAGAT                         GTCTGGCTCTGTCTGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTT
genomic: CCGTCCATCGGCTTCATCAACAAGATTTATCACCCAAATGTCGATGAGATgtgagcatta ... caaaatgcagGTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTT
EST: gi|6022600|gb|AW067412.1|AW067412
EST:     CCGTCCATCGGCTTCATCAACAAGATTTATCACCCTAATGTCGATGAGAT                         GTCTGGCTCTGTCTGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTT
genomic: CCGTCCATCGGCTTCATCAACAAGATTTATCACCCAAATGTCGATGAGATgtgagcatta ... caaaatgcagGTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTT
EST: gi|5713918|gb|AI943903.1|AI943903
EST:     CCGTCCATCGGCTTCATCAACAAGATTTATCACCCTAATGTCGATGAGAT                         GTCTGGCTCTGTCTGTTTAGATGTCATAAACCAAACATGGNAGCCCAATGT
genomic: CCGTCCATCGGCTTCATCAACAAGATTTATCACCCAAATGTCGATGAGATgtgagcatta ... caaaatgcagGTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGG-AGCCCAATGT
EST: gi|5895785|gb|AW037031.1|AW037031
EST:     CCGTCCATCGGCTTCATCAACAAGATTTATCACCCTAATGTCGATGAGAT                         GTCTGGCTCTGTCTGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTT
genomic: CCGTCCATCGGCTTCATCAACAAGATTTATCACCCAAATGTCGATGAGATgtgagcatta ... caaaatgcagGTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTT
EST: gi|60396538|gb|DN229407.1|DN229407
EST:     CCGTCCATCGGCTTCATCAACAAGATTTATCACCCAAATGTCGATGAGAT                         GTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTT
genomic: CCGTCCATCGGCTTCATCAACAAGATTTATCACCCAAATGTCGATGAGATgtgagcatta ... caaaatgcagGTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTT
EST: gi|60355446|gb|DN222419.1|DN222419
EST:     CCGTCCATCGGCTTCATCAACAAGATTTATCACCCAAATGTCGATGAGAT                         GTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTT
genomic: CCGTCCATCGGCTTCATCAACAAGATTTATCACCCAAATGTCGATGAGATgtgagcatta ... caaaatgcagGTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTT
EST: gi|5649980|gb|AI920340.1|AI920340
EST:     CCGTCCATCGGCTTCATCAACAAGATTTATCACCCAAATGTCGATGAGAT                         GTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTT
genomic: CCGTCCATCGGCTTCATCAACAAGATTTATCACCCAAATGTCGATGAGATgtgagcatta ... caaaatgcagGTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTT
EST: gi|71328419|gb|DR800850.1|DR800850
EST:     CCGTCCATCGGCTTCATCAACAAGATTTATCACCCAAATGTCGATGAGAT                         GTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTT
genomic: CCGTCCATCGGCTTCATCAACAAGATTTATCACCCAAATGTCGATGAGATgtgagcatta ... caaaatgcagGTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTT
EST: gi|5608383|gb|AI901960.1|AI901960
EST:     CATCAACAAGATTTATCACCCTAATGTCGATGAGAT                         GTCTGGCTCTGTCTGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTT
genomic: CATCAACAAGATTTATCACCCAAATGTCGATGAGATgtgagcatta ... caaaatgcagGTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTT
EST: gi|87156694|gb|DY401483.1|DY401483
EST:     CCGTCCATCGGCTTCATCAACAAGATTTATCACCCTAATGTCGATGAGAT                         GTCTGGCTCTGTCTGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTT
genomic: CCGTCCATCGGCTTCATCAACAAGATTTATCACCCAAATGTCGATGAGATgtgagcatta ... caaaatgcagGTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTT
EST: gi|5895786|gb|AW037032.1|AW037032
EST:     CCGTCCATCGGCTTCATCAACAAGATTTATCACCCTAATGTCGATGAGAT                         GTCTGGCTCTGTCTGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTT
genomic: CCGTCCATCGGCTTCATCAACAAGATTTATCACCCAAATGTCGATGAGATgtgagcatta ... caaaatgcagGTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTT
EST: gi|5917370|gb|AW054161.1|AW054161
EST:     CCGTCCATCGGCTTCATCAACAAGATTTATCACCCTAATGTCGATGAGAT                         GTCTGGCTCTGTCTGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTT
genomic: CCGTCCATCGGCTTCATCAACAAGATTTATCACCCAAATGTCGATGAGATgtgagcatta ... caaaatgcagGTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTT
EST: gi|22715330|gb|BU197707.1|BU197707
EST:     CCGTCCATCGGCTTCATCAACAAGATTTATCACCCTAATGTCGATGAGAT                         GTCTGGCTCTGTCTGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTT
genomic: CCGTCCATCGGCTTCATCAACAAGATTTATCACCCAAATGTCGATGAGATgtgagcatta ... caaaatgcagGTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTT
EST: gi|211363205|gb|FL271919.1|FL271919
EST:     CCGTCCATCGGCTTCATCAACAAGATTTATCACCCAAATGTCGATGAGAT                         GTCTGGCTCTGTATGTTTANATGTCATAAACCAAACATGGAGCCCAATGTT
genomic: CCGTCCATCGGCTTCATCAACAAGATTTATCACCCAAATGTCGATGAGATgtgagcatta ... caaaatgcagGTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTT

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: 47 (upstream exon), 49 (downstream exon)
Score: 178

GTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCATATCCTTACAAATCCCCGTCCATCGGCTTCATCAACAAGATTTATCACCCAAATGTCGATGAGATgtgagcatta ... caaaatgcagGTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 534

GTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCATATCCTTACAAATCCCCGTCCATCGGCTTCATCAACAAGATTTATCACCCAAATGTCGATGAGATgtgagcatta ... caaaatgcagGTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 658

GTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCATATCCTTACAAATCCCCGTCCATCGGCTTCATCAACAAGATTTATCACCCAAATGTCGATGAGATgtgagcatta ... caaaatgcagGTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 262

GTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCATATCCTTACAAATCCCCGTCCATCGGCTTCATCAACAAGATTTATCACCCAAATGTCGATGAGATgtgagcatta ... caaaatgcagGTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTG