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

GGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAGgtgtgtccctctttttaccatagtctcttggtgcaatttcttcttagttcttggagcgcacattgacttggtgttgtgacatttgtccttccacag

Basic information

species Zea mays
transcript GRMZM2G324540_T01
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G324540_T01 (Zea mays), 5'ss of exon 17
lower sequence: LOC_Os10g32880.1 (Oryza sativa), 5'ss of exon 15
GGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAGgtgtgtccctctttt-taccatagtctcttggtgca-atttcttcttagttcttggagcgcacattgacttggtgt-tgtgacatttgtccttccacag
||| ||||||||||| |||||||||   |||||||||||| ||||||| ||||| ||||| ||||| ||||||  |||||| | || |  |  |   ||| ||| |    ||    |  || |||| |    ||  | | ||||| | |||| | |      |||  |||
GGTTTACCAAGTAGCAAATGTTAAGCTTGAATGGAATCTTGTCAAGACCTTACCAGATTTGTCAGGCACAGgttcgtccctttcttatggcccacattctcggttcgtgattggcatctgtgcttgcacttaac--taatttggtttctgtggcgtacacttttct-cag
















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|166629274|gb|EG278733.1|EG278733
EST:     ATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAG                         GGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAG
genomic: ATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAGgtgtgtccct ... ccttccacagGGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAG
EST: gi|211125237|gb|FL005610.1|FL005610
EST:     TAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAG                         GGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAG
genomic: TAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAGgtgtgtccct ... ccttccacagGGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAG
EST: gi|211013333|gb|FL464492.1|FL464492
EST:     TAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAG                         GGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAG
genomic: TAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAGgtgtgtccct ... ccttccacagGGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAG
EST: gi|30052429|gb|AI065718.2|AI065718
EST:     TAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAG                         GGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAG
genomic: TAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAGgtgtgtccct ... ccttccacagGGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAG
EST: gi|211328788|gb|FL441397.1|FL441397
EST:     TAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAG                         GGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAG
genomic: TAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAGgtgtgtccct ... ccttccacagGGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAG
EST: gi|211328787|gb|FL441396.1|FL441396
EST:     TAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAG                         GGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAG
genomic: TAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAGgtgtgtccct ... ccttccacagGGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAG
EST: gi|211125230|gb|FL005603.1|FL005603
EST:     TAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAG                         GGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAG
genomic: TAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAGgtgtgtccct ... ccttccacagGGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAG
EST: gi|16379531|gb|BI993008.1|BI993008
EST:     TAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAG                         GGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAG
genomic: TAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAGgtgtgtccct ... ccttccacagGGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAG
EST: gi|37394216|gb|CF634379.1|CF634379
EST:     TAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAG                         GGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAG
genomic: TAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAGgtgtgtccct ... ccttccacagGGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAG
EST: gi|32932206|gb|CF037018.1|CF037018
EST:     TAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAG                         GGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAG
genomic: TAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAGgtgtgtccct ... ccttccacagGGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAG
EST: gi|32835196|gb|CD974874.1|CD974874
EST:     TAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAG                         GGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAG
genomic: TAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAGgtgtgtccct ... ccttccacagGGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAG
EST: gi|30052532|gb|AI065821.2|AI065821
EST:     ATTTATCAGGAACAG                         GGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAG
genomic: ATTTATCAGGAACAGgtgtgtccct ... ccttccacagGGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAG
EST: gi|32834072|gb|CD973750.1|CD973750
EST:     TAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAG                         GGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAG
genomic: TAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAGgtgtgtccct ... ccttccacagGGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAG
EST: gi|13490540|gb|BG517304.1|BG517304
EST:     TAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAG                         GGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAG
genomic: TAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAGgtgtgtccct ... ccttccacagGGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAG
EST: gi|211152716|gb|FL458060.1|FL458060
EST:     TAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAG                         GGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAG
genomic: TAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAGgtgtgtccct ... ccttccacagGGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAG
EST: gi|32931746|gb|CF036558.1|CF036558
EST:     TAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAG                         GGAAAGTAACTTCCGTAAAATTCGGAGT
genomic: TAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAGgtgtgtccct ... ccttccacagGGAAAGTAACTTCCGTAAAATTCGGAGT
EST: gi|13490541|gb|BG517305.1|BG517305
EST:     TAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAG                         GGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAG
genomic: TAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAGgtgtgtccct ... ccttccacagGGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAG
EST: gi|32939397|gb|CF044216.1|CF044216
EST:     TAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAG                         GGAAAGTAACTTCCGTAAAATTCGGAGTAGGCGCGAAATACATAGCCATAG
genomic: TAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAGgtgtgtccct ... ccttccacagGGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAG
EST: gi|116828456|gb|EC857640.1|EC857640
EST:     TAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAG                         GAAAAGTAACTTCCGTAAAATTTGGAGTAGACGCGAAATACATAGCCATAG
genomic: TAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAGgtgtgtccct ... ccttccacagGGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAG
EST: gi|32835644|gb|CD975322.1|CD975322
EST:     TAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAG                         GGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATA
genomic: TAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAGgtgtgtccct ... ccttccacagGGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATA

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), 49 (downstream exon)
Score: 214

GGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAGgtgtgtccct ... ccttccacagGGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAGGTTCTATGGACCGCAATCTACGGATATTTGGTCTCCCTGGAGATGATCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 74

GGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAGgtgtgtccct ... ccttccacagGGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAGGTTCTATGGACCGCAATCTACGGATATTTGGTCTCCCTGGAGATGATCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 102

GGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAGgtgtgtccct ... ccttccacagGGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAGGTTCTATGGACCGCAATCTACGGATATTTGGTCTCCCTGGAGATGATCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 83

GGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTTATCAAGACATTACCCGATTTATCAGGAACAGgtgtgtccct ... ccttccacagGGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAGGTTCTATGGACCGCAATCTACGGATATTTGGTCTCCCTGGAGATGATCA