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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTACCGCAAACCGCTTGCTAGCATCTAAACAGACCATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCAAgtatgtttctaacctaatatatgatttacagagctcttttcgttggtgggacagcacttctaactttgagttgtgtcattctaatccacag

Basic information

species Zea mays
transcript GRMZM2G161969_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G161969_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os02g01500.1 (Oryza sativa), 5'ss of exon 12
GTTACCGCAAACCGCTTGCTAGCATCTAAACAGACCATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCAAgtatgtttctaacctaatatatgatttacagagctcttttcgttggtgggacagcacttctaactttgagttgtgtcattctaatcc-acag------------------------------------
||||| ||||||||| |||||   |||||||| || ||||||||||| ||||||||||| || || |||||||| || ||| |||||||||||     |    | | | ||||| ||   || | |  |   | ||| | |  |   |   || | ||   |  | ||  |     ||                                    
GTTACTGCAAACCGCCTGCTAAGCTCTAAACAAACTATTCCTCATTATTACTTGACAGTTGACGCCCGTGTTGATAATCTTATCAAgtatgttgaagcctagctttgtaatttaaagcaatcctatattacataggaaacctatgtaatgattcaattccatactgctggttttgtagctttttaaaatagttctttatttcaatctaatccag

upper sequence: GRMZM2G161969_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA07G03930.2 (Glycine max), 5'ss of exon 12
GTTACCGCAAACCGCTTGCTAGCATCTAAACAGACCATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCAAgtatgtttctaacctaatatatgatttacagagctcttttcgttggtgggacagcacttctaactttgagttgtgtcattctaatccacag
|| || ||    ||  | |||  ||| ||||| || |||||||||||||| || ||||||||| || |||||||||||||    | ||| || |||    ||  | ||  |  ||||     ||  |  |  |   | |  | |||| |         | |   | || ||| | ||
GTCACAGCTTCACGGCTACTATTATCAAAACAAACTATTCCTCATTACTATTTAACAGTAGATACATGTGTTGACAAACTCACGAGgtaagtctctg--ttatcaaatattcgacagg---tttacctgtcattacatattatttctgat-----aacgcgaactccttatctatag
















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|20802763|gb|BQ293813.1|BQ293813
EST:     ATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCAA                         GTTGCGAGGTGAACTGAATCCACTGCAGGATGCTTCTGGTGGAAAGAAAAT
genomic: ATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCAAgtatgtttct ... taatccacagGTTGCGAGGTGAACTGAATCCACTGCAGGATGCTTCTGGTGGAAAGAAAAT
EST: gi|32932090|gb|CF036902.1|CF036902
EST:     ATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCAA                         GTTGCGAGGTGAACTGAATCCACTGCAGGATGCTTCTGGTGGAAAGAAAAT
genomic: ATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCAAgtatgtttct ... taatccacagGTTGCGAGGTGAACTGAATCCACTGCAGGATGCTTCTGGTGGAAAGAAAAT
EST: gi|32933945|gb|CF038757.1|CF038757
EST:     ATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCAA                         GTTGCGAGGTGAACTGAATCCACTGCAGGATGCTTCTGGTGGAAAGAAAAT
genomic: ATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCAAgtatgtttct ... taatccacagGTTGCGAGGTGAACTGAATCCACTGCAGGATGCTTCTGGTGGAAAGAAAAT
EST: gi|21809700|gb|BQ668018.1|BQ668018
EST:     ATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCAA                         GTTGCGAGGTGAACTGAATCCACTGCAGGATGCTTCTGGTGGAAAGAAAAT
genomic: ATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCAAgtatgtttct ... taatccacagGTTGCGAGGTGAACTGAATCCACTGCAGGATGCTTCTGGTGGAAAGAAAAT
EST: gi|32930018|gb|CF034830.1|CF034830
EST:     ATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCAA                         GTTGCGAGGTGAACTGAATCCACTGCAGGATGCTTCTGGTGGAAAGAAAAT
genomic: ATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCAAgtatgtttct ... taatccacagGTTGCGAGGTGAACTGAATCCACTGCAGGATGCTTCTGGTGGAAAGAAAAT
EST: gi|5343148|gb|AI795333.1|AI795333
EST:     TACTTGACAGTAGATGCACGTGTTGACAAACTTGTCAA                         GTTGCGAGGTGAACTGAATCCACTGCAGGATGCTTCTGGTGGAAAGAAAAT
genomic: TACTTGACAGTAGATGCACGTGTTGACAAACTTGTCAAgtatgtttct ... taatccacagGTTGCGAGGTGAACTGAATCCACTGCAGGATGCTTCTGGTGGAAAGAAAAT
EST: gi|32934396|gb|CF039208.1|CF039208
EST:     ATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCAA                         GTTGCGAGGTGAACTGAATCCACTGCAGGATGCTTCTGGTGGAAAGAAAAT
genomic: ATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCAAgtatgtttct ... taatccacagGTTGCGAGGTGAACTGAATCCACTGCAGGATGCTTCTGGTGGAAAGAAAAT
EST: gi|22472155|gb|BU036635.1|BU036635
EST:     ATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCAA                         GTTGCGAGGTGAACTGAATCCACTGCAGGATGCTTCTGGTGGAAAGAAAAT
genomic: ATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCAAgtatgtttct ... taatccacagGTTGCGAGGTGAACTGAATCCACTGCAGGATGCTTCTGGTGGAAAGAAAAT
EST: gi|20802898|gb|BQ293948.1|BQ293948
EST:     ATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCAA                         GTTGCGAGGTGAACTGAATCCACTGCAGGATGCTTCTGGTGGAAAGAAAAT
genomic: ATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCAAgtatgtttct ... taatccacagGTTGCGAGGTGAACTGAATCCACTGCAGGATGCTTCTGGTGGAAAGAAAAT
EST: gi|20208122|gb|BQ134196.1|BQ134196
EST:     ATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCAA                         GTTGCGAGGTGAACTGAATCCACTGCAGGATGCTTCTGGTGGAAAGAAAAT
genomic: ATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCAAgtatgtttct ... taatccacagGTTGCGAGGTGAACTGAATCCACTGCAGGATGCTTCTGGTGGAAAGAAAAT

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: 160

GTTACCGCAAACCGCTTGCTAGCATCTAAACAGACCATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCAAgtatgtttct ... taatccacagGTTGCGAGGTGAACTGAATCCACTGCAGGATGCTTCTGGTGGAAAGAAAATATCTATCAATGATCTTGTCATCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 244

GTTACCGCAAACCGCTTGCTAGCATCTAAACAGACCATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCAAgtatgtttct ... taatccacagGTTGCGAGGTGAACTGAATCCACTGCAGGATGCTTCTGGTGGAAAGAAAATATCTATCAATGATCTTGTCATCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 180

GTTACCGCAAACCGCTTGCTAGCATCTAAACAGACCATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCAAgtatgtttct ... taatccacagGTTGCGAGGTGAACTGAATCCACTGCAGGATGCTTCTGGTGGAAAGAAAATATCTATCAATGATCTTGTCATCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 301

GTTACCGCAAACCGCTTGCTAGCATCTAAACAGACCATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCAAgtatgtttct ... taatccacagGTTGCGAGGTGAACTGAATCCACTGCAGGATGCTTCTGGTGGAAAGAAAATATCTATCAATGATCTTGTCATCAAG