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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgtttcctctttcatttttttcgcttcttggtggcatgcccatcatatgcttcatctgatttttttggtgaaaaattatttcagAGACCTTTCCTCCAATTCTCTTACTGGCAATCTACCACAAAGTTTCACTTCTTTGTCAAGCCTGAAAACACT

Basic information

species Zea mays
transcript GRMZM2G004572_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G004572_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os10g25090.1 (Oryza sativa), 3'ss of exon 6
---------------------------------------------------gtgagtgtttcctctttcatttttttcgcttcttggtggcatgcccatcatatgcttcatctgatttttttggtgaaaaattatttcagAGACCTTTCCTCCAATTCTCTTACTGGCAATCTACCACAAAGTTTCACTTCTTTGTCAAGCCTGAAAACACT
                                                      | |  |||    |||  | ||| |  |||||    |    | |    |||  ||  ||| | | | ||  || | | ||  | ||| || || ||||  ||||||||||||||  |||| |||||||||||||||||| ||||||||||||||||  |
gtgagtactcttacttaaaacaagtattctaggttgatctcaatgtgcacacaaaattcttctaacttctctgtttgcatttcttacaagt---cacgatgtatctttgctcttactatatttctgtaca-ttgctacagTGATCTCTCCTTAAATTCTCTTACTGGTGATCTCCCACAAAGTTTCACTTCTCTGTCAAGCCTGAAAACTTT
















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|76018777|gb|DT945947.1|DT945947
EST:     TCAGGAGATATCACGGACATATTTTCCAACCTCCCAAGTTTAACCACAGT                         AGACCTTTCCTCCCATTCTCTTACTGGCAATCTACCACAAAGTTTCACTTC
genomic: TCAGGAGATATCACGGACATATTTTCCAACCTCCCAAGTTTAACCACAGTgtgagtgttt ... attatttcagAGACCTTTCCTCCAATTCTCTTACTGGCAATCTACCACAAAGTTTCACTTC
EST: gi|74245639|gb|DT653553.1|DT653553
EST:     TCAGGAGATATCACGGACATATTTTCCAACCTCCCAAGTTTAACCACAGT                         AGACCTTTCCTCCAATTCTCTTACTGGCAATCTACCACAAAGTTTCACTTC
genomic: TCAGGAGATATCACGGACATATTTTCCAACCTCCCAAGTTTAACCACAGTgtgagtgttt ... attatttcagAGACCTTTCCTCCAATTCTCTTACTGGCAATCTACCACAAAGTTTCACTTC
EST: gi|78116943|gb|DV535330.1|DV535330
EST:     TCAGGAGATATCACGGACATATTTTCCAACCTCCCAAGTTTAACCACAGT                         AGACCTTTCCTCCAATTCTCTTACTGGCAATCTACCACAAAGTTTCACTTC
genomic: TCAGGAGATATCACGGACATATTTTCCAACCTCCCAAGTTTAACCACAGTgtgagtgttt ... attatttcagAGACCTTTCCTCCAATTCTCTTACTGGCAATCTACCACAAAGTTTCACTTC
EST: gi|74241625|gb|DT649539.1|DT649539
EST:     TCAGGAGATATCACGGACATATTTTCCAACCTCCCAAGTTTAACCACAGT                         AGACCTTTCCTCCAATTCTCTTACTGGCAATCTACCACAAAGTTTCACTTC
genomic: TCAGGAGATATCACGGACATATTTTCCAACCTCCCAAGTTTAACCACAGTgtgagtgttt ... attatttcagAGACCTTTCCTCCAATTCTCTTACTGGCAATCTACCACAAAGTTTCACTTC

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), 48 (downstream exon)
Score: 50

AAACCTTAATCATAACCAGCTATCAGGAGATATCACGGACATATTTTCCAACCTCCCAAGTTTAACCACAGTgtgagtgttt ... attatttcagAGACCTTTCCTCCAATTCTCTTACTGGCAATCTACCACAAAGTTTCACTTCTTTGTCAAGCCTGAAAACACT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 18

AAACCTTAATCATAACCAGCTATCAGGAGATATCACGGACATATTTTCCAACCTCCCAAGTTTAACCACAGTgtgagtgttt ... attatttcagAGACCTTTCCTCCAATTCTCTTACTGGCAATCTACCACAAAGTTTCACTTCTTTGTCAAGCCTGAAAACACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 24

AAACCTTAATCATAACCAGCTATCAGGAGATATCACGGACATATTTTCCAACCTCCCAAGTTTAACCACAGTgtgagtgttt ... attatttcagAGACCTTTCCTCCAATTCTCTTACTGGCAATCTACCACAAAGTTTCACTTCTTTGTCAAGCCTGAAAACACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 139

AAACCTTAATCATAACCAGCTATCAGGAGATATCACGGACATATTTTCCAACCTCCCAAGTTTAACCACAGTgtgagtgttt ... attatttcagAGACCTTTCCTCCAATTCTCTTACTGGCAATCTACCACAAAGTTTCACTTCTTTGTCAAGCCTGAAAACACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtggcatgcccatcatatgcttcatctgatttttttggtgaaaaattatttcagAGACCTTTCCTCCAATTCTCTTACTGGCAATCTACCACAAAGTTTCACTTCTTTGTCAAGCCTGAAAACACT
                        atctgat  putative branch site (score: 139)
                                              ttatttc  putative PPT
                             atttttttggtgaaaa  TA-rich tract