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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgtgctgagaaatatgtcttacatttttttatatttatctcacctatttcctggctaatatgatttttgcatagcaattgcatgtctgtgatggagcatgttcattgaaacttgtatggttgtagtgattttgtcaatctgccttaccgttacaaatttatcacagGAAGATACAAGAGAATTTGTTGGAGAGTTGAATATCACACTGGTCAAAGGCACCAACTTGGCCGTTAGAGACATGCTAACAAGTGATCCATATGTTGTTT

Basic information

species Zea mays
transcript GRMZM2G161728_T04
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G161728_T04 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g49070.1 (Oryza sativa), 3'ss of exon 6
gtaagttgt---gctgagaaatatgtcttacatttttttatatttatctcacctatttcctggctaatatgatttttgcatagcaattgcatgtctgtgatggagcatgttcattgaaacttgtatggttgtagtgattttgtcaatctgccttaccgttacaaatttatcacagGAAGATACAAGAGAATTTGTTGGAGAGTTGAATATCACACTGGTCAAAGGCACCAACTTGGCCGTTAGAGACATGCTAACAAGTGATCCATATGTTGTTT
||||| |||   ||||| | |||| |  ||||  | |  | |||| ||| |||  |||  |      | ||  ||     |||| |||| |        ||||||||| || | |||   ||| ||| || |||||||   | ||||| |||||| | || |||||   |||||||| |||||||||||||||||||||||| |||| || ||| |||| | ||| |   | |||||||| |||||||||||||| || ||||||||||||||| 
gtaagctgttctgctgaaacatatatgatacagctgtgaagatttgtctaaccattttatt------tgtgggttcaagttagccattgaa--------atggagcatatttaatgattgttgcatgattttagtgatccagacaatcagccttaaccttgcaaatg-gtcacagGACGATACAAGAGAATTTGTTGGAGAGCTGAACATTACAGTGGTAAGAGGTATTCAGTTGGCCGTCAGAGACATGCTAACGAGCGATCCATATGTTGTTC
















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|74234877|gb|DT642791.1|DT642791
EST:     TGAAGAGTGTAGATAGCAATTTCTCTAGCACTTCAAGGAAGGATGTCTTT                         GAAGATACAAGAGAATTTGTTGGAGAGTTGAATATCACACTGGTCAAAGGC
genomic: TGAAGAGTGTAGATAGCAATTTCTCTAGCACTTCAAGGAAGGATGTCTTTgtaagttgtg ... tttatcacagGAAGATACAAGAGAATTTGTTGGAGAGTTGAATATCACACTGGTCAAAGGC
EST: gi|148970443|gb|EE021294.2|EE021294
EST:     TGAAGAGTGTAGATAGCAATTTCTCTAGCACTTCAAGGAAGGATGTCTTT                         GAAGATACAAGAGAATTTGTTGGAGAGTTGAATATCACACTGGTCAAAGGC
genomic: TGAAGAGTGTAGATAGCAATTTCTCTAGCACTTCAAGGAAGGATGTCTTTgtaagttgtg ... tttatcacagGAAGATACAAGAGAATTTGTTGGAGAGTTGAATATCACACTGGTCAAAGGC
EST: gi|148982152|gb|EE028182.2|EE028182
EST:     TGAAGAGTGTAGATAGCAATTTCTCTAGCACTTCAAGGAAGGATGTCTTT                         GAAGATACAAGAGAATTTGTTGGAGAGTTGAATATCACACTGGTCAAAGGC
genomic: TGAAGAGTGTAGATAGCAATTTCTCTAGCACTTCAAGGAAGGATGTCTTTgtaagttgtg ... tttatcacagGAAGATACAAGAGAATTTGTTGGAGAGTTGAATATCACACTGGTCAAAGGC
EST: gi|78079893|gb|DV508305.1|DV508305
EST:     TGAAGAGTGTAGATAGCAATTTCTCTAGCACTTCAAGGAAGGATGTCTTT                         GAAGATACAAGAGAATTTGTTGGAGAGTTGAATATCACACTGGTCAAAGGC
genomic: TGAAGAGTGTAGATAGCAATTTCTCTAGCACTTCAAGGAAGGATGTCTTTgtaagttgtg ... tttatcacagGAAGATACAAGAGAATTTGTTGGAGAGTTGAATATCACACTGGTCAAAGGC
EST: gi|76287384|gb|DV026952.1|DV026952
EST:     TGAAGAGTGTAGATAGCAATTTCTCTAGCACTTCAAGGAAGGATGTCTTT                         GAAGATACAAGAGAATTTGTTGGAGAGTTGAATATCACACTGGTCAAAGGC
genomic: TGAAGAGTGTAGATAGCAATTTCTCTAGCACTTCAAGGAAGGATGTCTTTgtaagttgtg ... tttatcacagGAAGATACAAGAGAATTTGTTGGAGAGTTGAATATCACACTGGTCAAAGGC

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: 48 (upstream exon), 49 (downstream exon)
Score: 179

GCCAAGTTTGCGCATTTCATCAAGATCATCTTTTAAATCTACCACTTCTGTGAAGAGTGTAGATAGCAATTTCTCTAGCACTTCAAGGAAGGATGTCTTTgtaagttgtg ... tttatcacagGAAGATACAAGAGAATTTGTTGGAGAGTTGAATATCACACTGGTCAAAGGCACCAACTTGGCCGTTAGAGACATGCTAACAAGTGATCCATATGTTGTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 342

GCCAAGTTTGCGCATTTCATCAAGATCATCTTTTAAATCTACCACTTCTGTGAAGAGTGTAGATAGCAATTTCTCTAGCACTTCAAGGAAGGATGTCTTTgtaagttgtg ... tttatcacagGAAGATACAAGAGAATTTGTTGGAGAGTTGAATATCACACTGGTCAAAGGCACCAACTTGGCCGTTAGAGACATGCTAACAAGTGATCCATATGTTGTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 303

GCCAAGTTTGCGCATTTCATCAAGATCATCTTTTAAATCTACCACTTCTGTGAAGAGTGTAGATAGCAATTTCTCTAGCACTTCAAGGAAGGATGTCTTTgtaagttgtg ... tttatcacagGAAGATACAAGAGAATTTGTTGGAGAGTTGAATATCACACTGGTCAAAGGCACCAACTTGGCCGTTAGAGACATGCTAACAAGTGATCCATATGTTGTTT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 209

GCCAAGTTTGCGCATTTCATCAAGATCATCTTTTAAATCTACCACTTCTGTGAAGAGTGTAGATAGCAATTTCTCTAGCACTTCAAGGAAGGATGTCTTTgtaagttgtg ... tttatcacagGAAGATACAAGAGAATTTGTTGGAGAGTTGAATATCACACTGGTCAAAGGCACCAACTTGGCCGTTAGAGACATGCTAACAAGTGATCCATATGTTGTTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtatggttgtagtgattttgtcaatctgccttaccgttacaaatttatcacagGAAGATACAAGAGAATTTGTTGGAGAGTTGAATATCACACTGGTCAAAGGCACCAACTTGGCCGTTAGAGACATGCTAACAAGTGATCCATATGTTGTTT
                             gccttac  putative branch site (score: 209)
                                      ttacaaatttatca  TA-rich tract