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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGACACCTAATATGGTTGCTTGCATTGCTGTAGAGGCAATTTCTATACTTGAGAAACTTCATGCAAAAGGgtaactagtatatttactgagtttatttgccatactgtatctcccgattatttatttattggtaattttctgtcag

Basic information

species Zea mays
transcript GRMZM2G116086_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116086_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os01g56580.2 (Oryza sativa), 5'ss of exon 7
GATGACACCTAATATGGTTGCTTGCATTGCTGTAGAGGCAATTTCTATACTTGAGAAACTTCATGCAAAAGGgtaactagtatatttactgagtttatttgccatactgtatctcccgattatttatttattggt--aattttctgtcag
|||||| || | ||||||||||||||| |||||||||||||||||||| |||||||||||||||||||| ||||||  ||    |||      | |||| |||   ||| || || |  ||  |  ||||||  |  ||  || |  |||
GATGACCCCAAGTATGGTTGCTTGCATCGCTGTAGAGGCAATTTCTATCCTTGAGAAACTTCATGCAAAGGGgtaagcaggccttttgaattttctattagcct--ctggatttcactgttcatgttttatttttggaacattttaccag

upper sequence: GRMZM2G116086_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA16G04580.1 (Glycine max), 5'ss of exon 7
GATGACACCTAATATGGTTGCTTGCATTGCTGTAGAGGCAATTTCTATACTTGAGAAACTTCATGCAAAAGGgtaa-ctagtatatttactgagtttatt-tgccatactgtatc--tcccgattattt----at-----ttattggtaattttctgtcag-----------------------
 ||| |||| ||||||||||| |||||||| ||||||||||| || || |||||||| || ||    ||||||||| |   | |  |   |   |  ||  || ||  || || |  | ||  ||||||    ||     | | ||   | ||| | | |                        
AATGTCACCAAATATGGTTGCGTGCATTGCAGTAGAGGCAATATCAATTCTTGAGAAGCTCCACTTGAAAGGgtaaacccttgtgatagttttttcaatcctgtcaacctttaacattaccatttattttggcatggttgtgactgactaatttttattaatgaaactcgtatcattgaattag

upper sequence: GRMZM2G116086_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 5'ss of exon 7
GATGACACCTAATATGGTTGCTTGCATTGCTGTAGAGGCAATTTCTATACTTGAGAAACTTCATGCAAAAGGgtaactagtat----atttactgagtttatttgc-------catactgtatctcccgattatttatttattggtaattt------tctgtcag-------------------------------
|||| |||| |||||||| ||||||||||| ||||||||||| || || || ||||| |||||    || |||| | || |||    | || |    || | || |       ||| |||| ||||  ||  | ||   |    ||   ||      ||||| |                                
GATGTCACCAAATATGGTGGCTTGCATTGCAGTAGAGGCAATATCAATTCTCGAGAAGCTTCACATGAAGGGgtgagtactattaataattccatgtttcactttctcagaatcatcctgtctctcttgagcactttcctcaaagtggcttcttcattctgttaattattgtcatcttttttcttcctcaaccaag

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|22935976|gb|BU572251.1|BU572251
EST:     TGCATTGCTGTAGAGGCAATTTCTATACTTGAGAAACTTCATGCAAAAGG                         GTTTGTTCATGGAGACGTTAAACCCGAGAATTTTCTACTCGGCCAGCCTGG
genomic: TGCATTGCTGTAGAGGCAATTTCTATACTTGAGAAACTTCATGCAAAAGGgtaactagta ... tttctgtcagGTTTGTTCATGGAGACGTTAAACCCGAGAATTTTCTACTTGGCCAGCCTGG
EST: gi|67028330|gb|CO457079.1|CO457079
EST:     TGCATTGCTGTAGAGGCAATTTCTATACTTGAGAAACTTCATGCAAAAGG                         GTTTGTTCATGGAGACGTTAAACCCGAGAATTTTCTACTTGGCCAGCCTGG
genomic: TGCATTGCTGTAGAGGCAATTTCTATACTTGAGAAACTTCATGCAAAAGGgtaactagta ... tttctgtcagGTTTGTTCATGGAGACGTTAAACCCGAGAATTTTCTACTTGGCCAGCCTGG
EST: gi|87155883|gb|DY400672.1|DY400672
EST:     TGCATTGCTGTAGAGGCAATTTCTATACTTGAGAAACTTCATGCAAAAGG                         GTTTGTTCATGGAGACGTTAAACCCGAGAATTTTCTACTTGGCCAGCCTGG
genomic: TGCATTGCTGTAGAGGCAATTTCTATACTTGAGAAACTTCATGCAAAAGGgtaactagta ... tttctgtcagGTTTGTTCATGGAGACGTTAAACCCGAGAATTTTCTACTTGGCCAGCCTGG
EST: gi|26559656|gb|CA831891.1|CA831891
EST:     TGCATTGCTGTAGAGGCAATTTCTATACTTGAGAAACTTCATGCAAAAGG                         GTTTGTTCATGGAGACGTTAAACCCGAGAATTTTCTACTTGGCCAGCCTGG
genomic: TGCATTGCTGTAGAGGCAATTTCTATACTTGAGAAACTTCATGCAAAAGGgtaactagta ... tttctgtcagGTTTGTTCATGGAGACGTTAAACCCGAGAATTTTCTACTTGGCCAGCCTGG

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), 48 (downstream exon)
Score: 329

GATGACACCTAATATGGTTGCTTGCATTGCTGTAGAGGCAATTTCTATACTTGAGAAACTTCATGCAAAAGGgtaactagta ... tttctgtcagGTTTGTTCATGGAGACGTTAAACCCGAGAATTTTCTACTTGGCCAGCCTGGATCCCCTGACGAGAAAAAACTTTTTCTGATTGATCTTGGGTTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 150

GATGACACCTAATATGGTTGCTTGCATTGCTGTAGAGGCAATTTCTATACTTGAGAAACTTCATGCAAAAGGgtaactagta ... tttctgtcagGTTTGTTCATGGAGACGTTAAACCCGAGAATTTTCTACTTGGCCAGCCTGGATCCCCTGACGAGAAAAAACTTTTTCTGATTGATCTTGGGTTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 174

GATGACACCTAATATGGTTGCTTGCATTGCTGTAGAGGCAATTTCTATACTTGAGAAACTTCATGCAAAAGGgtaactagta ... tttctgtcagGTTTGTTCATGGAGACGTTAAACCCGAGAATTTTCTACTTGGCCAGCCTGGATCCCCTGACGAGAAAAAACTTTTTCTGATTGATCTTGGGTTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 395

GATGACACCTAATATGGTTGCTTGCATTGCTGTAGAGGCAATTTCTATACTTGAGAAACTTCATGCAAAAGGgtaactagta ... tttctgtcagGTTTGTTCATGGAGACGTTAAACCCGAGAATTTTCTACTTGGCCAGCCTGGATCCCCTGACGAGAAAAAACTTTTTCTGATTGATCTTGGGTTAG