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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTACATGTATGGATTTTTTAAGAATAAACGCATAGTACTCTATGACACATTGATTCAGCAGgttcaatccttcaaacattttgtttcataaaaattggcatgcacagaattgacctgttttcttttgttgatttcag

Basic information

species Zea mays
transcript GRMZM2G702159_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G702159_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os02g45650.1 (Oryza sativa), 5'ss of exon 9
GCTTACATGTATGGATTTTTTAAGAATAAACGCATAGTACTCTATGACACATTGATTCAGCAGgttcaatccttcaaacattttgtttcataaaaattg------gcatgcacagaattgacctgttttcttttgttgatttcag
|||||||||||||| ||||| ||||| || ||||| || ||||||||||| |||||||||||||||  || ||  |    ||| ||||||| | ||||        ||||||   || | |||||  | ||||||| | ||||||
GCTTACATGTATGGGTTTTTCAAGAACAAGCGCATTGTTCTCTATGACACGTTGATTCAGCAGgttatatgcta-agttgtttagtttcattataattttgaattacatgcatgaaactcacctggatccttttgtcggtttcag

upper sequence: GRMZM2G702159_T01 (Zea mays), 5'ss of exon 9
lower sequence: AT4G01320.1 (Arabidopsis thaliana), 5'ss of exon 9
GCTTACATGTATGGATTTTTTAAGAATAAACGCATAGTACTCTATGACACATTGATTCAGCAGgt----------tcaatccttcaaacattttgt-ttcataaaaat-tggcatgcacagaattgacctgttttcttttgttgatttcag
|||||||||||||| || |||||||| ||| | || || || ||||| || ||||||||||||||          |  || ||||||||    | |  ||| |    | |  |  |  | |||        |  |||| | |||  | |||
GCTTACATGTATGGTTTCTTTAAGAACAAAAGGATTGTTCTTTATGATACGTTGATTCAGCAGgtactgtgactcttgatgcttcaaacgagctatactcacatttctgtttctggttctgaaacataacataatcttctattg--tgcag

upper sequence: GRMZM2G702159_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv15s0046g02040.t01 (Vitis vinifera), 5'ss of exon 9
GCTTACATGTATGGATTTTTTAAGAATAAACGCATAGTACTCTATGACACATTGATTCAGCAGgt----------tcaatccttcaaacattttgtttcataaaaattggcatgcacagaattgacctgttttcttttgttgatttcag---------------
|| || ||||||||||| ||||| || || || ||||| ||||||||||||||||||||||||||          |  ||  ||   | ||||| ||| |      |    || || |   || |    |||| | | ||| ||||                  
GCCTATATGTATGGATTCTTTAACAACAAGCGGATAGTCCTCTATGACACATTGATTCAGCAGgtgtggaggcattttattatttggaaattttatttaagctttttctaaatacatattctttaggc-ttttatatagttaatttttttttcttgccattatt

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|28188098|gb|CB179708.1|CB179708
EST:     GATTTTTTAAGAATAAACGCATAGTACTCTATGACACATTGATTCAGCAG                         TGTACCAATGAGGATGAGATAGTTTCTGTTATTGCACGTGAACTTGGGCAC
genomic: GATTTTTTAAGAATAAACGCATAGTACTCTATGACACATTGATTCAGCAGgttcaatcct ... ttgatttcagTGTACCAATGAGGATGAGATAGTTTCTGTTATTGCACATGAACTTGGGCAC
EST: gi|33285753|gb|CF075548.1|CF075548
EST:     GATTTTTTAAGAATAAACGCATAGTACTCTATGACACATTGATTCAGCAG                         TGTACCAATGAGGATGAGATAGTTTCTGTTATTGCACATGAACTTGGGCAC
genomic: GATTTTTTAAGAATAAACGCATAGTACTCTATGACACATTGATTCAGCAGgttcaatcct ... ttgatttcagTGTACCAATGAGGATGAGATAGTTTCTGTTATTGCACATGAACTTGGGCAC
EST: gi|28188199|gb|CB179809.1|CB179809
EST:     GATTTTTTAAGAATAAACGCATAGTACTCTATGACACATTGATTCAGCAG                         TGTACCAATGAGGATGAGATAGTTTCTGTTATTGCACATGAACTTGGGCAC
genomic: GATTTTTTAAGAATAAACGCATAGTACTCTATGACACATTGATTCAGCAGgttcaatcct ... ttgatttcagTGTACCAATGAGGATGAGATAGTTTCTGTTATTGCACATGAACTTGGGCAC
EST: gi|33770597|gb|CF272891.1|CF272891
EST:     GATTTTTTAAGAATAAACGCATAGTACTCTATGACACATTGATTCAGCAG                         TGTACCAATGAGGATGAGATAGTTTCTGTTATTGCACATGAACTTGGGCAC
genomic: GATTTTTTAAGAATAAACGCATAGTACTCTATGACACATTGATTCAGCAGgttcaatcct ... ttgatttcagTGTACCAATGAGGATGAGATAGTTTCTGTTATTGCACATGAACTTGGGCAC

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 3 RNA-Seq libraries.


Block sizes: 46 (upstream exon), 38 (downstream exon)
Score: 6

GCTTACATGTATGGATTTTTTAAGAATAAACGCATAGTACTCTATGACACATTGATTCAGCAGgttcaatcct ... ttgatttcagTGTACCAATGAGGATGAGATAGTTTCTGTTATTGCACATGAACTTGGGCACTGGAAACTCAATCATATTGTCTATTCCTTTGTAGCTGTCCAG


Block sizes: 46 (upstream exon), 26 (downstream exon)
Score: 3

GCTTACATGTATGGATTTTTTAAGAATAAACGCATAGTACTCTATGACACATTGATTCAGCAGgttcaatcct ... ttgatttcagTGTACCAATGAGGATGAGATAGTTTCTGTTATTGCACATGAACTTGGGCACTGGAAACTCAATCATATTGTCTATTCCTTTGTAGCTGTCCAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 19

GCTTACATGTATGGATTTTTTAAGAATAAACGCATAGTACTCTATGACACATTGATTCAGCAGgttcaatcct ... ttgatttcagTGTACCAATGAGGATGAGATAGTTTCTGTTATTGCACATGAACTTGGGCACTGGAAACTCAATCATATTGTCTATTCCTTTGTAGCTGTCCAG