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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGCTCTGGTCCCTGGCAATTTTGTTTACGAAACTCAGTGTGAGAGATGTTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCGgtgagcttctaatgccagctttcatattcatgaaatgatgaccatatgttgatttgccttttctttttgttcattccgcaaacgcttcacagttccattg...

Basic information

species Zea mays
transcript GRMZM2G453794_T01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G453794_T01 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os03g02756.1 (Oryza sativa), 5'ss of exon 16
-GCTGCTCTGGTCCCTGGCAATTTTGTTTACGAAACTCAGTGTGAGAGATGTTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCGgtgagcttctaatgccagctttcatattcat----gaaatgatgac-catatgttgatttgccttttctttttgttcattccgcaaacgcttcacagttccattg
 || |   ||||   ||||| || ||||||| |  || ||||| | |||||| |||||| ||||  ||||||||||||||||||| |||||| |  |||||||||| ||||| |   | | |  || | |||    || | ||||   || | ||  | |    |||     ||||||  | || |   | |     ||| ||   
GGCGGGCTTGGTTG-TGGCAGTTGTGTTTACAAGCCTTAGTGTCAAAGATGTGTTTGCTGCCATCTTAGCATTTGTGCCAACTGGCTGGGGAGTTCTTTCGgtgagtttcta-tagaaacatcaatgtccatctgagacaggatggtgcaaaagtgaactcagttttgaaaattgttc-ctgcgtagcagataatatgtttca---
















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|9732693|gb|BE511445.1|BE511445
EST:     TTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGTAATCATTTCG                         ATTGCCATGGCATGGCAAACCTGTCGTGCAAGAAATTGGGTTTGTGGAAAA
genomic: TTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGG-AATCATTTCGgtgagcttct ... ttttccacagATTGCCATGGCATGG-AAACCTGTCGTG-AAGAAATTGGGTTTGTGGAAAA
EST: gi|211198729|gb|FL476496.1|FL476496
EST:     TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCG                         ATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
genomic: TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCGgtgagcttct ... ttttccacagATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
EST: gi|32838544|gb|CD978222.1|CD978222
EST:     TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCG                         ATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
genomic: TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCGgtgagcttct ... ttttccacagATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
EST: gi|87155610|gb|DY400399.1|DY400399
EST:     TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCG                         ATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
genomic: TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCGgtgagcttct ... ttttccacagATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
EST: gi|22545826|gb|BU098200.1|BU098200
EST:     TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCG                         ATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
genomic: TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCGgtgagcttct ... ttttccacagATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
EST: gi|166604328|gb|EG119302.1|EG119302
EST:     TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCG                         ATTGCCATGGCATGGAAACC
genomic: TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCGgtgagcttct ... ttttccacagATTGCCATGGCATGGAAACC
EST: gi|67012517|gb|CO441266.1|CO441266
EST:     TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCG                         ATTGCCATGGCATGGAAACCTTTCGTGAAGAAATTGGGTTTGTGGAAAACT
genomic: TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCGgtgagcttct ... ttttccacagATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
EST: gi|32837612|gb|CD977290.1|CD977290
EST:     TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCG                         ATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
genomic: TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCGgtgagcttct ... ttttccacagATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
EST: gi|50322940|gb|CO518066.1|CO518066
EST:     TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCG                         ATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
genomic: TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCGgtgagcttct ... ttttccacagATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
EST: gi|166469222|gb|EG140445.1|EG140445
EST:     TTTTGCTTCCATTTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCG                         ATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAA-CT
genomic: TTTTGCTTCCA-TTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCGgtgagcttct ... ttttccacagATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
EST: gi|84980995|gb|DW531344.1|DW531344
EST:     TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCG                         ATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
genomic: TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCGgtgagcttct ... ttttccacagATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
EST: gi|60397477|gb|DN230293.1|DN230293
EST:     TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCG                         ATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
genomic: TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCGgtgagcttct ... ttttccacagATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
EST: gi|45568321|gb|CK986009.1|CK986009
EST:     TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCG                         ATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
genomic: TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCGgtgagcttct ... ttttccacagATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
EST: gi|67015741|gb|CO444490.1|CO444490
EST:     TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCG                         ATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
genomic: TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCGgtgagcttct ... ttttccacagATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
EST: gi|211408841|gb|FL082351.1|FL082351
EST:     TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCG                         ATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
genomic: TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCGgtgagcttct ... ttttccacagATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
EST: gi|211406286|gb|FL082346.1|FL082346
EST:     TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCG                         ATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
genomic: TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCGgtgagcttct ... ttttccacagATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
EST: gi|32796874|gb|CD949110.1|CD949110
EST:     TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCG                         ATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
genomic: TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCGgtgagcttct ... ttttccacagATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
EST: gi|5847010|gb|AW000089.1|AW000089
EST:     TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCG                         ATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
genomic: TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCGgtgagcttct ... ttttccacagATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
EST: gi|166583047|gb|EG072176.1|EG072176
EST:     GGGGTAATCATTTCG                         ATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
genomic: GGGG-AATCATTTCGgtgagcttct ... ttttccacagATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
EST: gi|78120961|gb|DV539345.1|DV539345
EST:     TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCG                         ATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
genomic: TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCGgtgagcttct ... ttttccacagATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
EST: gi|78022641|gb|DV491028.1|DV491028
EST:     GGGAATCATTTCG                         ATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
genomic: GGGAATCATTTCGgtgagcttct ... ttttccacagATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
EST: gi|6194536|gb|AW146640.1|AW146640
EST:     TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCG                         ATCGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
genomic: TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCGgtgagcttct ... ttttccacagATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
EST: gi|6526773|gb|AW216052.1|AW216052
EST:     CCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCG                         ATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
genomic: CCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCGgtgagcttct ... ttttccacagATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
EST: gi|67040750|gb|CO467005.1|CO467005
EST:     TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCG                         ATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGNGTTTGTGGAAAACT
genomic: TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCGgtgagcttct ... ttttccacagATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
EST: gi|60357590|gb|DN224563.1|DN224563
EST:     TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCG                         ATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
genomic: TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCGgtgagcttct ... ttttccacagATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACT
EST: gi|26558188|gb|CA830423.1|CA830423
EST:     TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCG                         ATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAA
genomic: TTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCGgtgagcttct ... ttttccacagATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAA

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), 49 (downstream exon)
Score: 560

GCTGCTCTGGTCCCTGGCAATTTTGTTTACGAAACTCAGTGTGAGAGATGTTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCGgtgagcttct ... ttttccacagATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACTGTTCGTGCCCTAGCTCGCCTCTATGATGCTGGAATGGGGATGGTCATTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 229

GCTGCTCTGGTCCCTGGCAATTTTGTTTACGAAACTCAGTGTGAGAGATGTTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCGgtgagcttct ... ttttccacagATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACTGTTCGTGCCCTAGCTCGCCTCTATGATGCTGGAATGGGGATGGTCATTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 387

GCTGCTCTGGTCCCTGGCAATTTTGTTTACGAAACTCAGTGTGAGAGATGTTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCGgtgagcttct ... ttttccacagATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACTGTTCGTGCCCTAGCTCGCCTCTATGATGCTGGAATGGGGATGGTCATTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 361

GCTGCTCTGGTCCCTGGCAATTTTGTTTACGAAACTCAGTGTGAGAGATGTTTTTGCTTCCATTCTAGCATTTGTGCCAACTGGGTGGGGAATCATTTCGgtgagcttct ... ttttccacagATTGCCATGGCATGGAAACCTGTCGTGAAGAAATTGGGTTTGTGGAAAACTGTTCGTGCCCTAGCTCGCCTCTATGATGCTGGAATGGGGATGGTCATTT