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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGGgtatgaatttaattaccaggccagtacatactggccagaaaacggggcatcaggtagactctcgtactgacttatgtgtgtctcag

Basic information

species Zea mays
transcript GRMZM2G143651_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143651_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os02g57180.2 (Oryza sativa), 5'ss of exon 8
GCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGGgtatgaatttaattaccaggccagtacatactggcca--gaaaacggggcatcaggtagactctcgtactgacttatgtgtgtctcag---------
|||||||||||||| |||||||| || ||||||||| | ||  || |||| ||||||||| ||||||||||||||| |||| ||  |          |  ||| ||  | || | | | ||  | | | |||   |  | ||  |  | ||  || |         
GCTGAGCTGATGTATGAGACAATACGTGAATGGCCACGGTACATCGATGTTCCTCTTCCTATTGCAAGGgtatgaacttaaataatatcttg-----tgttggtcaaggcaacctgagtattggattgtctcgtcttttaac--agttatgcttcgggttgtgcag
















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|71533831|gb|DR784590.1|DR784590
EST:     CAATCCGCGAATGGCCAAGATATGTCGATGTCCCTCTTCCTGTTGCAAGG                         GCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
genomic: CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGGgtatgaattt ... tgtgtctcagGCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
EST: gi|30031664|gb|CB833515.1|CB833515
EST:     CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGG                         GCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
genomic: CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGGgtatgaattt ... tgtgtctcagGCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
EST: gi|18164602|gb|BM334441.1|BM334441
EST:     CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGG                         GCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
genomic: CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGGgtatgaattt ... tgtgtctcagGCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
EST: gi|16927071|gb|BM080140.1|BM080140
EST:     TGTCAATGTCCCTTTTCCTGTTGCAAGG                         GCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
genomic: TGTCAATGTCCCTCTTCCTGTTGCAAGGgtatgaattt ... tgtgtctcagGCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
EST: gi|29545100|gb|CB605278.1|CB605278
EST:     CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGG                         GCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
genomic: CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGGgtatgaattt ... tgtgtctcagGCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
EST: gi|211264901|gb|FK979901.1|FK979901
EST:     CAATCCGYGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGG                         GCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
genomic: CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGGgtatgaattt ... tgtgtctcagGCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
EST: gi|60397747|gb|DN230563.1|DN230563
EST:     CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGG                         GCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
genomic: CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGGgtatgaattt ... tgtgtctcagGCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
EST: gi|67015444|gb|CO444193.1|CO444193
EST:     CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGG                         GCTATTGCTTCCCCAAGGGAGATGCTGCTCAATNA-GTGCCGTTCCCGCTT
genomic: CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGGgtatgaattt ... tgtgtctcagGCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
EST: gi|31350209|gb|CD434566.1|CD434566
EST:     CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGG                         GCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
genomic: CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGGgtatgaattt ... tgtgtctcagGCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
EST: gi|211264900|gb|FK979900.1|FK979900
EST:     CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGG                         GCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCCGCT
genomic: CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGGgtatgaattt ... tgtgtctcagGCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCC-GCT
EST: gi|120480121|gb|EH210746.1|EH210746
EST:     CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGG                         GCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
genomic: CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGGgtatgaattt ... tgtgtctcagGCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
EST: gi|30087962|gb|CB886167.1|CB886167
EST:     CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGG                         GCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
genomic: CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGGgtatgaattt ... tgtgtctcagGCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
EST: gi|71445607|gb|DR826657.1|DR826657
EST:     CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGG                         GCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
genomic: CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGGgtatgaattt ... tgtgtctcagGCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
EST: gi|211383681|gb|FL229452.1|FL229452
EST:     CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGG                         GCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
genomic: CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGGgtatgaattt ... tgtgtctcagGCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
EST: gi|31612342|gb|CD568964.1|CD568964
EST:     CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGG                         GCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
genomic: CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGGgtatgaattt ... tgtgtctcagGCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
EST: gi|149069993|gb|EE158393.2|EE158393
EST:     CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGG                         GCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
genomic: CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGGgtatgaattt ... tgtgtctcagGCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
EST: gi|211418862|gb|FL076974.1|FL076974
EST:     CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGG                         GCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
genomic: CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGGgtatgaattt ... tgtgtctcagGCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
EST: gi|31664373|gb|CD573098.1|CD573098
EST:     CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGG                         GCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
genomic: CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGGgtatgaattt ... tgtgtctcagGCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
EST: gi|149064146|gb|EE286442.2|EE286442
EST:     CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGG                         GCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
genomic: CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGGgtatgaattt ... tgtgtctcagGCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
EST: gi|31998441|gb|CD662076.1|CD662076
EST:     CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGG                         GCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
genomic: CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGGgtatgaattt ... tgtgtctcagGCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
EST: gi|4886142|gb|AI677262.1|AI677262
EST:     CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGG                         GCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT
genomic: CAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGGgtatgaattt ... tgtgtctcagGCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTT

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: 326

GCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGGgtatgaattt ... tgtgtctcagGCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTTCCAACACCATCCATTTTCAACCTAGACCAAATCAACGCATTTGCTGTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 347

GCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGGgtatgaattt ... tgtgtctcagGCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTTCCAACACCATCCATTTTCAACCTAGACCAAATCAACGCATTTGCTGTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 382

GCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGGgtatgaattt ... tgtgtctcagGCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTTCCAACACCATCCATTTTCAACCTAGACCAAATCAACGCATTTGCTGTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 403

GCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGGgtatgaattt ... tgtgtctcagGCTATTGCTTCCCCAAGGGAGATGCTGCTCAATAAAGTGCCGTTCCCGCTTCCAACACCATCCATTTTCAACCTAGACCAAATCAACGCATTTGCTGTGG