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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgactggcaaaaaaaaaaaactccagattattcagttctctctacgcaccaaattcatgatcttggcgagtttaagcgtacctgatctctgcatttcggttgtttcgcagTATCTGAAGAACATACAGATAAAAGAAATCCCCATACTGGAAAGGTTCTCCCTTTTCATCTGTGTCGCGTTGGTATGGGCGTACGCTCAGATCCTCACTT

Basic information

species Zea mays
transcript GRMZM2G437859_T04
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G437859_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g55500.4 (Oryza sativa), 3'ss of exon 6
gtctgactggcaaaaaaaaaaaactccagattattcagttctct--ctacgcaccaaattcatgatcttggcgagtttaagcgtacctgatctctgcatttcggttgtttcgcagTATCTGAAGAACATACAGATAAAAGAAATCCCCATACTGGAAAGGTTCTCCCTTTTCATCTGTGTCGCGTTGGTATGGGCGTACGCTCAGATCCTCACTT
    |  ||||||  ||      ||||| || ||  | |||| |  |||   |||| |||     |   | | |  |   || |     ||              |||||  ||||||||||||||  ||||||||| ||| || || |||||||| ||||||||||| ||||||||  |||||||||| ||||| || ||||| ||||||||| 
----gtttggcaagcaa------ctcca-atgatcgaattcttttgctagtgaccatatttgaagttgagtctaactcgtgcattgtcaatta------------tgtttttcagTATCTGAAGAATGTACAGATAAGAGATATTCCAATACTGGAGAGGTTCTCCCTGTTCATCTGCATCGCGTTGGTTTGGGCCTATGCTCAAATCCTCACTG
















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|74244049|gb|DT651963.1|DT651963
EST:     GCGTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAG                         TATCTGAAGAACATACAGATAAAAGAAATCCCCATACTGGAAAGGTTCTCC
genomic: GCGTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAGgtctgactgg ... tgtttcgcagTATCTGAAGAACATACAGATAAAAGAAATCCCCATACTGGAAAGGTTCTCC
EST: gi|78084450|gb|DV512843.1|DV512843
EST:     GCGTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAG                         TATCTGAAGAACATACAGATAAAAGAAATCCCCATACTGGGAAAGGTTCTC
genomic: GCGTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAGgtctgactgg ... tgtttcgcagTATCTGAAGAACATACAGATAAAAGAAATCCCCATACTGG-AAAGGTTCTC
EST: gi|74238881|gb|DT646795.1|DT646795
EST:     CGTGCTGTCTCAG                         TATCTGAAGAACATACAGATAAAAGAAATCCCCATACTGGAAAGGTTCTCC
genomic: CGTGCTGTCTCAGgtctgactgg ... tgtttcgcagTATCTGAAGAACATACAGATAAAAGAAATCCCCATACTGGAAAGGTTCTCC
EST: gi|76923378|gb|DV169457.1|DV169457
EST:     GCGTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAG                         TATCTGAAGAACATACAGATAAAAGAAATCCCCATACTGGAAAGGTTCTCC
genomic: GCGTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAGgtctgactgg ... tgtttcgcagTATCTGAAGAACATACAGATAAAAGAAATCCCCATACTGGAAAGGTTCTCC
EST: gi|74238882|gb|DT646796.1|DT646796
EST:     GCGTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAG                         TATCTGAAGAACATACAGATAAAAGAAATCCCCATACTGGAAAGGGTTCTC
genomic: GCGTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAGgtctgactgg ... tgtttcgcagTATCTGAAGAACATACAGATAAAAGAAATCCCCATACTGGAAAGG-TTCTC
EST: gi|211379070|gb|FL028411.1|FL028411
EST:     GTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAG                         TATCTGAAGAACATACAGATAAAAGGAATCCCCATACTGGAAAGGTTCTCC
genomic: GTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAGgtctgactgg ... tgtttcgcagTATCTGAAGAACATACAGATAAAAGAAATCCCCATACTGGAAAGGTTCTCC
EST: gi|5055765|gb|AI734652.1|AI734652
EST:     GCGTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAG                         TATCTGAAGAACATACAGATAAAAGAAATCCCCATACTGGAAAGGTTCTCC
genomic: GCGTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAGgtctgactgg ... tgtttcgcagTATCTGAAGAACATACAGATAAAAGAAATCCCCATACTGGAAAGGTTCTCC
EST: gi|71310987|gb|DR791795.1|DR791795
EST:     GCGTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAG                         TATCTGAAGAACATACAGATAAAAGAAATCCCCATACTGGAAAGGTTCTCC
genomic: GCGTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAGgtctgactgg ... tgtttcgcagTATCTGAAGAACATACAGATAAAAGAAATCCCCATACTGGAAAGGTTCTCC
EST: gi|71438783|gb|DR819833.1|DR819833
EST:     GCGTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAG                         TATCTGAAGAACATACAGATAAAAGAAATCCCCATACTGGAAAGGTTCTCC
genomic: GCGTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAGgtctgactgg ... tgtttcgcagTATCTGAAGAACATACAGATAAAAGAAATCCCCATACTGGAAAGGTTCTCC

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: 132

GTTGGGAGATGCGTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAGgtctgactgg ... tgtttcgcagTATCTGAAGAACATACAGATAAAAGAAATCCCCATACTGGAAAGGTTCTCCCTTTTCATCTGTGTCGCGTTGGTATGGGCGTACGCTCAGATCCTCACTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 36

GTTGGGAGATGCGTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAGgtctgactgg ... tgtttcgcagTATCTGAAGAACATACAGATAAAAGAAATCCCCATACTGGAAAGGTTCTCCCTTTTCATCTGTGTCGCGTTGGTATGGGCGTACGCTCAGATCCTCACTT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 11

GTTGGGAGATGCGTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAGgtctgactgg ... tgtttcgcagTATCTGAAGAACATACAGATAAAAGAAATCCCCATACTGGAAAGGTTCTCCCTTTTCATCTGTGTCGCGTTGGTATGGGCGTACGCTCAGATCCTCACTT


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 9

GTTGGGAGATGCGTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAGgtctgactgg ... tgtttcgcagTATCTGAAGAACATACAGATAAAAGAAATCCCCATACTGGAAAGGTTCTCCCTTTTCATCTGTGTCGCGTTGGTATGGGCGTACGCTCAGATCCTCACTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgatcttggcgagtttaagcgtacctgatctctgcatttcggttgtttcgcagTATCTGAAGAACATACAGATAAAAGAAATCCCCATACTGGAAAGGTTCTCCCTTTTCATCTGTGTCGCGTTGGTATGGGCGTACGCTCAGATCCTCACTT
                        acctgat  putative branch site (score: 9)
                                            ttgtttc  putative PPT
             agtttaa  TA-rich tract