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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaagattttaacaatggttatgttatttaatagttgtcctgtatgtattaatatcgctgttttgatatgatgtgctgcagATTGGCCCTTTCCAAACCTCCAAAGGAGAGAAGGCCAAACTGAAAGTGAAAGTGCGTCTCAACATCCATGGGACCGTTACAGTTGATTCAGCAATA

Basic information

species Zea mays
transcript GRMZM2G023232_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023232_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g08840.1 (Oryza sativa), 3'ss of exon 2
gtaagcaagattttaa--------caatggttatgttatttaatagttgt----cctgtatgtattaata-tcgctgttttgatatgatgtg---------ctgcagATTGGCCCTTTCCAAACCTCCAAAGGAGAGAAGGCCAAACTGAAAGTGAAAGTGCGTCTCAACATCCATGGGACCGTTACAGTTGATTCAGCAATA
|||||||| |||  ||        || |  | |       |  || ||||    | |   ||  | || | | |||| |||| |||| ||||          |||||||||||||||||||| ||  ||||   |||||||| ||| |||| |||||||   ||||||||||||||||||  ||  |  |||| |||||||| 
gtaagcaacattgcaaactttcgccagtattcaaacctgatgttatttgtggttcttaactggttcaacagttgctgatttgctatgctgtgattgaccgtatgcagATTGGCCCTTTCCAATCCAGCAAACCTGAGAAGGCAAAAGTGAATGTGAAAGCATGTCTCAACATCCATGGGATAGTCTCTATTGAATCAGCAATG
















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|32931686|gb|CF036498.1|CF036498
EST:     ATGTCGACCCAAACGGCTTACAAATTCCACAAAAAATAAGCACATACACA                         ATTGGCCCTTTCCAAACCTCCAAAGGAGAGAAGGCCAAACTGAAAGTGAAA
genomic: ATGTCGACCCAAACGGCTTACAAATTCCACAAAAAATAAGCACATACACAgtaagcaaga ... tgtgctgcagATTGGCCCTTTCCAAACCTCCAAAGGAGAGAAGGCCAAACTGAAAGTGAAA
EST: gi|89251181|gb|DY622967.1|DY622967
EST:     GGCTTACAAATTCCACAAAAAATAAGCACATACACA                         ATTGGCCCTTTCCAAACCTCCAAAGGAGAGAAGGCCAAACTGAAAGTGAAA
genomic: GGCTTACAAATTCCACAAAAAATAAGCACATACACAgtaagcaaga ... tgtgctgcagATTGGCCCTTTCCAAACCTCCAAAGGAGAGAAGGCCAAACTGAAAGTGAAA
EST: gi|211491249|gb|FK959664.1|FK959664
EST:     ATGTCGACCCAAACGGCTTACAAATTCCACAAAAAATAAGCACATACACA                         ATTGGCCCTTTCCAAACCTCCAAAGGAGAGAAGGCCAAACTG
genomic: ATGTCGACCCAAACGGCTTACAAATTCCACAAAAAATAAGCACATACACAgtaagcaaga ... tgtgctgcagATTGGCCCTTTCCAAACCTCCAAAGGAGAGAAGGCCAAACTG
EST: gi|32945492|gb|CF050311.1|CF050311
EST:     ATGTCGACCCAAACGGCCTACAAATTCCACAAAAAATAAGCACATACACA                         ATTGGCCCTTTCCAAACCTCCAAAGGAGAGAAGGCCAAACTGAAAGTGAAA
genomic: ATGTCGACCCAAACGGCTTACAAATTCCACAAAAAATAAGCACATACACAgtaagcaaga ... tgtgctgcagATTGGCCCTTTCCAAACCTCCAAAGGAGAGAAGGCCAAACTGAAAGTGAAA
EST: gi|211491250|gb|FK959665.1|FK959665
EST:     ATGTCGACCCAAACGGCTTACAAATTCCACAAAAAATAAGCACATACACA                         ATTGGCCCTTTCCAAACCTCCAAAGGAGAGAAGGC
genomic: ATGTCGACCCAAACGGCTTACAAATTCCACAAAAAATAAGCACATACACAgtaagcaaga ... tgtgctgcagATTGGCCCTTTCCAAACCTCCAAAGGAGAGAAGGC
EST: gi|67021901|gb|CO450650.1|CO450650
EST:     CAAAAAATAAGCACATACACA                         ATTGGCCCTTTCCAAACCTCCAAAGGAGAGAAGGCCAAACTGAAAGTGAAA
genomic: CAAAAAATAAGCACATACACAgtaagcaaga ... tgtgctgcagATTGGCCCTTTCCAAACCTCCAAAGGAGAGAAGGCCAAACTGAAAGTGAAA
EST: gi|67016035|gb|CO444784.1|CO444784
EST:     ATGTCGACCCAAACGGCTTACAAATTCCACAAAAAATAAGCACATACACA                         ATTGGCCCTTTCCAAACCTCCAAAGGAGAGAAGGCCAAACTGAAAGTGAAA
genomic: ATGTCGACCCAAACGGCTTACAAATTCCACAAAAAATAAGCACATACACAgtaagcaaga ... tgtgctgcagATTGGCCCTTTCCAAACCTCCAAAGGAGAGAAGGCCAAACTGAAAGTGAAA
EST: gi|67025370|gb|CO454119.1|CO454119
EST:     ATGTCGACCCAAACGGCTTACAAATTCCACAAAAAATAAGCACATACACA                         ATTGGCCCTTTCCAAACCTCCAAAGGAGAGAAGGCCAAACTGAAAGTGAAA
genomic: ATGTCGACCCAAACGGCTTACAAATTCCACAAAAAATAAGCACATACACAgtaagcaaga ... tgtgctgcagATTGGCCCTTTCCAAACCTCCAAAGGAGAGAAGGCCAAACTGAAAGTGAAA
EST: gi|18175444|gb|BM350773.1|BM350773
EST:     ATGTCGACCCAAACGGCTTACAAATTCCACAAAAAATAAGCACATACACA                         ATTGGCCCTTTCCAAACCTCCAAAGGAGAGAAGGCCAAACTGAAAGTGAAA
genomic: ATGTCGACCCAAACGGCTTACAAATTCCACAAAAAATAAGCACATACACAgtaagcaaga ... tgtgctgcagATTGGCCCTTTCCAAACCTCCAAAGGAGAGAAGGCCAAACTGAAAGTGAAA
EST: gi|18163486|gb|BM333325.1|BM333325
EST:     ATGTCGACCCAAACGGCTTACAAATTCCACAAAAAATAAGCACATACACA                         ATTGGCCCTTTCCAAACCTCCAAAGGAGAGAAGGCCAAACTGAAAGTGAAA
genomic: ATGTCGACCCAAACGGCTTACAAATTCCACAAAAAATAAGCACATACACAgtaagcaaga ... tgtgctgcagATTGGCCCTTTCCAAACCTCCAAAGGAGAGAAGGCCAAACTGAAAGTGAAA
EST: gi|211494120|gb|FK959666.1|FK959666
EST:     ATGTCGACCCAAACGGCTTACAAATTCCACAAAAAATAAGCACATACACA                         ATTGGNCCCTTTCCAAACCTCCAAAGGAGAGAAGGCCAAACTGAAAGTGAA
genomic: ATGTCGACCCAAACGGCTTACAAATTCCACAAAAAATAAGCACATACACAgtaagcaaga ... tgtgctgcagATTGG-CCCTTTCCAAACCTCCAAAGGAGAGAAGGCCAAACTGAAAGTGAA
EST: gi|211491247|gb|FK959662.1|FK959662
EST:     ATGTCGACCCAAACGGCTTACAAATTCCACAAAAAATAAGCACATACACA                         ATTGGNCCTTTCCAAACCTCCAAAGGAGAGAAGGCCAAACTGGAAAGTGAA
genomic: ATGTCGACCCAAACGGCTTACAAATTCCACAAAAAATAAGCACATACACAgtaagcaaga ... tgtgctgcagATTGGCCCTTTCCAAACCTCCAAAGGAGAGAAGGCCAAACTG-AAAGTGAA
EST: gi|22520708|gb|BU079519.1|BU079519
EST:     ATGTCGACCCAAACGGCTTACAAATTCCACAAAAAATAAGCACATACACA                         ATTGGCCCTTTCCAAACCTCCAAAGGAGAGAAGGCCAAACTGAAAGTGAAA
genomic: ATGTCGACCCAAACGGCTTACAAATTCCACAAAAAATAAGCACATACACAgtaagcaaga ... tgtgctgcagATTGGCCCTTTCCAAACCTCCAAAGGAGAGAAGGCCAAACTGAAAGTGAAA
EST: gi|78106114|gb|DV524532.1|DV524532
EST:     ATGTCGACCCAAACGGCTTACAAATTCCACAAAAAATAAGCACATACACA                         ATTGGCCCTTTCCAAACCTCCAAAGGAGAGAAGGCCAAACTGAAAGTGAAA
genomic: ATGTCGACCCAAACGGCTTACAAATTCCACAAAAAATAAGCACATACACAgtaagcaaga ... tgtgctgcagATTGGCCCTTTCCAAACCTCCAAAGGAGAGAAGGCCAAACTGAAAGTGAAA

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: 289

TAAAGTTCTTACCTTCTTTAAATCCAGTACATTTGAAGTTGATGTTTTGTATGTCGACCCAAACGGCTTACAAATTCCACAAAAAATAAGCACATACACAgtaagcaaga ... tgtgctgcagATTGGCCCTTTCCAAACCTCCAAAGGAGAGAAGGCCAAACTGAAAGTGAAAGTGCGTCTCAACATCCATGGGACCGTTACAGTTGATTCAGCAATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 133

TAAAGTTCTTACCTTCTTTAAATCCAGTACATTTGAAGTTGATGTTTTGTATGTCGACCCAAACGGCTTACAAATTCCACAAAAAATAAGCACATACACAgtaagcaaga ... tgtgctgcagATTGGCCCTTTCCAAACCTCCAAAGGAGAGAAGGCCAAACTGAAAGTGAAAGTGCGTCTCAACATCCATGGGACCGTTACAGTTGATTCAGCAATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 109

TAAAGTTCTTACCTTCTTTAAATCCAGTACATTTGAAGTTGATGTTTTGTATGTCGACCCAAACGGCTTACAAATTCCACAAAAAATAAGCACATACACAgtaagcaaga ... tgtgctgcagATTGGCCCTTTCCAAACCTCCAAAGGAGAGAAGGCCAAACTGAAAGTGAAAGTGCGTCTCAACATCCATGGGACCGTTACAGTTGATTCAGCAATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 128

TAAAGTTCTTACCTTCTTTAAATCCAGTACATTTGAAGTTGATGTTTTGTATGTCGACCCAAACGGCTTACAAATTCCACAAAAAATAAGCACATACACAgtaagcaaga ... tgtgctgcagATTGGCCCTTTCCAAACCTCCAAAGGAGAGAAGGCCAAACTGAAAGTGAAAGTGCGTCTCAACATCCATGGGACCGTTACAGTTGATTCAGCAATA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaatagttgtcctgtatgtattaatatcgctgttttgatatgatgtgctgcagATTGGCCCTTTCCAAACCTCCAAAGGAGAGAAGGCCAAACTGAAAGTGAAAGTGCGTCTCAACATCCATGGGACCGTTACAGTTGATTCAGCAATA
              tgtatgtattaatat  TA-rich tract