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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttcttcgttgcattttcaactctgtgtacattcatgtgtgactctgacataaatcatttgtcgactgaaagATCAATGAGGATGACCGGAGAGACCATAATAACAGGTAGTGATGATTGGACTGCTAGAGTGTGGTCCCTTAACCGGGGAACATGTGATGCAGTGTTAGCA

Basic information

species Zea mays
transcript GRMZM2G074466_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074466_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g39380.1 (Oryza sativa), 3'ss of exon 28
gtaatttcttcgttgcattttcaactctgtg-------------tacattcatgtgt----gactctgacataaatcatttgtcgactgaaagATCAATGAGGATGACCGGAGAGACCATAATAACAGGTAGTGATGATTGGACTGCTAGAGTGTGGTCCCTTAACCGGGGAACATGTGATGCAGTGTTAGCA
||||| ||| |||| || | ||| | || | | || || ||| |||| || || || |||| |||||||||||||||| || || ||||||||||| || |||||||||||||| ||||| |||||||| |||| ||| ||||||||||| || |||||||||
gtaatgtcta-actgcagttatgggtgggtgggtcggagcaacttgcacccgtaatctacagatgcttacacaaatt-ttggttgattgaa-gATCAATGAGGATGACGGGTGAAACCATAATAACTGGGAGTGATGATTGGACGGCTAGGGTGTGGTCTCTTACCCGAGGAACATGTGACGCTGTGTTAGCA
















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|211489769|gb|FL012890.1|FL012890
EST:     CGCTCCAGCAAGCAGATGTTCAAGCTTCAAGGGCATACAAAGTGGATAAG                         ATCAATGAGGATGACCGGAGAGACCAT
genomic: CGCTCCAGCAAGCAGATGTTCAAGCTTCAAGGGCATACAAAGTGGATAAGgtaatttctt ... cgactgaaagATCAATGAGGATGACCGGAGAGACCAT
EST: gi|32933778|gb|CF038590.1|CF038590
EST:     CGCTCCAGCAAGCAGATGTTCAAGCTTCAAGGGCATACAAAGTGGATAAG                         ATCAATGAGGATGACCGGAGAGACCATAATAACAGGTAGTGATGATTGGAC
genomic: CGCTCCAGCAAGCAGATGTTCAAGCTTCAAGGGCATACAAAGTGGATAAGgtaatttctt ... cgactgaaagATCAATGAGGATGACCGGAGAGACCATAATAACAGGTAGTGATGATTGGAC
EST: gi|67010825|gb|CO439574.1|CO439574
EST:     CGCTCCAGCAAGCAGATGTTCAAGCTTCAAGGGCATACAAAGTGGATAAG                         ATCAATGAGGATGACCGGAGAGACCATAATAACAGGTAGTGATGATTGGAC
genomic: CGCTCCAGCAAGCAGATGTTCAAGCTTCAAGGGCATACAAAGTGGATAAGgtaatttctt ... cgactgaaagATCAATGAGGATGACCGGAGAGACCATAATAACAGGTAGTGATGATTGGAC
EST: gi|71331763|gb|DR802742.1|DR802742
EST:     AAGCAGATGTTCAAGC-TCAAGGGGCATACAAAGTGGATAAG                         ATCAATGAGGATGACCGGAGAGACCATAATAACAGGTAGTGATGATTGGAC
genomic: AAGCAGATGTTCAAGCTTCAA-GGGCATACAAAGTGGATAAGgtaatttctt ... cgactgaaagATCAATGAGGATGACCGGAGAGACCATAATAACAGGTAGTGATGATTGGAC
EST: gi|32850651|gb|CD990332.1|CD990332
EST:     CGCTCCAGCAAGCAGATGTTCAAGCTTCAAGGGCATACAAAGTGGATAAG                         ATCAATGAGGGTGACCGGAGAGACCATAATAACAGGTAGTGATGATTGGAC
genomic: CGCTCCAGCAAGCAGATGTTCAAGCTTCAAGGGCATACAAAGTGGATAAGgtaatttctt ... cgactgaaagATCAATGAGGATGACCGGAGAGACCATAATAACAGGTAGTGATGATTGGAC
EST: gi|211489771|gb|FL012892.1|FL012892
EST:     CGCTCCAGCAAGCAGATGTTCAAGCTTCAAGGGCATACAAAGTGGATAAG                         ATCAATGAGGATGACCGGAGAGACCATAATAACAGGTAGTGATGATTGGAC
genomic: CGCTCCAGCAAGCAGATGTTCAAGCTTCAAGGGCATACAAAGTGGATAAGgtaatttctt ... cgactgaaagATCAATGAGGATGACCGGAGAGACCATAATAACAGGTAGTGATGATTGGAC
EST: gi|211489770|gb|FL012891.1|FL012891
EST:     CGCTCCAGCAAGCAGATGTTCAAGCTTCAAGGGCATACAAAGTGGATAAG                         ATCAATGAGGATGACCGGAGAGACCATAATAACAGGTAGTGATGATTGGAC
genomic: CGCTCCAGCAAGCAGATGTTCAAGCTTCAAGGGCATACAAAGTGGATAAGgtaatttctt ... cgactgaaagATCAATGAGGATGACCGGAGAGACCATAATAACAGGTAGTGATGATTGGAC

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), 45 (downstream exon)
Score: 93

CACGGCACATGTCTGGGATATTCGCTCCAGCAAGCAGATGTTCAAGCTTCAAGGGCATACAAAGTGGATAAGgtaatttctt ... cgactgaaagATCAATGAGGATGACCGGAGAGACCATAATAACAGGTAGTGATGATTGGACTGCTAGAGTGTGGTCCCTTAACCGGGGAACATGTGATGCAGTGTTAGCA


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 81

CACGGCACATGTCTGGGATATTCGCTCCAGCAAGCAGATGTTCAAGCTTCAAGGGCATACAAAGTGGATAAGgtaatttctt ... cgactgaaagATCAATGAGGATGACCGGAGAGACCATAATAACAGGTAGTGATGATTGGACTGCTAGAGTGTGGTCCCTTAACCGGGGAACATGTGATGCAGTGTTAGCA


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 98

CACGGCACATGTCTGGGATATTCGCTCCAGCAAGCAGATGTTCAAGCTTCAAGGGCATACAAAGTGGATAAGgtaatttctt ... cgactgaaagATCAATGAGGATGACCGGAGAGACCATAATAACAGGTAGTGATGATTGGACTGCTAGAGTGTGGTCCCTTAACCGGGGAACATGTGATGCAGTGTTAGCA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 59

CACGGCACATGTCTGGGATATTCGCTCCAGCAAGCAGATGTTCAAGCTTCAAGGGCATACAAAGTGGATAAGgtaatttctt ... cgactgaaagATCAATGAGGATGACCGGAGAGACCATAATAACAGGTAGTGATGATTGGACTGCTAGAGTGTGGTCCCTTAACCGGGGAACATGTGATGCAGTGTTAGCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caactctgtgtacattcatgtgtgactctgacataaatcatttgtcgactgaaagATCAATGAGGATGACCGGAGAGACCATAATAACAGGTAGTGATGATTGGACTGCTAGAGTGTGGTCCCTTAACCGGGGAACATGTGATGCAGTGTTAGCA
                         ctctgac  putative branch site (score: 59)
 ataaatcattt  TA-rich tract