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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtattgactattgagcttcgaattcacatttatgtcgatttagcccattacatgcatgatccatgagcaaatttgcccaaattatttatgtctggaggagtggatcagttgctagagttatattgcaataattcttctgcagGTTGCACGGACAGGCCGGATTGCTCTGCTCCGAGAGTCTGGAGTTGACTCCAAGTACCTCCGCGGGTTTTCCCTCCCGCTGTAATTCTCCATTTCCAGAC

Basic information

species Zea mays
transcript GRMZM2G077215_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G077215_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os11g14950.1 (Oryza sativa), 3'ss of exon 11
gtttgtattgactattgagcttcgaattcacatttatgtcga-tttagcccattacatgcatgatccatgagca--aatttgcccaaattatttatgtctggaggagtggatcagttgctagagttatattgcaataattcttc-----tgcagGTTGCACGGACAGGCCGGATTGCTCTGCTCCGAGAGTCTGGAGTTGACTCCAAGTACCTCCGCGGGTTTTCCCTCCCGCTGTAATTCTCCATTTCCAGAC--
                                ||| | | ||  ||| | | || ||| | ||  |||||      ||    |   | | | |      |  |  | | | |||| || | |   ||||||||  |   || ||     ||||||||||||| || ||| || ||||  ||| ||| ||||| ||||| || ||||| |||||||| ||||||||||| || ||||| ||     ||  |||    
-------------------------------gtttgtattgagcttatcactttgcat-cttgcaccatgtttttcaaccaacagtagtgaatccaacgtaaatca-tagttcagatggttgcaatatattgctcttgatcctcctctttgcagGTTGCACGAACTGGCAGGGTTGCGTTGCGCCGTGAGTCAGGAGTCGATTCCAAATACCTCCGTGGGTTTTCCCTTCCTCTGTAGTTTGT--TTGTCAGTTGG
















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|71424777|gb|DR806432.1|DR806432
EST:     ACAGAATGGTTAGATTGCAAAAGATGCTAGAGCAGTATGGCATCTGTGAG                         GTTGCACGGACAGGCCGGATTGTTCTGCTCCGAGAGTCTGGAGTTGACTCC
genomic: ACAGAATGGTTAGATTGCAAAAGATGCTAGAGCAGTATGGCATCTGTGAGgtttgtattg ... tcttctgcagGTTGCACGGACAGGCCGGATTGCTCTGCTCCGAGAGTCTGGAGTTGACTCC
EST: gi|211138943|gb|FL439641.1|FL439641
EST:     ACAGAATGGTTAGATTGCAAAAGATGCTAGAGCAGTATGGCATCTGTGAG                         GTTGCACGGACAGGCCGGATTGCTCTGCTCCGAGAGTCTGGAGTTGACTCC
genomic: ACAGAATGGTTAGATTGCAAAAGATGCTAGAGCAGTATGGCATCTGTGAGgtttgtattg ... tcttctgcagGTTGCACGGACAGGCCGGATTGCTCTGCTCCGAGAGTCTGGAGTTGACTCC
EST: gi|71435321|gb|DR816371.1|DR816371
EST:     ACAGAATGGTTAGATTGCAAAAGATGCTAGAGCAGTATGGCATCTGTGAG                         GTTGCACGGACAGGGCCGGATTGCTCTGCTCCGAGAGTCTGGAGTTG
genomic: ACAGAATGGTTAGATTGCAAAAGATGCTAGAGCAGTATGGCATCTGTGAGgtttgtattg ... tcttctgcagGTTGCACGGACAGG-CCGGATTGCTCTGCTCCGAGAGTCTGGAGTTG
EST: gi|211088666|gb|FL440752.1|FL440752
EST:     ACAGAATGGTTAGATTGCAAAAGATGCTAGAGCAGTATGGCATCTGTGAG                         GTTGCACGGACAGGCCGGATTGCTCTGCTCCGAGAGTCTGGAGTTGACTCC
genomic: ACAGAATGGTTAGATTGCAAAAGATGCTAGAGCAGTATGGCATCTGTGAGgtttgtattg ... tcttctgcagGTTGCACGGACAGGCCGGATTGCTCTGCTCCGAGAGTCTGGAGTTGACTCC
EST: gi|71435320|gb|DR816370.1|DR816370
EST:     ACAGAATGGTTAGATTGCAAAAGATGCTAGAGCAGTATGGCATCTGTGAG                         GTTGCACGGACAGGCCGGATTGTTCTGCTCCGAGAGTCTGGAGTTGACTCC
genomic: ACAGAATGGTTAGATTGCAAAAGATGCTAGAGCAGTATGGCATCTGTGAGgtttgtattg ... tcttctgcagGTTGCACGGACAGGCCGGATTGCTCTGCTCCGAGAGTCTGGAGTTGACTCC

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: 37

CTCACCGGAGACATTGACAGAATGGTTAGATTGCAAAAGATGCTAGAGCAGTATGGCATCTGTGAGgtttgtattg ... tcttctgcagGTTGCACGGACAGGCCGGATTGCTCTGCTCCGAGAGTCTGGAGTTGACTCCAAGTACCTCCGCGGGTTTTCCCTCCCGCTGTAATTCTCCATTTCCAGAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 96

CTCACCGGAGACATTGACAGAATGGTTAGATTGCAAAAGATGCTAGAGCAGTATGGCATCTGTGAGgtttgtattg ... tcttctgcagGTTGCACGGACAGGCCGGATTGCTCTGCTCCGAGAGTCTGGAGTTGACTCCAAGTACCTCCGCGGGTTTTCCCTCCCGCTGTAATTCTCCATTTCCAGAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 70

CTCACCGGAGACATTGACAGAATGGTTAGATTGCAAAAGATGCTAGAGCAGTATGGCATCTGTGAGgtttgtattg ... tcttctgcagGTTGCACGGACAGGCCGGATTGCTCTGCTCCGAGAGTCTGGAGTTGACTCCAAGTACCTCCGCGGGTTTTCCCTCCCGCTGTAATTCTCCATTTCCAGAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 48

CTCACCGGAGACATTGACAGAATGGTTAGATTGCAAAAGATGCTAGAGCAGTATGGCATCTGTGAGgtttgtattg ... tcttctgcagGTTGCACGGACAGGCCGGATTGCTCTGCTCCGAGAGTCTGGAGTTGACTCCAAGTACCTCCGCGGGTTTTCCCTCCCGCTGTAATTCTCCATTTCCAGAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtctggaggagtggatcagttgctagagttatattgcaataattcttctgcagGTTGCACGGACAGGCCGGATTGCTCTGCTCCGAGAGTCTGGAGTTGACTCCAAGTACCTCCGCGGGTTTTCCCTCCCGCTGTAATTCTCCATTTCCAGAC
                                            ttcttctgc  CT-rich tract
                              ttatattgcaataatt  TA-rich tract