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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATGACTATTCAGGATATGGGCAATCATCAGGAAAGgtatgatcaaatcttgaagttgaacaatgttatttttcataacaaaactaagtgtctactttgctgagtgtttgcgctgtcccattttag

Basic information

species Zea mays
transcript GRMZM2G039214_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G039214_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os12g18860.1 (Oryza sativa), 5'ss of exon 2
GTATGACTATTCAGGATATGGGCAATCATCAGGAAAGgtatgatcaaatc--ttgaagttgaacaatgttatttttcataacaaaactaagtgtctactttgctgagtgtttgcgctgtcccattttag
 |||||||||||||||||||| |||||||||||||||||||| | || |   |||          ||  ||  |  ||| |  |  || |  |  |  || ||| ||| ||| |  | ||   ||| ||
ATATGACTATTCAGGATATGGACAATCATCAGGAAAGgtatgctgaagtttgttgtgagcagtgcatactacgtgacattaacacgctgaa-gcttggttagcttagtttttcccttctctgctttcag

upper sequence: GRMZM2G039214_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT4G24760.1 (Arabidopsis thaliana), 5'ss of exon 2
GTATGACTATTCAGGATATGGGCAATCATCAGGAAAGgta--tgatca--aatcttgaagttgaac-aatgttatttttcataacaaaactaagtgtctactttgc-tgagtgtttgcgctgtcccattttag-----
||||||||||||||| ||||| ||||||||||| |||||   | | ||   ||| | ||| |     | |  |    |||| ||      |   | |  ||| ||    | ||           |||||||       
GTATGACTATTCAGGGTATGGCCAATCATCAGGGAAGgtgagtaaccacagatcctaaagctctcttagttctgagattca-aatgttggtccatttacactgtgaacaactgaacataaatctccattttgttgcag
















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|211422808|gb|FL239276.1|FL239276
EST:     GTATGACTATTCAGGATATGGGCAATCATCAGGAAAG                         CCGAGTGAACACAATACT
genomic: GTATGACTATTCAGGATATGGGCAATCATCAGGAAAGgtatgatcaa ... cccattttagCCGAGTGAACACAATACT
EST: gi|211425408|gb|FL239281.1|FL239281
EST:     GTATGACTATTCAGGATATGGGCAATCATCAGGAAAG                         CCGAGTGAACACAATACTTATGCTGAC
genomic: GTATGACTATTCAGGATATGGGCAATCATCAGGAAAGgtatgatcaa ... cccattttagCCGAGTGAACACAATACTTATGCTGAC
EST: gi|211422809|gb|FL239277.1|FL239277
EST:     GTATGACTATTCAGGATATGGGCAATCATCAGGAAAG                         CCGAGTGAACACAATACTTATGCTGACATAGAGGCAGCTTACAAGTGCCTC
genomic: GTATGACTATTCAGGATATGGGCAATCATCAGGAAAGgtatgatcaa ... cccattttagCCGAGTGAACACAATACTTATGCTGACATAGAGGCAGCTTACAAGTGCCTC
EST: gi|211425406|gb|FL239279.1|FL239279
EST:     GTATGACTATTCAGGATATGGGCAATCATCAGGAAAG                         CCGAGTGAACACAATACTTATGCTGACATAGAGGCAGCTTACAAGTGCCTC
genomic: GTATGACTATTCAGGATATGGGCAATCATCAGGAAAGgtatgatcaa ... cccattttagCCGAGTGAACACAATACTTATGCTGACATAGAGGCAGCTTACAAGTGCCTC
EST: gi|160481624|gb|EY254456.1|EY254456
EST:     GTATGACTATTCAGGATATGGGCAATCATCAGGAAAG                         CCGAGTGAACACAATACTTATGCTGACATAGAGGCAGCTTACAAGTGCCTC
genomic: GTATGACTATTCAGGATATGGGCAATCATCAGGAAAGgtatgatcaa ... cccattttagCCGAGTGAACACAATACTTATGCTGACATAGAGGCAGCTTACAAGTGCCTC
EST: gi|211425405|gb|FL239278.1|FL239278
EST:     GTATGACTATTCAGGATATGGGCAATCATCAGGAAAG                         CCGAGTGAACACAATACTTATGCTGACATAGAGGCAGCTTACAAGTGCCTC
genomic: GTATGACTATTCAGGATATGGGCAATCATCAGGAAAGgtatgatcaa ... cccattttagCCGAGTGAACACAATACTTATGCTGACATAGAGGCAGCTTACAAGTGCCTC
EST: gi|211425407|gb|FL239280.1|FL239280
EST:     GTATGACTATTCAGGATATGGGCAATCATCAGGAAAG                         CCGAGTGAACACAATACTTATGCTGACAT
genomic: GTATGACTATTCAGGATATGGGCAATCATCAGGAAAGgtatgatcaa ... cccattttagCCGAGTGAACACAATACTTATGCTGACAT
EST: gi|149076908|gb|EE165564.2|EE165564
EST:     GTATGACTATTCAGGATATGGGCAATCATCAGGAAAG                         CCGAGTGAACACAATACTTATGCTGACATAGAGGCAGCTTACAAGTGCCTC
genomic: GTATGACTATTCAGGATATGGGCAATCATCAGGAAAGgtatgatcaa ... cccattttagCCGAGTGAACACAATACTTATGCTGACATAGAGGCAGCTTACAAGTGCCTC
EST: gi|94475263|gb|EB704221.1|EB704221
EST:     GTATGACTATTCAGGATATGGGCAATCATCAGGAAAG                         CCGAGTGAACACAATACTTATGCTGACATAGAGGCAGCTTACAAGTGCCTC
genomic: GTATGACTATTCAGGATATGGGCAATCATCAGGAAAGgtatgatcaa ... cccattttagCCGAGTGAACACAATACTTATGCTGACATAGAGGCAGCTTACAAGTGCCTC

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), 47 (downstream exon)
Score: 74

GTATGACTATTCAGGATATGGGCAATCATCAGGAAAGgtatgatcaa ... cccattttagCCGAGTGAACACAATACTTATGCTGACATAGAGGCAGCTTACAAGTGCCTCATAGAGAAATTTGGTGCCAAGGAAGAAGAAATAATTCTTTATGGACAAT


Block sizes: 47 (upstream exon), 43 (downstream exon)
Score: 61

GTATGACTATTCAGGATATGGGCAATCATCAGGAAAGgtatgatcaa ... cccattttagCCGAGTGAACACAATACTTATGCTGACATAGAGGCAGCTTACAAGTGCCTCATAGAGAAATTTGGTGCCAAGGAAGAAGAAATAATTCTTTATGGACAAT


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 84

GTATGACTATTCAGGATATGGGCAATCATCAGGAAAGgtatgatcaa ... cccattttagCCGAGTGAACACAATACTTATGCTGACATAGAGGCAGCTTACAAGTGCCTCATAGAGAAATTTGGTGCCAAGGAAGAAGAAATAATTCTTTATGGACAAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 85

GTATGACTATTCAGGATATGGGCAATCATCAGGAAAGgtatgatcaa ... cccattttagCCGAGTGAACACAATACTTATGCTGACATAGAGGCAGCTTACAAGTGCCTCATAGAGAAATTTGGTGCCAAGGAAGAAGAAATAATTCTTTATGGACAAT