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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGAAATCCATGAATCTGAGCCTTTTACTCGTCAAAGCGACGTATATAGTTTGGGTGTGGTGATGCTAGAACTTCTTACTGGTCGTAAGCCATATGACAGgtcagagatccattgcaatatgcatgttgaacaagagccttttgcaattatttgaatcacttctctcctaaaaattcatttttagtacttctttatgttggaatatgcag

Basic information

species Zea mays
transcript GRMZM2G335638_T01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G335638_T01 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os02g07960.2 (Oryza sativa), 5'ss of exon 15
CTGAAATCCATGAATCTGAGCCTTTTACTCGTCAAAGCGACGTATATAGTTTGGGTGTGGTGATGCTAGAACTTCTTACTGGTCGTAAGCCATATGACAGgtcagagatccattgcaatatgcatgt-tgaacaagagccttttgcaattat-ttgaatcacttctctcctaaaaattcat-----ttttag--tacttctttat-----gttggaatatgcag
|||||||||||||| ||| | |||||||    | ||| || || || ||||| || ||||| |||||||||||||| ||||| ||||| |||||||||||||||| ||| ||  | ||||||||| | | ||    ||  |||   |||| | ||  |||| || ||||| ||   |   |     || |||  | |||  ||||     |||  |||||||||
CTGAAATCCATGAAGCTGGGACTTTTACCTACCGAAGTGATGTTTACAGTTTTGGCGTGGTAATGCTAGAACTTCTCACTGGCCGTAAACCATATGACAGgtcagtgattcaccgtaatatgcatttcttaattttag--tttcataattgtgttagatcaattgtctccaaatgttgtctgaactttctagtttgcttgcttattttccgttacaatatgcag
















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|148967602|gb|EE018855.2|EE018855
EST:     TTGGGTGTGGTGATGCTAGAACTTTTTACTGGTCGTAAGCCATATGACAG                         TTTTTGTCCACGTGATGAACAACATCTTGTTCGATGGGCTAATTTTCAGCT
genomic: TTGGGTGTGGTGATGCTAGAACTTCTTACTGGTCGTAAGCCATATGACAGgtcagagatc ... gaatatgcagTTCTCGTCCACGTGATGAACAACATCTTGTTCGATGGGCTAATTCTCAGCT
EST: gi|4681241|gb|AI629911.1|AI629911
EST:     TTGGGTGTGGTGATGCTAGAACTTCTTACTGGTCGTAAGCCATATGACAG                         TTCTCGTCCACGTGATGAACAACATCTTGTTCGATGGGCTAATTCTCAGCT
genomic: TTGGGTGTGGTGATGCTAGAACTTCTTACTGGTCGTAAGCCATATGACAGgtcagagatc ... gaatatgcagTTCTCGTCCACGTGATGAACAACATCTTGTTCGATGGGCTAATTCTCAGCT
EST: gi|32850663|gb|CD990344.1|CD990344
EST:     TTGGGTGTGGTGATGCTAGAACTTCTTACTGGTCGTAAGCCATATGACAG                         TTCTCGTTCACGTGATGAACAACATCTTGTTCGATGGGCTAATTCTCAGCT
genomic: TTGGGTGTGGTGATGCTAGAACTTCTTACTGGTCGTAAGCCATATGACAGgtcagagatc ... gaatatgcagTTCTCGTCCACGTGATGAACAACATCTTGTTCGATGGGCTAATTCTCAGCT
EST: gi|44682246|gb|CK787294.1|CK787294
EST:     TTGGGTGTGGTGATGCTAGAACTTCTTACTGGTCGTAAGCCATATGACAG                         TTCTCGTCCACGTGATGAACAACATCTTGTTCGATGGGCTGATTCTCAGCT
genomic: TTGGGTGTGGTGATGCTAGAACTTCTTACTGGTCGTAAGCCATATGACAGgtcagagatc ... gaatatgcagTTCTCGTCCACGTGATGAACAACATCTTGTTCGATGGGCTAATTCTCAGCT
EST: gi|60345562|gb|DN212535.1|DN212535
EST:     TTGGGTGTGGTGATGCTAGAACTTCTTACTGGTCGTAAGCCATATGACAG                         TTCTCGTCCACGTGATGAACAACATCTTGTTCGATGGGCTAATTCTCAGCT
genomic: TTGGGTGTGGTGATGCTAGAACTTCTTACTGGTCGTAAGCCATATGACAGgtcagagatc ... gaatatgcagTTCTCGTCCACGTGATGAACAACATCTTGTTCGATGGGCTAATTCTCAGCT
EST: gi|40302989|gb|CK347376.1|CK347376
EST:     TTGGGTGTGGTGATGCTAGAACTTCTTACTGGTCGTAAGCCATATGACAG                         TTCTCGTCCACGTGATGAACAACATCTTGTTCGATGGGCTAATTCTCAGCT
genomic: TTGGGTGTGGTGATGCTAGAACTTCTTACTGGTCGTAAGCCATATGACAGgtcagagatc ... gaatatgcagTTCTCGTCCACGTGATGAACAACATCTTGTTCGATGGGCTAATTCTCAGCT

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), 49 (downstream exon)
Score: 123

CTGAAATCCATGAATCTGAGCCTTTTACTCGTCAAAGCGACGTATATAGTTTGGGTGTGGTGATGCTAGAACTTCTTACTGGTCGTAAGCCATATGACAGgtcagagatc ... gaatatgcagTTCTCGTCCACGTGATGAACAACATCTTGTTCGATGGGCTAATTCTCAGCTTCATGACATGGAGTCCCTGTCAAAGATGGTTGATCCTTCTATCCGAGGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 42

CTGAAATCCATGAATCTGAGCCTTTTACTCGTCAAAGCGACGTATATAGTTTGGGTGTGGTGATGCTAGAACTTCTTACTGGTCGTAAGCCATATGACAGgtcagagatc ... gaatatgcagTTCTCGTCCACGTGATGAACAACATCTTGTTCGATGGGCTAATTCTCAGCTTCATGACATGGAGTCCCTGTCAAAGATGGTTGATCCTTCTATCCGAGGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 34

CTGAAATCCATGAATCTGAGCCTTTTACTCGTCAAAGCGACGTATATAGTTTGGGTGTGGTGATGCTAGAACTTCTTACTGGTCGTAAGCCATATGACAGgtcagagatc ... gaatatgcagTTCTCGTCCACGTGATGAACAACATCTTGTTCGATGGGCTAATTCTCAGCTTCATGACATGGAGTCCCTGTCAAAGATGGTTGATCCTTCTATCCGAGGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 150

CTGAAATCCATGAATCTGAGCCTTTTACTCGTCAAAGCGACGTATATAGTTTGGGTGTGGTGATGCTAGAACTTCTTACTGGTCGTAAGCCATATGACAGgtcagagatc ... gaatatgcagTTCTCGTCCACGTGATGAACAACATCTTGTTCGATGGGCTAATTCTCAGCTTCATGACATGGAGTCCCTGTCAAAGATGGTTGATCCTTCTATCCGAGGA