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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCAGCGATTAAATCTGCCTACCCAGACATCAACATTATATCAAGTTGTGATAGGCCAACTATTTCGCCATCCAACCCTGCCGATCTTTATGATGTTCATgtaatgtctcaacgctatgttccttgcttgcttgagcaatgttttagttatggttgaaaaagacatcatcttttgctgcag

Basic information

species Zea mays
transcript GRMZM2G097277_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G097277_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os07g48750.1 (Oryza sativa), 5'ss of exon 13
CTCAGCGATTAAATCTGCCTACCCAGACATCAACATTATATCAAGTTGTGATAGGCCAACTATTTCGCCATCCAACCCTGCCGATCTTTATGATGTTCATgtaatgtctcaacgctatgttcc-----ttgcttgcttgagcaat----------------------gttttagttatggttgaaaaagacatcatcttttgctgcag
 || ||||||||| ||||||| |||||||||||| |  | |||||||||||||   | |||||||| || ||||||||||||||||| |||||||||||||||||||||   |  ||||||||     ||| ||| ||   ||||                      ||||   |||||| ||| ||| ||||||||| |  |  |||
TTCCGCGATTAAAGCTGCCTATCCAGACATCAACGTCGTGTCAAGTTGTGATAAATCCACTATTTCTCCGTCCAACCCTGCCGATCTATATGATGTTCATgtaatgtctattcattatgttcctttccttgtttgttttcacaatttcgtgttttttccaaattatggtttcgtttatggctgacaaaaacatcatctat-accacag
















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|67024258|gb|CO453007.1|CO453007
EST:     ATAGGCCAACTATTTCGGCATCCAACCCTGCCGATCTTTATGATGTTCAT                         GTCTACACCTCTTCGACTAATATGTTTTCAAAAGCTAGTATGTTTGACAAC
genomic: ATAGGCCAACTATTTCGCCATCCAACCCTGCCGATCTTTATGATGTTCATgtaatgtctc ... tttgctgcagGTCTACACCTCTTCGACTAATATGTTTTCAAAAGCTAGTATGTTTGACAAC
EST: gi|211168064|gb|FL062250.1|FL062250
EST:     ATAGGCCAACTATTTCGCCATCCAACCCTGCCGATCTTTATGATGTTCAT                         GTCTACACCTCTTCGACTAATATGTTTTCAAAAGCTAGTATGTTTGACAAC
genomic: ATAGGCCAACTATTTCGCCATCCAACCCTGCCGATCTTTATGATGTTCATgtaatgtctc ... tttgctgcagGTCTACACCTCTTCGACTAATATGTTTTCAAAAGCTAGTATGTTTGACAAC
EST: gi|67026679|gb|CO455428.1|CO455428
EST:     ATAGGCCAACTATTTCGGCATCCAACCCTGCCGATCTTTATGATGTTCAT                         GTCTACACCTCTTCGACTAATATGTTTTCAAAAGCTAGTATGTTTGACAAC
genomic: ATAGGCCAACTATTTCGCCATCCAACCCTGCCGATCTTTATGATGTTCATgtaatgtctc ... tttgctgcagGTCTACACCTCTTCGACTAATATGTTTTCAAAAGCTAGTATGTTTGACAAC
EST: gi|71757747|gb|DR955684.1|DR955684
EST:     ATAGGCCAACTATTTCGCCATCCAACCCTGCCGATCTTTATGATGTTCAT                         GTCTACACCTCTTCGACTAATATGTTTTCAAAAGCTAGTATGTTTGACAAC
genomic: ATAGGCCAACTATTTCGCCATCCAACCCTGCCGATCTTTATGATGTTCATgtaatgtctc ... tttgctgcagGTCTACACCTCTTCGACTAATATGTTTTCAAAAGCTAGTATGTTTGACAAC
EST: gi|5895641|gb|AW036887.1|AW036887
EST:     ATAGGCCAACTATTTCGCCATCCAACCCTGCCGATCTTTATGATGTTCAT                         GTCTACACCTCTTCGACTAATATGTTTTCAAAAGCTAGTATGTTTGACAAC
genomic: ATAGGCCAACTATTTCGCCATCCAACCCTGCCGATCTTTATGATGTTCATgtaatgtctc ... tttgctgcagGTCTACACCTCTTCGACTAATATGTTTTCAAAAGCTAGTATGTTTGACAAC
EST: gi|67042721|gb|CO468976.1|CO468976
EST:     ATAGGCCAACTATTTCGGCATCCAACCCTGCCGATCTTTATGATGTTCAT                         GTCTACACCTCTTCGACTAATATGTTTTCAAAAGCTANGTATGTT-GACAA
genomic: ATAGGCCAACTATTTCGCCATCCAACCCTGCCGATCTTTATGATGTTCATgtaatgtctc ... tttgctgcagGTCTACACCTCTTCGACTAATATGTTTTCAAAAGCTA-GTATGTTTGACAA

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: 39 (upstream exon), 49 (downstream exon)
Score: 18

CTCAGCGATTAAATCTGCCTACCCAGACATCAACATTATATCAAGTTGTGATAGGCCAACTATTTCGCCATCCAACCCTGCCGATCTTTATGATGTTCATgtaatgtctc ... tttgctgcagGTCTACACCTCTTCGACTAATATGTTTTCAAAAGCTAGTATGTTTGACAACACACCACGTGGAGCACCGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 71

CTCAGCGATTAAATCTGCCTACCCAGACATCAACATTATATCAAGTTGTGATAGGCCAACTATTTCGCCATCCAACCCTGCCGATCTTTATGATGTTCATgtaatgtctc ... tttgctgcagGTCTACACCTCTTCGACTAATATGTTTTCAAAAGCTAGTATGTTTGACAACACACCACGTGGAGCACCGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 30

CTCAGCGATTAAATCTGCCTACCCAGACATCAACATTATATCAAGTTGTGATAGGCCAACTATTTCGCCATCCAACCCTGCCGATCTTTATGATGTTCATgtaatgtctc ... tttgctgcagGTCTACACCTCTTCGACTAATATGTTTTCAAAAGCTAGTATGTTTGACAACACACCACGTGGAGCACCGAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 57

CTCAGCGATTAAATCTGCCTACCCAGACATCAACATTATATCAAGTTGTGATAGGCCAACTATTTCGCCATCCAACCCTGCCGATCTTTATGATGTTCATgtaatgtctc ... tttgctgcagGTCTACACCTCTTCGACTAATATGTTTTCAAAAGCTAGTATGTTTGACAACACACCACGTGGAGCACCGAAG