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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGGAGTGAAGAGAACAGTAGAGTCGTACTCCCATCTACAAGCTCAGAATCATAGGAGTATATCAAAGGCTTCAATTTTCCTCGGGAATGGAAATCgtatgaaactgccttcatcccttgtgcccacacataccctgtatattcatagtacttttgtacttcatttgaaatccttaccaatttatctattcatatgcag

Basic information

species Zea mays
transcript GRMZM2G149224_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149224_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os03g29170.1 (Oryza sativa), 5'ss of exon 8
GATGGAGTGAAGAGAACAGTAGAGTCGTACTCCCATCTACAAGCTCAGAATCATAGGAGTATATCAAAGGCTTCAATTTTCCTCGGGAATGGAAATCgtatgaaactgccttcatcccttgtgcccacacataccctgtatattcatagtacttttgtacttcatttgaaatccttaccaatttatctattcatatgcag
|||||| | ||||||||| ||||||| ||  ||||||| ||||| || ||||| ||||| |||||||| || ||||||||||| || |||||||||||||||||         ||| ||    | ||||   |   || ||   |||    | ||   ||     |||| ||  | |  ||| |   | ||    |||||
GATGGACTTAAGAGAACAATAGAGTCATATCCCCATCTGCAAGCACAAAATCAAAGGAGCATATCAAAAGCCTCAATTTTCCTTGGCAATGGAAATCgtatgaa--------tatctctcacacacacatgca---tgcatgcccatg---ccttcacacccttcttgagattataatgaatattgatcttggc-tgcag
















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|87151705|gb|DY396494.1|DY396494
EST:     GAATCATAGGAGTATATCAAAGGCTTCAATTTTCCTCGGGAATGGAAATC                         TTGCAAAAACAGTACTTTGGGAAGATGCGAAGCAAACTGTGACAGTGCTTC
genomic: GAATCATAGGAGTATATCAAAGGCTTCAATTTTCCTCGGGAATGGAAATCgtatgaaact ... tcatatgcagTTGCAAAAACAGTACTTTGGGAAGATGCGAAGCAAACTGTGACAGTGCTTC
EST: gi|32863056|gb|CF002738.1|CF002738
EST:     GAATCATAGGAGTATATCAAAGGCTTCAATTTTCCTCGGGAATGGAAATC                         TTGCAAAAACAGTACTTTGGGAAGATGCGAAGCAAACTGTGACAGTGCTTC
genomic: GAATCATAGGAGTATATCAAAGGCTTCAATTTTCCTCGGGAATGGAAATCgtatgaaact ... tcatatgcagTTGCAAAAACAGTACTTTGGGAAGATGCGAAGCAAACTGTGACAGTGCTTC
EST: gi|149072463|gb|EE160739.2|EE160739
EST:     CGGGAATGGAAATC                         TTGCAAAAACAGTACTTTGGGAAGATGCGAAGCAAACTGTGACAGTGCTTC
genomic: CGGGAATGGAAATCgtatgaaact ... tcatatgcagTTGCAAAAACAGTACTTTGGGAAGATGCGAAGCAAACTGTGACAGTGCTTC
EST: gi|18450804|gb|BM429082.1|BM429082
EST:     GAATCATAGGAGTATATCAAAGGCTTCAATTTTCCTCGGGAATGGAAATC                         TTGCAAAAACAGTACTTTGGGAAGATGCGAAGCAAACTGTGACAGTGCTTC
genomic: GAATCATAGGAGTATATCAAAGGCTTCAATTTTCCTCGGGAATGGAAATCgtatgaaact ... tcatatgcagTTGCAAAAACAGTACTTTGGGAAGATGCGAAGCAAACTGTGACAGTGCTTC
EST: gi|166483903|gb|EG135197.1|EG135197
EST:     GAATCATAGGAGTATATCAAAGGCTTCAATTTTCCTCGGGAATGGAAATC                         TTGCAAAAACNGTACTTTGGGAAGA
genomic: GAATCATAGGAGTATATCAAAGGCTTCAATTTTCCTCGGGAATGGAAATCgtatgaaact ... tcatatgcagTTGCAAAAACAGTACTTTGGGAAGA
EST: gi|22489855|gb|BU049778.1|BU049778
EST:     GAATCATAGGAGTATATCAAAGGCTTCAATTTTCCTCGGGAATGGAAATC                         TTGCAAAAACAGTACTTTGGGAAGATGCGAAGCAAACTGTGACAGTGCTTC
genomic: GAATCATAGGAGTATATCAAAGGCTTCAATTTTCCTCGGGAATGGAAATCgtatgaaact ... tcatatgcagTTGCAAAAACAGTACTTTGGGAAGATGCGAAGCAAACTGTGACAGTGCTTC
EST: gi|60337162|gb|DN204135.1|DN204135
EST:     TTCCTCGGGAATGGAAATC                         TTGCAAAAACAGTACTTTGGGAAGATGCGAAGCAAACTGTGACAGTGCTTC
genomic: TTCCTCGGGAATGGAAATCgtatgaaact ... tcatatgcagTTGCAAAAACAGTACTTTGGGAAGATGCGAAGCAAACTGTGACAGTGCTTC

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: 125

GATGGAGTGAAGAGAACAGTAGAGTCGTACTCCCATCTACAAGCTCAGAATCATAGGAGTATATCAAAGGCTTCAATTTTCCTCGGGAATGGAAATCgtatgaaact ... tcatatgcagTTGCAAAAACAGTACTTTGGGAAGATGCGAAGCAAACTGTGACAGTGCTTCTACTGTTGGCTGTTATCTACTACCACTTATTTACATGTGGTTACACCTT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 87

GATGGAGTGAAGAGAACAGTAGAGTCGTACTCCCATCTACAAGCTCAGAATCATAGGAGTATATCAAAGGCTTCAATTTTCCTCGGGAATGGAAATCgtatgaaact ... tcatatgcagTTGCAAAAACAGTACTTTGGGAAGATGCGAAGCAAACTGTGACAGTGCTTCTACTGTTGGCTGTTATCTACTACCACTTATTTACATGTGGTTACACCTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 102

GATGGAGTGAAGAGAACAGTAGAGTCGTACTCCCATCTACAAGCTCAGAATCATAGGAGTATATCAAAGGCTTCAATTTTCCTCGGGAATGGAAATCgtatgaaact ... tcatatgcagTTGCAAAAACAGTACTTTGGGAAGATGCGAAGCAAACTGTGACAGTGCTTCTACTGTTGGCTGTTATCTACTACCACTTATTTACATGTGGTTACACCTT


Block sizes: 47 (upstream exon), 43 (downstream exon)
Score: 81

GATGGAGTGAAGAGAACAGTAGAGTCGTACTCCCATCTACAAGCTCAGAATCATAGGAGTATATCAAAGGCTTCAATTTTCCTCGGGAATGGAAATCgtatgaaact ... tcatatgcagTTGCAAAAACAGTACTTTGGGAAGATGCGAAGCAAACTGTGACAGTGCTTCTACTGTTGGCTGTTATCTACTACCACTTATTTACATGTGGTTACACCTT