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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATTGGTTGGATGATGGGGCAAAAGATGGACTTGAATTTCCAACTATTCGAAACAGCAACGCTCTTCATAACAGTACTAGTCGTGGCATTTATGCTACAGgtaggttattgtgtgaaatattaagaattattttgataagggatgcctgcttaatgaagagtttgtcaagctgtgtttgtttttgtatgccttggcacat...

Basic information

species Oryza sativa
transcript LOC_Os04g55940.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g55940.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G040017_T01 (Zea mays), 5'ss of exon 10
CATTGGTTGGATGATGGGGCAAAAGATGGACTTGAATTTCCAACTATTCGAAACAGCAACGCTCTTCATAACAGTACTAGTCGTGGCATTTATGCTACAGgtaggttattgtgtgaaatattaagaattattttgataagggatgcctgcttaatgaagagtttgtcaagct-gtgtttgtttttgtatgccttg-gcacat
 ||||||||||||||||| |||| ||||||||||||||| || ||||| || |||||||| |||||||||||||| || || || |||||||||||||||||||||| ||  |    ||||||| ||  | ||| ||||    || ||| |   |     ||| || | | |  |   ||   |  ||||   || | | ||
TATTGGTTGGATGATGGGACAAAGGATGGACTTGAATTTTCAGCTATTTGAGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAGgtaggttcttaaggtggatattaataaaaacttttataaaatgtgtctgtt--gttgcctgttggtaaggtttattgatgccatcatatggactgtgaaaat

upper sequence: LOC_Os04g55940.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G143356_T02 (Zea mays), 5'ss of exon 11
CATTGGTTGGATGATGGGGCAAAAGATGGACTTGAATTTCCAACTATTCGAAACAGCAACGCTCTTCATAACAGTACTAGTCGTGGCATTTATGCTACAGgtaggttatt---gtgtgaaatattaagaattattttgataagggatgcctgcttaatgaagagtttgtcaagct-gtgtttgtttttgtatgccttggcacat
 |||||||||| |||||| |||||||||||||||||||| || ||||| || |||||||| ||||||||||||||||| || |||||||||||| |||||||||||| ||   |||    ||||||||||  | ||| |||     ||  || |   |     |||  | | | |  | ||     |  | | |    || || 
TATTGGTTGGACGATGGGACAAAAGATGGACTTGAATTTTCAGCTATTTGAGACAGCAACTCTCTTCATAACAGTACTTGTGGTGGCATTTATGTTACAGgtaggttcttaaggtggatgatattaagaaaaacttttatataacgtgtatggt--gttgcctgttgctaaggtttatattgaccctgatttactgctgc-ca-

upper sequence: LOC_Os04g55940.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G143356_T01 (Zea mays), 5'ss of exon 11
CATTGGTTGGATGATGGGGCAAAAGATGGACTTGAATTTCCAACTATTCGAAACAGCAACGCTCTTCATAACAGTACTAGTCGTGGCATTTATGCTACAGgtaggttatt---gtgtgaaatattaagaattattttgataagggatgcctgcttaatgaagagtttgtcaagct-gtgtttgtttttgtatgccttggcacat
                         |||||||||||||| || ||||| || |||||||| ||||||||||||||||| || |||||||||||| |||||||||||| ||   |||    ||||||||||  | ||| |||     ||  || |   |     |||  | | | |  | ||     |  | | |    || || 
-------------------------ATGGACTTGAATTTTCAGCTATTTGAGACAGCAACTCTCTTCATAACAGTACTTGTGGTGGCATTTATGTTACAGgtaggttcttaaggtggatgatattaagaaaaacttttatataacgtgtatggt--gttgcctgttgctaaggtttatattgaccctgatttactgctgc-ca-

upper sequence: LOC_Os04g55940.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA13G44960.1 (Glycine max), 5'ss of exon 9
CATTGGTTGGATGATGGGGCAAAAGATGGACTTGAATTTCCAACTATTCGAAACAGCAACGCTCTTCATAACAGTACTAGTCGTGGCATTTATGCTACAGgtaggttattgtgtga--aatattaagaattattttgataagggatgcctgcttaatgaagagtttgtcaagctgtgtttgtttttgtatgccttggcacat
  |||| |||   |||||  || | |||||||||||||| ||||||||||| || || ||||| || || || ||  |||| || ||||||||| | |||||| ||||||   |         |   |||| | ||| ||   | |       |  |    |  |   ||| |  || | |   |  |  | |   |||   
TGTTGGATGGTGCATGGGAAAAGAAATGGACTTGAATTTTCAACTATTCGAGACTGCCACGCTTTTTATCACTGTGTTAGTAGTTGCATTTATGATGCAGgtatgttatttcttacttgcgcctgtaaattgtgttggtagcagttattaatgttttttcaacataaacaatcgatggtcgagatgtttggtcaaagcat--

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|86484481|gb|CI127114.1|CI127114
EST:     AAACAGCAACGCTCTTCATACCAGTACTAGTCGTGGCATTTATGCTACAG                         GATGGTGTTGCGAACTACTTGAAAGGACTTATGCTGATCTTGTGTTATCTA
genomic: AAACAGCAACGCTCTTCATAACAGTACTAGTCGTGGCATTTATGCTACAGgtaggttatt ... gtttccacagGATGGTGTTGCGAACTACTTGAAAGGACTTATGCTGATCTTGTGTTATCTA
EST: gi|88262940|gb|CI366566.1|CI366566
EST:     TCTTCATAACAGTACTACTCGT-GCATTTATGCTACAG                         GATGGT-TTGCGAACTACTTGAAA-GACTTATGCTGATCTTGTGTTATCTA
genomic: TCTTCATAACAGTACTAGTCGTGGCATTTATGCTACAGgtaggttatt ... gtttccacagGATGGTGTTGCGAACTACTTGAAAGGACTTATGCTGATCTTGTGTTATCTA
EST: gi|66923908|gb|CX110756.1|CX110756
EST:     AAACAGCAACGCTCTTCATAACAGTACTAGTCGTGGCATTTATGCTACAG                         GATGGTGTTGCGAACTACTTGAAAGGACTTATGCTGATCTTGTGTTATCTA
genomic: AAACAGCAACGCTCTTCATAACAGTACTAGTCGTGGCATTTATGCTACAGgtaggttatt ... gtttccacagGATGGTGTTGCGAACTACTTGAAAGGACTTATGCTGATCTTGTGTTATCTA
EST: gi|86832984|gb|CI333583.1|CI333583
EST:     TTTATGCTACAG                         GATGGTGGTTGCGAACTACTTGAAAGGACTTATGCTGATCTTGTGTTATCT
genomic: TTTATGCTACAGgtaggttatt ... gtttccacagGATGGT-GTTGCGAACTACTTGAAAGGACTTATGCTGATCTTGTGTTATCT
EST: gi|86258579|gb|CI064932.1|CI064932
EST:     AAACAGCAACGCTCTTCATAACAGTACTAGTCGTGGCATTTATGCTACAG                         GATGGTGTTGCGAACTACTTGAAAGGACTTATGCTGATCTTGTGTTATCTA
genomic: AAACAGCAACGCTCTTCATAACAGTACTAGTCGTGGCATTTATGCTACAGgtaggttatt ... gtttccacagGATGGTGTTGCGAACTACTTGAAAGGACTTATGCTGATCTTGTGTTATCTA
EST: gi|33381504|gb|CF196847.1|CF196847
EST:     AAACAGCAACGCTCTTCATAACAGTACTAGTCGTGGCATTTATGCTACAG                         GATGGTGTTGCGAACTACTTGAAAGGACTTATGCTGATCTTGTGTTATCTA
genomic: AAACAGCAACGCTCTTCATAACAGTACTAGTCGTGGCATTTATGCTACAGgtaggttatt ... gtttccacagGATGGTGTTGCGAACTACTTGAAAGGACTTATGCTGATCTTGTGTTATCTA
EST: gi|58669001|gb|CK057687.1|CK057687
EST:     AAACAGCAACGCTCTTCATAACAGTACTAGTCGTGGCATTTATGCTACAG                         GATGGTGTTGCGAACTACTTGAAAGGACTTATGCTGATCTTGTGTTATCTA
genomic: AAACAGCAACGCTCTTCATAACAGTACTAGTCGTGGCATTTATGCTACAGgtaggttatt ... gtttccacagGATGGTGTTGCGAACTACTTGAAAGGACTTATGCTGATCTTGTGTTATCTA