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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_Os04g55940.1
intron # 10
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

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 1 RNA-Seqlibrary.


Block sizes: 74 (upstream exon), 62 (downstream exon)
Score: 26

CATTGGTTGGATGATGGGGCAAAAGATGGACTTGAATTTCCAACTATTCGAAACAGCAACGCTCTTCATAACAGTACTAGTCGTGGCATTTATGCTACAGgtaggttatt ... gtttccacagGATGGTGTTGCGAACTACTTGAAAGGACTTATGCTGATCTTGTGTTATCTAATAGTTGCCGCCAGTTTCTTCGTTCACGTTGATCCACAATCCA




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