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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTATGGAAAGGCTCCCAGGAGTAAGAATTGCTTTTGTTGGTGACGGACCATACAGgtgcattccttaatgttaaatatttttcgttatcaacaagactcatacatgataacatatatattgaaatgacactatttggagcacttcagttttatct...

Basic information

species Oryza sativa
transcript LOC_Os03g15840.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g15840.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G049190_T01 (Zea mays), 5'ss of exon 10
GGTTATGGAAAGGCTCCCAGGAGTAAGAATTGCTTTTGTTGGTGACGGACCATACAGgtgca---ttccttaat-gttaaatatttttcgttatcaacaagactcatacatgataacatatatattgaaatgacactatttggagcacttcagttttatct
||||||||| ||||||||||||| ||| ||||| |||||||| ||||| |||||||||||||   ||||| | | ||||  ||| | |  || | |  | ||  || || |||| | || | |||  |  | |  |   |   || ||||   |  |    
GGTTATGGAGAGGCTCCCAGGAGCAAGGATTGCCTTTGTTGGAGACGGGCCATACAGgtgcaccattcctcagtcgttagctatatgttttttttagtatgatgcacacctgatgagatttttatgtatgttaaccacatattagtacttacatgct----

upper sequence: LOC_Os03g15840.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G117153_T01 (Zea mays), 5'ss of exon 10
GGTTATGGAAAGGCTCCCAGGAGTAAGAATTGCTTTTGTTGGTGACGGACCATACAGgtgca---ttccttaat-gttaa--atatttttcgttatcaacaagactcatacatgataacatatatattgaaatgacactatttggagcacttcagttttatct
||||||||| ||||||||||||| ||| ||||| || ||||| ||||| |||||||||||||   ||||| | | ||||   |||| ||   || | |  | ||  || || |||| | || | |||    |||    || |   |   |   | ||  |   
GGTTATGGAGAGGCTCCCAGGAGCAAGGATTGCCTTCGTTGGAGACGGGCCATACAGgtgcaccattcctcagtcgttagctatatgttatttttttagtaggatgcagacctgatgagatttgtatatgtatg---ttaatcacaaatcagtatttaca---

upper sequence: LOC_Os03g15840.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA07G17680.1 (Glycine max), 5'ss of exon 9
GGTTATGGAAAGGCTCCCAGGAGTAAGAATTGCTTTTGTTGGTGACGGACCATACAGgtg-----------cattccttaatgttaaa-tatttttcgttatcaacaagactcata-catgataa-------------catatatat-tgaaatgacactatttggagcacttcagttttatct------------------------------
            ||| || |  |   |||||||||| |||||||| ||||||||||||||           ||| ||||||    ||| |||||   |||     || |  |  || | | |||              ||||| ||  | ||   |   || |   |  ||||  |     | |                              
------------GCTTCCTGATGCCCGAATTGCTTTCGTTGGTGATGGACCATACAGgtgactaattctgccatcccttaaaaaaaaagtatttggtgtttgtttcatgctttttatctttatattactcccctcttccatatctacataaagcaatgttaatataaaaactttggcaacttttagtaatatgagttgctttgctaactactag

upper sequence: LOC_Os03g15840.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA18G42540.1 (Glycine max), 5'ss of exon 10
GGTTATGGAAAGGCTCCCAGGAGTAAGAATTGCTTTTGTTGGTGACGGACCATACAGgtgcattcct-taatgttaaatatttttcgttatcaacaagactcatacatgataacatatatattgaaatgacactatttggagcacttcagttttatct
| | ||||| ||||| || |  |   |||||||||| |||||||| ||||||||||||||  |   | | |       ||         |   |   |     |   |||| | |   ||  |   ||    |  ||||  |    | |      |  
GCTCATGGATAGGCTTCCTGATGCCCGAATTGCTTTCGTTGGTGATGGACCATACAGgtgactaattctgacaccccttaaaaaaaagaaagtatttggtatttgtttgatgataatgatcctatcatctatcagtttgaggggggtaacagaggtt-

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|29682747|gb|CB679022.1|CB679022
EST:     GAAAGGCTCCCAGGAGTAAGAATTGCTTTTGTTGGTGACGGACCATACAG                         GGCTGAGCTGGAAAGAATGTTTACTGGCATGCCTGCAGTATTCACTGGAAT
genomic: GAAAGGCTCCCAGGAGTAAGAATTGCTTTTGTTGGTGACGGACCATACAGgtgcattcct ... tctttggcagGGCTGAGCTGGAAAGAATGTTTACTGGCATGCCTGCAGTATTCACTGGAAT
EST: gi|29682379|gb|CB678654.1|CB678654
EST:     GAAAGGCTCCCAGGAGTAAGAATTGCTTTTGTTGGTGACGGACCATACAG                         GGCTGAGCTGGAAAGAATGTTTACTGGCATGCCTGCAGTATTCACTGGAAT
genomic: GAAAGGCTCCCAGGAGTAAGAATTGCTTTTGTTGGTGACGGACCATACAGgtgcattcct ... tctttggcagGGCTGAGCTGGAAAGAATGTTTACTGGCATGCCTGCAGTATTCACTGGAAT
EST: gi|9864970|gb|AU100720.1|AU100720
EST:     TAAGAATTGCTTTTTGTTGGTGACGGACCATACAG                         GGCTGAGCTGGAAAGAATGTTTACTGGCATGCCTGCAGTATTCACTGGAAT
genomic: TAAGAATTGC-TTTTGTTGGTGACGGACCATACAGgtgcattcct ... tctttggcagGGCTGAGCTGGAAAGAATGTTTACTGGCATGCCTGCAGTATTCACTGGAAT
EST: gi|58691923|gb|CK080610.1|CK080610
EST:     GAAAGGCTCCCAGGAGTAAGAATTGCTTTTGTTGGTGACGGACCATACAG                         GGCTGAGCTGGAAAGAATGTTTACTGGCATGCCTGCAGTATTCACTGGAAT
genomic: GAAAGGCTCCCAGGAGTAAGAATTGCTTTTGTTGGTGACGGACCATACAGgtgcattcct ... tctttggcagGGCTGAGCTGGAAAGAATGTTTACTGGCATGCCTGCAGTATTCACTGGAAT
EST: gi|33794374|gb|CF323073.1|CF323073
EST:     GAAAGGCTCCCAGGAGTAAGAATTGCTTTTGTTGGTGACGGACCATACAG                         GGCTGAGCTGGAAAGAATGTTTACTGGCATGCCTGCAGTATTCACTGGAAT
genomic: GAAAGGCTCCCAGGAGTAAGAATTGCTTTTGTTGGTGACGGACCATACAGgtgcattcct ... tctttggcagGGCTGAGCTGGAAAGAATGTTTACTGGCATGCCTGCAGTATTCACTGGAAT

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: 57 (upstream exon), 74 (downstream exon)
Score: 12

GGTTATGGAAAGGCTCCCAGGAGTAAGAATTGCTTTTGTTGGTGACGGACCATACAGgtgcattcct ... tctttggcagGGCTGAGCTGGAAAGAATGTTTACTGGCATGCCTGCAGTATTCACTGGAATGCTCCAAGGCGAGGAGCTCTCACAAGCATATGCCAGTGGCGACTTGTTT




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