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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCCTGGTGGCTGCGCTAACTGCAAGCGCATATGGCAGCTTCTTGAGCTGCATTCTCGCATGTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAGgtgagcacttctgtttgctgcacattgttctgtgtttctgttgcattctttgacattcttttggtcactgtgacccagcatatctagttatctactctgaccatgctacttgttcagcatttctgctctgaatttttgtgctgttttactcctacag

Basic information

species Oryza sativa
transcript LOC_Os01g66890.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g66890.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM5G807064_T01 (Zea mays), 5'ss of exon 5
TGCCTGGTGGCTGCGCTAACTGCAAGCGCATATGGCAGCTTCTTGAGCTGCATTCTCGCATGTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAGgtgagcacttctgtttgctgcacattgttctgtgtttctgttgcattctttgacattcttttggtcac--tgtgacccagcatatctagttatctactctgaccatgctacttgtt-cagcatttctgctctgaatttttgtgctgttttactcctacag
|||| || ||||| || ||||||| ||| || |||||||| || ||||||||||| ||||||||||     |  || || ||| | ||||| ||||| ||||||||          || || ||| | ||| | || |    ||  |     |         |   |   | ||  |  |||||||| |      | |     |||   |  | |  ||| |    || | | | || | |     |||    | | |||
TGCCCGGCGGCTGTGCCAACTGCAGGCGGATGTGGCAGCTCCTCGAGCTGCATTCCCGCATGTGCTTCCTCCCGGACACCTGCAAGGTTCCTCTCTGCAGgtgagc----------gcggcgcatcgatctct-ttgccaaagcggtagcaaatggggagaggaagaggatatgctctggcatatcttg------atttcattcatataagatataacagaacacgtgtttttatttatcgcaaattttacgacttgcag

upper sequence: LOC_Os01g66890.3 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv05s0094g00950.t01 (Vitis vinifera), 5'ss of exon 6
TGCCTGGTGGCTGCGCTAACTGCAAGCGCATATGGCAGCTTCTTGAGCTGCATTCTCGCATGTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAGgtgagcacttctgtttgctgcacattgttctgtgtttctgttgc--attctttgacattcttttggtcactgtgacccagcatatctagttatctactctgaccatgctacttgttcagcatttctgctctgaatttttgtgctgttttactcctacag
| || || || || | | ||||||||||||| |||||||||||||| ||||| || || ||||||  || || |||   |||| | || || |||||||||| |||  | | | ||   || |||  |  ||  || |  ||    |  | ||   || || ||    |         | ||||| |  |  | || | |                                                           
TCCCCGGCGGATGTGTTCACTGCAAGCGCATGTGGCAGCTTCTTGAACTGCACTCCCGGATGTGCAGTGAACCTGATTGTTGCAAGGTCCCTCTCTGTAGgtaagc--tacagattagcgc-catcatattgaattccgattatttacacattcttatcctcttcccaaaaaaattttaacatattttttattttattttatt--------------------------------------------------------

upper sequence: LOC_Os01g66890.3 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S365_10V6.1 (Physcomitrella patens), 5'ss of exon 7
TGCCTGGTGGCTGCGCTAACTGCAAGCGCATATGGCAGCTTCTTGAGCTGCATTCTCGCATGTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAGgtgagcacttctgtttgctgcacattgttctgtgtttctgttgcattctttgacattcttttggtcactgtgacccagcatatctagttatctactctgaccatgctacttgttcagcatttctgctctgaatttttgtgctgttttactcctacag
|| ||||||| || |   | || |||||||| ||||||||||| ||||| |||||||| |||||| |  ||  |||  ||||| | || ||||||||  ||||||   ||| | |  ||     | ||| | ||        | || ||      | ||||||  |   |      || | |  |  || |     | ||    || |                                                 
TGGCTGGTGGATGTGTGCATTGTAAGCGCATGTGGCAGCTTCTCGAGCTTCATTCTCGTATGTGCACGACAAGTGATTCTTGCAAAGTGCCCCTCTGCGGgtgagt-tttcagatacct-----tcgttgtatgaagtatgcgtatactac----tgcttttgaacgaggcacagtaggaaacatcattttgagtacagatttcgcgagg-----------------------------------------------

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|55438956|gb|CV732778.1|CV732778
EST:     CATTCTCGCATGTGCTCTGCACTTGAAACTTGCCGTGTTCCCCTCTGTAG                         GCATTTCAAGGAGAAAATGCAACATCTGAGCAGAAAGGAGGAGGCCAAGTG
genomic: CATTCTCGCATGTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAGgtgagcactt ... actcctacagGCATTTCAAGGAGAAAATGCAACATCTGAGCAGAAAGGAGGAGGCCAAGTG
EST: gi|88268662|gb|CI378597.1|CI378597
EST:     CATTCTCGCATGTGCTCTGCACTTGAAACTTTCCATGTTCCCCTCTGTAG                         GCATTTCAAGGAGAAAATGCAACATCTGAGCAGAAAGGAGGAGGCCAAGTG
genomic: CATTCTCGCATGTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAGgtgagcactt ... actcctacagGCATTTCAAGGAGAAAATGCAACATCTGAGCAGAAAGGAGGAGGCCAAGTG
EST: gi|88282380|gb|CI403776.1|CI403776
EST:     CATTCTCGCATGTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAG                         GCATTTCAAGGAGAAAATGCAACATCTGAGCAGAAAGGAGGAGGCCAAGTG
genomic: CATTCTCGCATGTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAGgtgagcactt ... actcctacagGCATTTCAAGGAGAAAATGCAACATCTGAGCAGAAAGGAGGAGGCCAAGTG
EST: gi|86892962|gb|CI318869.1|CI318869
EST:     CATTCTCGCATGTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAG                         GCATTTCAAGGAGAAAATGCAACATCTGAGCAGAAAGGAGGAGGCCAAGTG
genomic: CATTCTCGCATGTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAGgtgagcactt ... actcctacagGCATTTCAAGGAGAAAATGCAACATCTGAGCAGAAAGGAGGAGGCCAAGTG
EST: gi|88832167|gb|CI017401.1|CI017401
EST:     CATTCTCGCATGTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAG                         GCATTTCAAGGAGAAAATGCAACATCTGAGCAGAAAGGAGGAGGCCAAGTG
genomic: CATTCTCGCATGTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAGgtgagcactt ... actcctacagGCATTTCAAGGAGAAAATGCAACATCTGAGCAGAAAGGAGGAGGCCAAGTG
EST: gi|55438958|gb|CV732779.1|CV732779
EST:     CATTCTCGCATGTGCTCTGCACTTGAAACTTGCCGTGTTCCCCTCTGTAG                         GCATTTCAAGGAGAAAATGCAACATCTGAGCAGAAAGGAGGAGGCCAAGTG
genomic: CATTCTCGCATGTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAGgtgagcactt ... actcctacagGCATTTCAAGGAGAAAATGCAACATCTGAGCAGAAAGGAGGAGGCCAAGTG
EST: gi|88276362|gb|CI396966.1|CI396966
EST:     CATTCTCGCATTTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAG                         GCATTTCAAGGAGAAAATGCAACATCTGAGCAGAAAGGAGGAGGCCAAGTG
genomic: CATTCTCGCATGTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAGgtgagcactt ... actcctacagGCATTTCAAGGAGAAAATGCAACATCTGAGCAGAAAGGAGGAGGCCAAGTG
EST: gi|88966559|gb|CI353111.1|CI353111
EST:     CATTCTCGCATGTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAG                         GCATTTCAAGGAGAAAATGCAACATCTGAGCAGAAAGGAGGAGGCCAAGTG
genomic: CATTCTCGCATGTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAGgtgagcactt ... actcctacagGCATTTCAAGGAGAAAATGCAACATCTGAGCAGAAAGGAGGAGGCCAAGTG
EST: gi|86853111|gb|CI324813.1|CI324813
EST:     CATTCTCGCATGTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAG                         GCATTTCAAGGAGAAAATGCAACATCTGAGCAGAAAGGAGGAGGCCAAGTG
genomic: CATTCTCGCATGTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAGgtgagcactt ... actcctacagGCATTTCAAGGAGAAAATGCAACATCTGAGCAGAAAGGAGGAGGCCAAGTG

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: 46 (upstream exon), 49 (downstream exon)
Score: 13

TGCCTGGTGGCTGCGCTAACTGCAAGCGCATATGGCAGCTTCTTGAGCTGCATTCTCGCATGTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAGgtgagcactt ... actcctacagGCATTTCAAGGAGAAAATGCAACATCTGAGCAGAAAGGAGGAGGCCAAGTGGAATCTTTTGGTGTCCAAGGTGTTGGAGAGCAAAGCAACAACCAGTTCC




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