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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCGACAGCAGTTAAAGATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTCTTTTGACCGGAAAGgtttggcttcttttgtttaactgtttttcttgtaaacttggttttcctgttcttatttttgtcggcatttagctgctagtgtggactgataggtatttgtttgtttcag

Basic information

species Oryza sativa
transcript LOC_Os02g10070.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G063851_T04 (Zea mays), 5'ss of exon 7
GGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCGACAGCAGTTAAAGATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTCTTTTGACCGGAAAGgttt--ggcttcttttgtttaactgtttttcttgtaaacttggttttcctgttcttatttttgtcggcatttagctgctag-tgtggactgataggtatttgtt-tgtttcag----------------------------------------------------------------
||| ||||| |||||||| ||||| ||||||||||| ||||||||||| |  || || ||||||||||||||||| ||||||||||||||||| || ||||| |  | |||| | | || |     |||   | ||||  ||       |||  |   ||  |    |||||  |  |||  | || | |   |    |||  | | ||| ||                                                                
GGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGCCAACAGCAGTTAAGGGCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAGgtatatgccttcctatattcattcaatttaaatttaaaaatgtgccaaatgtgttctgttaagaatacatttctcgcctatctttgtatttccattcctttaatatattttagtttttttcccaattctcatcctatttctataagttttaaggctgtgttttttttcttgtttcag

upper sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G064023_T04 (Zea mays), 5'ss of exon 7
GGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCGACAGCAGTTAAAGATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTCTTTTGACCGGAAAGgttt--ggcttcttttgtttaactgttttt--cttgtaaacttggttttcctgttctt---atttttgtcggcatttagctgctagtgtggactgataggtatttgtttgtttcag
|||||||||||||||||||||||| ||||||||||| ||||||||||| | ||| || ||||||||||||||||| ||||||||||||||||| || ||||| |  | || | | | ||    |  | ||   ||  |||  ||     | |||||     |  |  | |   |||||  || |  |   || ||   |  |              
GGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCAACAGCAGTTAAGGGTGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACAGGGAAGgtatatgcctgcctatattcttttaatcttaatttacaaatgtgtcaaacgtgttccataaaactaggacaatattta-ttgttgataaagaatgg-ggaca--------------

upper sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G063909_T03 (Zea mays), 5'ss of exon 6
GGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCGACAGCAGTTAAAGATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTCTTTTGACCGGAAAGgttt--ggcttcttttgtttaactgtttttct-tgtaaacttggttttcctgttcttatttttgtcggcatttagctgctagtgtggactgataggtatttgtttgtttcag
||| ||||| |||||||||||||  ||||||||||| ||||||||| | | ||| || ||||||||||||||||| || |||||||||||||| || ||||| |  | || | | | || |  |  |||    |||       || ||||       |  |  |     |||||  || |  |   || ||    ||               
GGGCCTCTCAATTCCAGAGTGCCGAAAAGTGCTGCCAACAGCAGTTGAGGGTGGTGAACCTTTGCCTGAGGGTCTCCTCTGGCTTCTTTTGACAGGGAAGgtatatgcctgcctatattcatttaatttcgaatgtgccaaaagtgttcca---taaaactaggaaaatattta-ttgttgattaagaatggggagtggggaca--------

upper sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA08G16770.1 (Glycine max), 5'ss of exon 7
GGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCGACAGCAGTTAAAGATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTCTTTTGACCGGAAAGgtttg-gcttcttttgtttaactgttttt--cttgtaaacttggttttcctgttcttatttttgtcggcatttagc-----tgctagtgtggactgataggtatttgtttgtttcag---------------------------------------
|||  | || ||||| || |||||||||  ||| ||    ||  ||   | |||||||||||||||||||| | |||| |||||||| ||||| |||||||| ||   |  ||||    ||     ||    |  | |  |||  | |    | |||| |  ||     || ||       | | |  |||   | |||  ||    | |||||                                          
GGGCATGTCAATTCCTGAATGCCAGAAAAAGCTTCCAGGTGCTTTTCCTGGTGGGGAGCCTTTGCCTGAGGCTGTACTGTGGCTTCTATTGACAGGAAAGgtatgcaatagttttagaaaatcaaattgaattaattattttgaatattgcttacttaataatgcatatatataatccttgtacaaaggtgttttaatatctacac-tctgtttagattttgttgtataatctttgattcatacacttggtcacag

upper sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA15G42300.2 (Glycine max), 5'ss of exon 7
GGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCGACAGCAGTTAAAGATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTCTTTTGACCGGAAAGgtttggcttctttt-----------gtttaactgtttttcttgtaaact-----tggttttcctgttcttatttt-tgtcggcattt-------agctgctagtgtggactgataggtatt-tgtttgtttcag--------------
|||  | || ||||| || |||||||||  ||| ||    ||  |||  | |||||||||||| ||||||| | |||| |||||||| ||||| |||||||| ||   |  |||            || || |  || | ||| | | |     |  |     | |  |  |||| ||  ||  |||       | |   | || | || |     ||||  | |||| ||||               
GGGCATGTCAATTCCTGAATGCCAGAAAAAGCTTCCAGGTGCTTTTACTGGTGGGGAGCCTTTACCTGAGGCTGTACTGTGGCTTCTATTGACAGGAAAGgtatgcaatagttttagaaaatcaaattgaattaattattttgaatattactcataatgcatatataatccttttatgaaggtgttttaatatcaacacttggtttagattttgttgtataatctttgattcatacatttggtcacag

upper sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 5'ss of exon 7
GGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCGACAGCAGTTAAAGATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTCTTTTGACCGGAAAGgtttggct-tcttttgtttaactgtttttcttgtaaacttggttttcctgttcttatttttgtcggcatttagctgctagtgtggactgataggtatttgtttgtttcag
|||| | || || || || ||||| |||||  | || |  |||      | ||| |||||| ||||||||||||| ||||||||||||||||| ||||||||  |  | | ||      ||  |   ||   | | || ||  |       |   | |         |  | ||   |  | || |   || ||| | ||   ||||   
GGGTATGTCTATCCCTGAATGCCAAAAAGTATTACCAAATGCAACACCTGGTGGAGAGCCTCTGCCTGAGGGTCTGCTTTGGCTTCTTTTGACAGGAAAGgtgggtttgtgttaaaaacaaaagacattacaggatacctgaatg----aatgaaaataggaggaagacattgcatgtcatatgaa--aattggtttatgag-gttt---

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|58693317|gb|CK082004.1|CK082004
EST:     ATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTCTTTTGACCGGAAAG                         GTGCCAACCAAAGAGCAAGTTGATGCTCTATCAAAGGAATTGGCTAGTCGT
genomic: ATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTCTTTTGACCGGAAAGgtttggcttc ... tttgtttcagGTGCCAACCAAAGAGCAAGTTGATGCTCTATCAAAGGAATTGGCTAGTCGT
EST: gi|29614058|gb|CB619071.1|CB619071
EST:     ATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTCTTTTGACCGGAAAG                         GTGCCAACCAAAGAGCAAGTTGATGCTCTATCAAAGGAATTGGCTAGTCGT
genomic: ATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTCTTTTGACCGGAAAGgtttggcttc ... tttgtttcagGTGCCAACCAAAGAGCAAGTTGATGCTCTATCAAAGGAATTGGCTAGTCGT
EST: gi|29667252|gb|CB663527.1|CB663527
EST:     ATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTCTTTTGACCGGAAAG                         GTGCCAACCAAAGAGCAAGTTGATGCTCTATCAAAGGAATTGGCTAGTCGT
genomic: ATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTCTTTTGACCGGAAAGgtttggcttc ... tttgtttcagGTGCCAACCAAAGAGCAAGTTGATGCTCTATCAAAGGAATTGGCTAGTCGT
EST: gi|14571277|gb|BI118645.1|BI118645
EST:     ATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTCTTTTGACCGGAAAG                         GTGCCAACCAAAGAGCAAGTTGATGCTCTATCAAAGGAATTGGCTAGTCGT
genomic: ATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTCTTTTGACCGGAAAGgtttggcttc ... tttgtttcagGTGCCAACCAAAGAGCAAGTTGATGCTCTATCAAAGGAATTGGCTAGTCGT
EST: gi|88573691|gb|CI665460.1|CI665460
EST:     ATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTCTTTTGACCGGAAAG                         GTGCCAACCAAAGAGCAAGTTGATGCTCTATCAAAGGAATTGGCTAGTCGT
genomic: ATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTCTTTTGACCGGAAAGgtttggcttc ... tttgtttcagGTGCCAACCAAAGAGCAAGTTGATGCTCTATCAAAGGAATTGGCTAGTCGT
EST: gi|58658570|gb|CK047250.1|CK047250
EST:     ATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTCTTTTGACCGGAAAG                         GTGCCAACCAAAGAGCAAGTTGATGCTCTATCAAAGGAATTGGCTAGTCGT
genomic: ATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTCTTTTGACCGGAAAGgtttggcttc ... tttgtttcagGTGCCAACCAAAGAGCAAGTTGATGCTCTATCAAAGGAATTGGCTAGTCGT
EST: gi|58599089|gb|CK009617.1|CK009617
EST:     ATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTCTTTTGACCGGAAAG                         GTGCCAACCAAAGAGCAAGTTGATGCTCTATCAAAGGAATTGGCTAGTCGT
genomic: ATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTCTTTTGACCGGAAAGgtttggcttc ... tttgtttcagGTGCCAACCAAAGAGCAAGTTGATGCTCTATCAAAGGAATTGGCTAGTCGT
EST: gi|58611144|gb|CK038856.1|CK038856
EST:     ATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTCTTTTGACCGGAAAG                         GTGCCAACCAAAGAGCAAGTTGATGCTCTATCAAAGGAATTGGCTAGTCGT
genomic: ATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTCTTTTGACCGGAAAGgtttggcttc ... tttgtttcagGTGCCAACCAAAGAGCAAGTTGATGCTCTATCAAAGGAATTGGCTAGTCGT
EST: gi|29614020|gb|CB619033.1|CB619033
EST:     ATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTCTTTTGACCGGAAAG                         GTGCCAACCAAAGAGCAAGTTGATGCTCTATCAAAGGAATTGGCTAGTCGT
genomic: ATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTCTTTTGACCGGAAAGgtttggcttc ... tttgtttcagGTGCCAACCAAAGAGCAAGTTGATGCTCTATCAAAGGAATTGGCTAGTCGT
EST: gi|58690828|gb|CK079515.1|CK079515
EST:     ATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTCTTTTGACCGGAAAG                         GTGCCAACCAAAGAGCAAGTTGATGCTCTATCAAAGGAATTGGCTAGTCGT
genomic: ATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTCTTTTGACCGGAAAGgtttggcttc ... tttgtttcagGTGCCAACCAAAGAGCAAGTTGATGCTCTATCAAAGGAATTGGCTAGTCGT
EST: gi|33794508|gb|CF323141.1|CF323141
EST:     ATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTCTTTTGACCGGAAAG                         GTGCCAACCAAAGAGCAAGTTGATGCTCTATCAAAGGAATTGGCTAGTCGT
genomic: ATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTCTTTTGACCGGAAAGgtttggcttc ... tttgtttcagGTGCCAACCAAAGAGCAAGTTGATGCTCTATCAAAGGAATTGGCTAGTCGT
EST: gi|58678175|gb|CK066862.1|CK066862
EST:     ATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTCTTTTGACCGGAAAG                         GTGCCAACCAAAGAGCAAGTTGATGCTCTATCAAAGGAATTGGCTAGTCGT
genomic: ATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTCTTTTGACCGGAAAGgtttggcttc ... tttgtttcagGTGCCAACCAAAGAGCAAGTTGATGCTCTATCAAAGGAATTGGCTAGTCGT
EST: gi|58668188|gb|CK056874.1|CK056874
EST:     ATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTCTTTTGACCGGAAAG                         GTGCCAACCAAAGAGCAAGTTGATGCTCTATCAAAGGAATTGGCTAGTCGT
genomic: ATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTCTTTTGACCGGAAAGgtttggcttc ... tttgtttcagGTGCCAACCAAAGAGCAAGTTGATGCTCTATCAAAGGAATTGGCTAGTCGT

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: 69 (upstream exon), 43 (downstream exon)
Score: 60

GGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCGACAGCAGTTAAAGATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTCTTTTGACCGGAAAGgtttggcttc ... tttgtttcagGTGCCAACCAAAGAGCAAGTTGATGCTCTATCAAAGGAATTGGCTAGTCGTTCGAGTGTTCCAG




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