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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTTTTTGAAAATCCAGCATTCCGAGCTGATGGTCTAAAGATTTATCCAACTCTTGTGATTCGTGGAACTGGCCTTTATGAGCTCTGGAAAACTGGCAGgtacttattttatctagcacttgatattctagattgctagtcttgtgttcactgttgtgtttgttctctagaactttttagtgagaacttaggccctgccaatgtttgttgtgtttcag

Basic information

species Oryza sativa
transcript LOC_Os04g40840.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g40840.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G359735_T01 (Zea mays), 5'ss of exon 5
AATTTTTTGAAAATCCAGCATTCCGAGCTGATGGTCTAAAGATTTATCCAACTCTTGTGATTCGTGGAACTGGCCTTTATGAGCTCTGGAAAACTGGCAGgtacttattttatctagcacttgatattctagattgctagtcttgtgttcactgttgtgtttgttctctagaactttttagtgagaacttaggccctgccaatgtttgttgtgtttcag
||||||||| || |||||| ||||| ||||||||||| |||||||||||||| |||||||||||||||||||| |||||||||||||||||||||||||||||||  | | ||||||         | ||| ||       |||   | |  | ||| | || || |    ||  ||   || ||||||||    ||    |     ||   |||    
AATTTTTTGGAAGTCCAGCGTTCCGGGCTGATGGTCTGAAGATTTATCCAACACTTGTGATTCGTGGAACTGGTCTTTATGAGCTCTGGAAAACTGGCAGgtactcctctaatctagtgtcc----tgctaaat-------cttacttacgttcttggggttattttt--aaatcttaaggtaagaacttatatactaatgacaa--gtcaggtt----

upper sequence: LOC_Os04g40840.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G100872_T01 (Zea mays), 5'ss of exon 5
AATTTTTTGAAAATCCAGCATTCCGAGCTGATGGTCTAAAGATTTATCCAACTCTTGTGATTCGTGGAACTGGCCTTTATGAGCTCTGGAAAACTGGCAGgtacttattttatctagcacttgatattctagattgctagtcttgtgttcactgttgtgtttgttctctagaactttttagtgagaacttaggccct---gccaatgtttgttgtgtttcag------------------------------
| |||||||||| |||||||||||| ||||||||||| |||||||||||||| ||||| |||||||||||||| |||||||||||||||||||||||||||||||| | | |||||| |      ||||    |    | |||| |   || |  |||| || ||      || |||  ||| |||||||  |  ||   | ||| |  |  |   |    |                              
AGTTTTTTGAAAGTCCAGCATTCCGGGCTGATGGTCTGAAGATTTATCCAACACTTGTTATTCGTGGAACTGGTCTTTATGAGCTCTGGAAAACTGGCAGgtacttctctaatctagtatc----attcagtgtcttgaatcttataaacattcctgtggttatttct---aattttacagtaagaacttctgtacttatgacaagggctcataaatccagggttaacccggtaacttttgctgtgctgcag

upper sequence: LOC_Os04g40840.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA04G36790.1 (Glycine max), 5'ss of exon 5
AATTTTTTGAAAATCCAGCATTCCGAGCTGATGGTCTAAAGATTTATCCAACTCTTGTGATTCGTGGAACTGGCCTTTATGAGCTCTGGAAAACTGGCAGgtacttattttatctagcacttgatattctagattgctagtctt------gtgttcactgttgtgtt--tgttctctagaactttttagtg------agaacttaggccctgccaatgtttgttgtgttt-cag
| |||||||| |  ||    ||  |||| ||||| || || || ||||| || ||||| |||||||||||||| |||||||||||||||||||||||||||||  |||   || |    |||  |||  | || ||||  |          | |  | | |  | ||  | ||   |||   |||||| ||      |||| |||         | |  ||  |||  ||  ||
AGTTTTTTGAGAGCCCCATGTTTAGAGCAGATGGGCTTAAAATATATCCTACACTTGTAATTCGTGGAACTGGGCTTTATGAGCTCTGGAAAACTGGCAGgtatatatcaaatgtttt-cttattat--tggactgctttttcctcaaacatctcaattttcatcttagtatttattagttttttttaatgtcctgtagaaattaaaaaaaaaaattcattaatgtaattgtag

upper sequence: LOC_Os04g40840.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA06G18150.1 (Glycine max), 5'ss of exon 5
AATTTTTTGAAAATCCAGCATTCCGAGCTGATGGTCTAAAGATTTATCCAACTCTTGTGATTCGTGGAACTGGCCTTTATGAGCTCTGGAAAACTGGCAGgtacttat----tttatctagcacttga--------tattctagattgctagtcttgtgttcactgttgtgtttgttctctagaactttttagtgagaacttaggccctgccaatgtttgttgtgtttcag
| |||||||| | |||    ||  |||| ||||| || || || ||||| || ||||| |||||||||||||| |||||||||||||||||||||||||||||  |||    ||| | ||  | | ||        |  || |  ||   | | ||    | | | || | || ||| | |  ||   | | ||   || | |         ||| |   ||||       
AGTTTTTTGAGAGTCCCTTGTTTAGAGCAGATGGGCTTAAAATATATCCTACACTTGTAATTCGTGGAACTGGGCTTTATGAGCTCTGGAAAACTGGCAGgtatatatcaattttttttaatattggactgctttttcctcaaacttctcaattttcatcttagtatt-tattagtttttttaaatggtct-gtagaaagtaaaaaaacattaatata-attgtag-----

upper sequence: LOC_Os04g40840.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT5G50320.1 (Arabidopsis thaliana), 5'ss of exon 5
AATTTTTTGAAAATCCAGCATTCCGAGCTGATGGTCTAAAGATTTATCCAACTCTTGTGATTCGTGGAACTGGCCTTTATGAGCTCTGGAAAACTGGCAGgtacttattttatctagcacttgatattctagattgctagtcttgtgttcactgttgtgtttg--ttctctagaactttttagtgagaacttaggccctgccaatgtttgttgtgtttcag
| ||||| || |  ||| | ||  |||| |||||  |||| || ||||| || |||||||| ||||||||||| |||||||| || ||||||||||| ||||||     |  ||| |   || |   |   || |||| | | |||    || |    | ||   |  | | |||  |||  |                                      
AGTTTTTCGAGAGCCCATCTTTTAGAGCAGATGGGTTAAAAATATATCCCACCCTTGTGATCCGTGGAACTGGACTTTATGAACTATGGAAAACTGGGAGgtacga---tactcttgtgtttaaagat---gaatgcttg-catgtcacaacggaaaaggttaaatcatattgaaaatttctgcag-----------------------------------

upper sequence: LOC_Os04g40840.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv17s0000g10190.t01 (Vitis vinifera), 5'ss of exon 5
AATTTTTTGAAAATCCAGCATTCCGAGCTGATGGTCTAAAGATTTATCCAACTCTTGTGATTCGTGGAACTGGCCTTTATGAGCTCTGGAAAACTGGCAGgtacttattttatctagcacttgatattctag--attgctagtcttgtgttcactgttgtgtttgttctctagaactttttagtgagaacttaggccctgccaatgtttgttgtgtttcag
| ||||||||||  ||    ||  |||||||||| || || || |||||||| ||||| |||||||||||||| ||||||||||| |||||||| ||||||||   || | ||       |  |||  || |  | |||  | ||       |  |   |  ||     |  |  || |||   |                                    
AGTTTTTTGAAAGCCCTATGTTTAGAGCTGATGGGCTCAAAATATATCCAACACTTGTAATTCGTGGAACTGGGCTTTATGAGCTTTGGAAAACGGGCAGgtaaa-atgtcattcc-tgttcaataagctggcaactgcatggctcaatgagaaagcaataattacatccatgtcctgtttgcag------------------------------------

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|29682940|gb|CB679215.1|CB679215
EST:     ACTCTTGTGATTCGTGGAACTGGCCTTTATGAGCTCTGGAAAACTGGCAG                         ATACCGAAACTATCCACCTGAACTTCTGGTGGATATTGTTGCAAGAATTCT
genomic: ACTCTTGTGATTCGTGGAACTGGCCTTTATGAGCTCTGGAAAACTGGCAGgtacttattt ... tgtgtttcagATACCGAAACTATCCACCTGAACTTCTGGTGGATATTGTTGCAAGAATTCT
EST: gi|29666831|gb|CB663106.1|CB663106
EST:     CCTTTATGAGCTCTGGAAAACTGGCAG                         ATACCGAAACTATCCACCTGAACTTCTGGTGGATATTGTTGCAAGAATTCT
genomic: CCTTTATGAGCTCTGGAAAACTGGCAGgtacttattt ... tgtgtttcagATACCGAAACTATCCACCTGAACTTCTGGTGGATATTGTTGCAAGAATTCT
EST: gi|27577984|gb|CB000679.1|CB000679
EST:     ACTCTTGTGATTCGTGGAACTGGCCTTTATGAGCTCTGGAAAACTGGCAG                         ATACCGAAACTATCCACCTGAACTTCTGGTGGATATTGTTGCGAGAATTCT
genomic: ACTCTTGTGATTCGTGGAACTGGCCTTTATGAGCTCTGGAAAACTGGCAGgtacttattt ... tgtgtttcagATACCGAAACTATCCACCTGAACTTCTGGTGGATATTGTTGCAAGAATTCT
EST: gi|218500846|gb|FG954979.1|FG954979
EST:     CTGGAAAACTGGCAG                         ATACCGAAACTATCCACCTGAACTTCTGGTGGATATTGTTGCGAGAATTCT
genomic: CTGGAAAACTGGCAGgtacttattt ... tgtgtttcagATACCGAAACTATCCACCTGAACTTCTGGTGGATATTGTTGCAAGAATTCT
EST: gi|27576345|gb|CA999039.1|CA999039
EST:     ACTCTTGTGATTCGTGGAACTGGCCTTTATGAGCTCTGGAAAACTGGCAG                         ATACCGAAACTATCCACCTGAACTTCTGGTGGATATTGTTGCGAGAATTCT
genomic: ACTCTTGTGATTCGTGGAACTGGCCTTTATGAGCTCTGGAAAACTGGCAGgtacttattt ... tgtgtttcagATACCGAAACTATCCACCTGAACTTCTGGTGGATATTGTTGCAAGAATTCT

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: 64 (upstream exon), 70 (downstream exon)
Score: 15

AATTTTTTGAAAATCCAGCATTCCGAGCTGATGGTCTAAAGATTTATCCAACTCTTGTGATTCGTGGAACTGGCCTTTATGAGCTCTGGAAAACTGGCAGgtacttattt ... tgtgtttcagATACCGAAACTATCCACCTGAACTTCTGGTGGATATTGTTGCAAGAATTCTATCCATGGTACCACCTTGGACACGAGTTTACCGTGTACAAAGAGATATC




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