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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGTGGTCTTTTTGGCTGAGCTATTAGCAACTTGTTTGGGCTCTATTGATCCTGACTGTCATGCATCATTCTGAATCTATGAGGTCAGATACACTCTGAGgtgagatgtgccatggacatgaagtatcacgcatcttggtgtctaccagcaactgatagtgttctttag

Basic information

species Oryza sativa
transcript LOC_Os04g41100.4
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g41100.4 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G179097_T02 (Zea mays), 5'ss of exon 7
CCGTGGTCTTTTTGGCTGAGCTATTAGCAACTTGTTTGGGCTCTATTGATCCTGACTGTCATGCATCA--------TTCTGAATCTATGAGGTCAGATACACTCTGAGgtgagatgtgccatggacatgaagtatcacg-catcttggtgtctaccagcaactgatagtgttctttag---
       |||||||||||| |||  |||| |||| |||||  || |   |||| ||||| |||| |||        | |||| |  ||||||| |||||   |||||||||||  |||||||||||||||||||||||  | ||| |||||||| |||||||||||||||||||||||   
-------CTTTTTGGCTGAACTAGAAGCA-CTTGATTGGGTCCTGTCCGTCCTAACTGTTATGCTTCACACTGAAATCCTGAGTTCATGAGGTTAGATATCTTCTGAGgtgag--gtgccatggacatgaagtatcacatcttctcggtgtctagcagcaactgatagtgttctttagcag

upper sequence: LOC_Os04g41100.4 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G179097_T08 (Zea mays), 5'ss of exon 7
CCGTGGTCTTTTTGGCTGAGCTATTAGCAACTTGTTTGGGCTCTATTGATCCTGACTGTCATGCATCA--------TTCTGAATCTATGAGGTCAGATACACTCTGAGgtgagatgtgccatggacatgaagtatcacg-catcttggtgtctaccagcaactgatagtgttctttag-------------------------------------------------------------------
       |||||||||||| |||  |||| |||| |||||  || |   |||| ||||| |||| |||        | |||| |  ||||||| |||||   |||||||||||  |||||||||||||||||||||||  | ||| |||||||| |||||||||||||||||||||||                                                                   
-------CTTTTTGGCTGAACTAGAAGCA-CTTGATTGGGTCCTGTCCGTCCTAACTGTTATGCTTCACACTGAAATCCTGAGTTCATGAGGTTAGATATCTTCTGAGgtgag--gtgccatggacatgaagtatcacatcttctcggtgtctagcagcaactgatagtgttctttagcaggcttggtaccggtttaaatggataaggtttctccttgtggcccatcatagaaattttgttgcag

upper sequence: LOC_Os04g41100.4 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G139038_T01 (Zea mays), 5'ss of exon 7
CCGTGGTCTTTTTGGCTGAGCTATTAGCAACTTGTTTGGGCTCTATTGATCCTGACTGTCATGCATCATTCTGAATCTATGAGGTCAGATACACTCTGAGgtgagatgtgccatggacatgaagtatcacg-catcttggtgtctaccagcaactgatagtgttctttag---
|||||| |||||||||||| |||  || |  |  || |    || |   | || ||||| |||| |||  ||||||| | ||||||||||    |||||||||||  |||||||||||||||||||||||  | ||| |||||||| |||| ||||||||||||||||||   
CCGTGGGCTTTTTGGCTGAACTAAGAGTACTTGATTGGATTCCTGTCCGTACTAACTGTTATGCTTCACCCTGAATCCACGAGGTCAGATGTCTTCTGAGgtgag--gtgccatggacatgaagtatcacatcttctcggtgtctagcagcgactgatagtgttctttagcag

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|29631145|gb|CB636154.1|CB636154
EST:     CCTGACTGTCATGCATCATTCTGAATCTATGAGGTCAGATACACTCTGAG                         --G-CATGGTGCTGGTTTAAGTTGATAGGTACCTGGCCCATCATAGAAATT
genomic: CCTGACTGTCATGCATCATTCTGAATCTATGAGGTCAGATACACTCTGAGgtgagatgtg ... tgttctttagCAGGCATGGTGCTGGTTTAAGTTGATAGGTACCTGGCCCATCATAGAAATT
EST: gi|44675738|gb|CR289172.1|CR289172
EST:     CCTGACTGTCATGCATCATTCTGAATCTATGAGGTCAGATACACTCTGAG                         CAGGCATGGTGCTGGTT-AAGTTGATAGG-ACCTG
genomic: CCTGACTGTCATGCATCATTCTGAATCTATGAGGTCAGATACACTCTGAGgtgagatgtg ... tgttctttagCAGGCATGGTGCTGGTTTAAGTTGATAGGTACCTG
EST: gi|29626550|gb|CB631561.1|CB631561
EST:     CCTGACTGTCATGCATCATTCTGAATCTATGAGGTCAGATACACTCTGAG                         CAGGCATGGTGCTGGTTTAAGTTGATAGGTACCTGGCCCATCATAGAAATT
genomic: CCTGACTGTCATGCATCATTCTGAATCTATGAGGTCAGATACACTCTGAGgtgagatgtg ... tgttctttagCAGGCATGGTGCTGGTTTAAGTTGATAGGTACCTGGCCCATCATAGAAATT
EST: gi|29631235|gb|CB636244.1|CB636244
EST:     CCTGACTGTCATGCATCATTCTGAATCTATGAGGTCAGATACACTCTGAG                         --G-CATGGTGCTGGTTTAAGTTGATAGGTACCTGGCCCATCATAGAAATT
genomic: CCTGACTGTCATGCATCATTCTGAATCTATGAGGTCAGATACACTCTGAGgtgagatgtg ... tgttctttagCAGGCATGGTGCTGGTTTAAGTTGATAGGTACCTGGCCCATCATAGAAATT
EST: gi|88979130|gb|CI025633.1|CI025633
EST:     CCTGACTGTCATGCATCATTCTGAATCTATGAGGTCAGATACACTCTGAG                         --G-CATGGTGCTGGTTTAAGTTGATAGGTACCTGGCCCATCATAGAAATT
genomic: CCTGACTGTCATGCATCATTCTGAATCTATGAGGTCAGATACACTCTGAGgtgagatgtg ... tgttctttagCAGGCATGGTGCTGGTTTAAGTTGATAGGTACCTGGCCCATCATAGAAATT
EST: gi|29631272|gb|CB636281.1|CB636281
EST:     CCTGACTGTCATGCATCATTCTGAATCTATGAGGTCAGATACACTCTGAG                         --G-CATGGTGCTGGTTTAAGTTGATAGGTACCTGGCCCATCATAGAAATT
genomic: CCTGACTGTCATGCATCATTCTGAATCTATGAGGTCAGATACACTCTGAGgtgagatgtg ... tgttctttagCAGGCATGGTGCTGGTTTAAGTTGATAGGTACCTGGCCCATCATAGAAATT

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: 73 (upstream exon), 54 (downstream exon)
Score: 5

CCGTGGTCTTTTTGGCTGAGCTATTAGCAACTTGTTTGGGCTCTATTGATCCTGACTGTCATGCATCATTCTGAATCTATGAGGTCAGATACACTCTGAGgtgagatgtg ... tgttctttagCAGGCATGGTGCTGGTTTAAGTTGATAGGTACCTGGCCCATCATAGAAATTTTGTTGCAGGATTAACTCCAACCAGATTGATCATAAAAGCAGTCTAATC




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