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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCAGTGGCATCTTCAGCCAATCTTTGGGCCCTTATTATGGACGCGGGAACTGGGTTCACATCCCAAGTTTATGAACTCTCACCAATATTTCTTCATAAGgtactcttactcttgagcaaagattccctcttttctctggagcgttctgagttgcctattcttgtacttttag

Basic information

species Oryza sativa
transcript LOC_Os01g56580.2
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56580.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G116086_T01 (Zea mays), 5'ss of exon 13
CTCAGTGGCATCTTCAGCCAATCTTTGGGCCCTTATTATGGACGCGGGAACTGGGTTCACATCCCAAGTTTATGAACTCTCACCAATATTTCTTCATAAGgtac--tctt-actcttgagcaaag-attccctcttttctctggagcgttc-tgagttgc------ctattcttgtacttttag
 ||||| ||||||||||||||||||||||| || |||||||| || || ||||| |||||||||||||| |||||||| ||||| ||||| ||||||||||||   |||  | |||   ||| ||   |   |||   |   |   | ||  | || | |      || |||||| |||||   
TTCAGTAGCATCTTCAGCCAATCTTTGGGCTCTCATTATGGATGCAGGGACTGGTTTCACATCCCAAGTATATGAACTGTCACCCATATTCCTTCATAAGgtatggtctcgattctcatgcatagtgctttttctaagcaaggctacatttataagctacaagtgtcttttcttgcactttag-

upper sequence: LOC_Os01g56580.1 (Oryza sativa), 5'ss of exon 13
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 5'ss of exon 13
CTCAGTGGCATCTTCAGCCAATCTTTGGGCCCTTATTATGGACGCGGGAACTGGGTTCACATCCCAAGTTTATGAACTCTCACCAATATTTCTTCATAAGgt-actcttactcttgagcaaagattccctcttttctctgga-gcgttctgagttgcct---attcttgtacttttag-----------------
||  ||||| |||||| | ||||||||||||||||||||||| |||||||| || |  |  ||||| || |||||||| ||| |  | || || |||||||| | | ||  || || |   |  |    | | |||| ||   | ||||     | |||   | |  ||  |||| |                  
CTGTGTGGCCTCTTCATCAAATCTTTGGGCCCTTATTATGGATGCGGGAACAGGTTATAGTTCCCAGGTCTATGAACTATCAGCTGTCTTCCTGCATAAGgttattttttttcatgtgttgatttctattatcttctgtgagtgggttcatgcatacctgatactactgacctttcacttttggattttcactag

upper sequence: LOC_Os01g56580.1 (Oryza sativa), 5'ss of exon 13
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 5'ss of exon 12
CTCAGTGGCATCTTCAGCCAATCTTTGGGCCCTTATTATGGACGCGGGAACTGGGTTCACATCCCAAGTTTATGAACTCTCACCAATATTTCTTCATAAGgta--ctcttactc-ttgagcaaagattcc-ctcttttctctggagcgttctgagttgcctattcttgtacttttag--------------------------
|   ||||| ||||   | ||||| ||||| ||||||||||| ||||| || || |||||| |||||||||| || || || |   | || || |||||||||    || | |  |||   |  | |||  ||  ||  | | ||  | |||   | |||   |  | |  |   |                           
CAGTGTGGCTTCTTGTACAAATCTGTGGGCTCTTATTATGGATGCGGGGACGGGATTCACAGCCCAAGTTTACGAGCTGTCTCATGTTTTCCTCCATAAGgtaagtgctcagtgattgtttagtgtttctgcttgttgtttttgaaggatctagttggccctcttcttttgtggaaattaacatggtcattggtattctacag

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|58683649|gb|CK072336.1|CK072336
EST:     CTGGGTTCACATCCCAAGTTTATGAACTCTCACCAATATTTCTTCATAAG                         GATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCG
genomic: CTGGGTTCACATCCCAAGTTTATGAACTCTCACCAATATTTCTTCATAAGgtactcttac ... gtacttttagGATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCG
EST: gi|218504544|gb|FG949399.1|FG949399
EST:     CCAATATTTCTTCATAAG                         GATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCG
genomic: CCAATATTTCTTCATAAGgtactcttac ... gtacttttagGATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCG
EST: gi|218502457|gb|FG966789.1|FG966789
EST:     CACCAATATTTCTTCATAAG                         GATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCG
genomic: CACCAATATTTCTTCATAAGgtactcttac ... gtacttttagGATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCG
EST: gi|58598509|gb|CK009037.1|CK009037
EST:     CTGGGTTCACATCCCAAGTTTATGAACTCTCACCAATATTTCTTCATAAG                         GATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCG
genomic: CTGGGTTCACATCCCAAGTTTATGAACTCTCACCAATATTTCTTCATAAGgtactcttac ... gtacttttagGATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCG
EST: gi|12623249|gb|AU173462.1|AU173462
EST:     CTGGGTTCACATCCCAAGTTTATGAACTCTCACCAATATTTCTTCATAAG                         GATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCG
genomic: CTGGGTTCACATCCCAAGTTTATGAACTCTCACCAATATTTCTTCATAAGgtactcttac ... gtacttttagGATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCG
EST: gi|58609933|gb|CK037966.1|CK037966
EST:     CTGGGTTCACATCCCAAGTTTATGAACTCTCACCAATATTTCTTCATAAG                         GATTGGATTATGGAGCAATGGGAGAATAATTACTACATC
genomic: CTGGGTTCACATCCCAAGTTTATGAACTCTCACCAATATTTCTTCATAAGgtactcttac ... gtacttttagGATTGGATTATGGAGCAATGGGAGAATAATTACTACATC
EST: gi|66914155|gb|CX101003.1|CX101003
EST:     TGGGTTCACATCCCAAGTTTATGAACTCTCACCAATATTTCTTCATAANG                         GATGGGAT-ATGGAGCAATGGGAGAAATAAT-ACTACATCAGTGCCATAG
genomic: TGGGTTCACATCCCAAGTTTATGAACTCTCACCAATATTTCTTCATAA-Ggtactcttac ... gtacttttagGATTGGATTATGGAGCAATGGGAGAA-TAATTACTACATCAGTGCCATAG
EST: gi|5005377|gb|AU070539.1|AU070539
EST:     CTGGGTTCACATCCCAAGTTTATGAACTCTCACCAATATTTCTTCATAAG                         GATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAANTGCCATAGC
genomic: CTGGGTTCACATCCCAAGTTTATGAACTCTCACCAATATTTCTTCATAAGgtactcttac ... gtacttttagGATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAG-TGCCATAGC
EST: gi|58609988|gb|CK038021.1|CK038021
EST:     GTTTATGAACTCTCACCAATATTTCTTCATAAG                         GATTGGATTATGGAGCAATGGGAGAATGATTACTACATCAGTGCCATAGCG
genomic: GTTTATGAACTCTCACCAATATTTCTTCATAAGgtactcttac ... gtacttttagGATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCG