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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattatccttgttcataccaatttgttttcctacttgttttttttttcctgagatgctttgacatgaaggggaaccattttcccaattcttttctagGATCTTTTCATTATTGGAGCTACAAATAGGCCTGACCTTCTTGATTCTGCACTTCTCCGGCCTGGCCGCTTTGATAAGCTTCTCTATGTTGGTGTAAATT

Basic information

species Oryza sativa
transcript LOC_Os04g52690.3
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g52690.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G058141_T02 (Zea mays), 3'ss of exon 3
gtattatccttgttcatacca-atttgttttcctacttgttttttttttcctgagatgctttgacatgaaggggaaccattttcccaattcttttctagGATCTTTTCATTATTGGAGCTACAAATAGGCCTGACCTTCTTGATTCTGCACTTCTCCGGCCTGGCCGCTTTGATAAGCTTCTCTATGTTGGTGTAAATT
|| ||  |||  | |||  || | |||||||  || |||   ||| ||      || |||| |||||| ||             | || |   || ||||| |||||||||||||| ||||| |||||||||||||||||||||||||| ||||| || | ||| || || || |||||||| ||||| ||||||||| 
gtgtttccctactccatgtcatacttgtttt--taattgccatttcttc-----gacgctt-gacatggaga------------caaaattgattgtagGACCTTTTCATTATTGGGGCTACCAATAGGCCTGACCTTCTTGATTCTGCCCTTCTTCGCCTTGGTCGGTTCGACAAGCTTCTTTATGTCGGTGTAAATA

upper sequence: LOC_Os04g52690.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G445617_T01 (Zea mays), 3'ss of exon 12
gtattatccttgttcatacca-atttgttttcctacttgttttttttttcctgagatgctttgacatgaaggggaaccattttcccaattcttttctagGATCTTTTCATTATTGGAGCTACAAATAGGCCTGACCTTCTTGATTCTGCACTTCTCCGGCCTGGCCGCTTTGATAAGCTTCTCTATGTTGGTGTAAATT
|| ||  |||  | |||  || | |||||||  || |||   ||| ||      |  |||| |||||| ||          || | || |   || ||||| |||||||||||||| ||||| |||||||||||||||||||||||||| ||||| || ||||| || || || |||||||| ||||| ||||||||| 
gtgtttccctactccatgtcatacttgtttt--taattgccatttcttc-----ggcgctt-gacatgtag------ttcctttcaaaattgattgtagGACCTTTTCATTATTGGGGCTACCAATAGGCCTGACCTTCTTGATTCTGCCCTTCTTCGCCCTGGTCGGTTCGACAAGCTTCTTTATGTCGGTGTAAATA

upper sequence: LOC_Os04g52690.1 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv07s0104g01610.t01 (Vitis vinifera), 3'ss of exon 12
---------------------------------------------gtattatcct-tgttcataccaatttgttttc-ctacttgttttttttttcctgagatgctttgacatgaa------ggggaaccattttcccaattc--ttttctagGATCTTTTCATTATTGGAGCTACAAATAGGCCTGACCTTCTTGATTCTGCACTTCTCCGGCCTGGCCGCTTTGATAAGCTTCTCTATGTTGGTGTAAATT
                                             || |  | || |||||||     ||  || || ||  || |||| |||||||     |  ||||     ||           ||  ||||  |  |    ||| | ||||  | || ||||| || || |  || || ||||| ||| ||||  ||||||||||||| |||||||| ||||| ||||| || |||||||| || || |
gttctttaaacttcttaatatattcattttccttcttttttttcagtttctttctatgttcatgttgtttctttctctctttttcttttctttttcccctccttttttgcttctaatcccacaatacactcttttttctttctggtttaccagGACTTGTTTATTATAGGGGCAAGCAACAGACCTGATCTTATTGACCCTGCACTTCTCCGACCTGGCCGATTTGACAAGCTGCTATATGTTGGAGTTAACT

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|29675898|gb|CB672173.1|CB672173
EST:     TTGCTTGTGGAGATTGATGGGTTAAGCGATAACAGTCAG                         GATCTTTTCATTATTGGAGCTACAAATAGGCCTGACCTTCTTGATTCTGCA
genomic: TTGCTTGTGGAGATTGATGGGTTAAGCGATAACAGTCAGgtattatcct ... tcttttctagGATCTTTTCATTATTGGAGCTACAAATAGGCCTGACCTTCTTGATTCTGCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttcctgagatgctttgacatgaaggggaaccattttcccaattcttttctagGATCTTTTCATTATTGGAGCTACAAATAGGCCTGACCTTCTTGATTCTGCACTTCTCCGGCCTGGCCGCTTTGATAAGCTTCTCTATGTTGGTGTAAATT
              ctttgac  putative branch site (score: 4)
                                ccattttcccaattct  putative PPT
                                          aattctttt  TA-rich tract