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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtctgtgatttcatggttgtactttgcactaggaaggccccgaatttgctaattgagaccttgttttggtcctgcagGATTTACATGATCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTATAACCATGCTTGTGCAGACTATGCCAAGCAGAAATTGTCAGCACCAAACT

Basic information

species Oryza sativa
transcript LOC_Os10g06130.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g06130.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G103430_T04 (Zea mays), 3'ss of exon 4
gtgtg-tctgtgatttcatggttgtact---ttgcactaggaaggccccgaatttgctaat--tgagaccttgttttggtcctgcagGATTTACATGATCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTATAACCATGCTTGTGCAGACTATGCCAAGCAGAAATTGTCAGCACCAAACT------
||||| | |||| |||| || ||||  |   ||| ||     | |  ||  |||  |||||  |||||   |||||        ||||||   ||||| |||| |||||||||||| |||||||||||||||||||| |||||||| || ||||||||||||| ||||||| | ||| | |||||||      
gtgtgctttgtggtttcgtgcttgttttcgtttgtacaccacaagttccagattcactaatattgagatgctgtttg-----cacaggatcagCATGACCCAAACCGTAACCGTGGCTTCCTCTTTGTTGAGTATTACAACCATGCCTGCGCAGACTATGCCAGGCAGAAACTTTCATCTCCAAACTTCAAGG

upper sequence: LOC_Os10g06130.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G103430_T05 (Zea mays), 3'ss of exon 3
gtgtg-tctgtgatttcatggttgtact---ttgcactaggaaggccccgaatttgctaat--tgagaccttgttttggtcctgcagGATTTACATGATCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTATAACCATGCTTGTGCAGACTATGCCAAGCAGAAATTGTCAGCACCAAACT
||||| | |||| |||| || ||||  |   ||| ||     | |  ||  |||  |||||  |||||   |||||        ||||||   ||||| |||| |||||||||||| |||||||||||||||||||| |||||||| || ||||||||||||| ||||||| | ||| | |||||||
gtgtgctttgtggtttcgtgcttgttttcgtttgtacaccacaagttccagattcactaatattgagatgctgtttg-----cacagGATCAGCATGACCCAAACCGTAACCGTGGCTTCCTCTTTGTTGAGTATTACAACCATGCCTGCGCAGACTATGCCAGGCAGAAACTTTCATCTCCAAACT

upper sequence: LOC_Os10g06130.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv15s0048g02700.t01 (Vitis vinifera), 3'ss of exon 4
gtgtgtctgtgatttca---tggttgt--actttgcactaggaaggccccga-atttgctaat-tgagaccttg-----ttttggtc--ctgcagGATTTACATGATCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTATAACCATGCTTGTGCAGACTATGCCAAGCAGAAATTGTCAGCACCAAACT
|||    | ||| || |   ||  | |  || ||    || ||| |    ||    |||| || |||||   |      ||||| |    | ||||||   ||  ||||||||||||| ||||| ||    |||||||||||||| ||| ||||||||||||| ||||  | ||||||| ||||     |||| |
gtgcagttttgaattgaaattgactatccaccttattttaagaatgaatagacgaatgcttatgtgagagtctaatgccttttgtttaattacagGATCCTCAAAATCCAAGCCGTAATCGTGGTTTTGCTTTTGTTGAGTATTACAACAATGCTTGTGCAGATTATGGGAGGCAGAAAATGTCTAGTTCAAATT

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|29663246|gb|CB659521.1|CB659521
EST:     ACATAATCCAGGGGAAGGGCCCAGGTGTTGTGAACATTGAGATGTTCAAG                         GATTTACATGATCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
genomic: ACATAATCCAGGGGAAGGGCCCAGGTGTTGTGAACATTGAGATGTTCAAGgtgtgtctgt ... ggtcctgcagGATTTACATGATCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
EST: gi|58604638|gb|CK015166.1|CK015166
EST:     ACATAATCCAGGGGAAGGGCCCAGGTGTTGTGAACATTGAGATGTTCAAG                         GATTTACATGATCCAAGCCGTAACCGCGGGTTCCTCTTTGTTGAGTATTAT
genomic: ACATAATCCAGGGGAAGGGCCCAGGTGTTGTGAACATTGAGATGTTCAAGgtgtgtctgt ... ggtcctgcagGATTTACATGATCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
EST: gi|33808240|gb|CF330009.1|CF330009
EST:     GGAAGGGCCCAGGTGTTGTGAACATTGAGATGTTCAAG                         GATTTACATGATCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
genomic: GGAAGGGCCCAGGTGTTGTGAACATTGAGATGTTCAAGgtgtgtctgt ... ggtcctgcagGATTTACATGATCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgcactaggaaggccccgaatttgctaattgagaccttgttttggtcctgcagGATTTACATGATCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTATAACCATGCTTGTGCAGACTATGCCAAGCAGAAATTGTCAGCACCAAACT
                        tgctaat  putative branch site (score: 2)
                           taattga  TA-rich tract