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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaatttttattagaccaatgctgtctttggcccattatcatgacataattaatttctgaatactaaatagtaaagcttctctttcctgcaacattttgcagATATCGAAGGGTTTGTTAGACAAATATGGCCCTGATAGGGTTCTTGACACACCAATCACAGAG

Basic information

species Oryza sativa
transcript LOC_Os08g42410.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g42410.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G043198_T02 (Zea mays), 3'ss of exon 4
gtgagtaatttttatta-gaccaatgctgtctttggcccattatcatgacat-----aattaatttctgaatactaaata-gtaaagcttctctttcctgcaacattttgcagATATCGAAGGGTTTGTTAGACAAATATGGCCCTGATAGGGTTCTTGACACACCAATCACAGAG
|| |||||| |||   | ||   |||||   |||   || |   | || ||      || |||| |   |||  |       | |||||||||||   ||       ||||||||||| ||||||||| | ||||| |||||||| ||||||||||| || || || ||||| |||
gtcagtaatatttccaaagatttatgcttcattttttccctccccgtggcaactgaaaagtaatatacaaatgttgccggtattaagcttctcttcattg-------ttgcagATATCCAAGGGTTTGCTTGACAAGTATGGCCCCGATAGGGTTCTCGATACTCCGATCACTGAG

upper sequence: LOC_Os08g42410.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G043198_T03 (Zea mays), 3'ss of exon 4
gtgagtaatttttatta-gaccaatgctgtctttggcccattatcatgacat-----aattaatttctgaatactaaata-gtaaagcttctctttcctgcaacattttgcagATATCGAAGGGTTTGTTAGACAAATATGGCCCTGATAGGGTTCTTGACACACCAATCACAGAG---
|| |||||| |||   | ||   |||||   |||   || |   | || ||      || |||| |   |||  |       | |||||||||||   ||       ||||||||||| ||||||||| | ||||| |||||||| ||||||||||| || || || ||||| |||   
gtcagtaatatttccaaagatttatgcttcattttttccctccccgtggcaactgaaaagtaatatacaaatgttgccggtattaagcttctcttcattg-------ttgcagATATCCAAGGGTTTGCTTGACAAGTATGGCCCCGATAGGGTTCTCGATACTCCGATCACTGAGGTT

upper sequence: LOC_Os08g42410.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv01s0146g00310.t01 (Vitis vinifera), 3'ss of exon 5
gtgagta--atttttattagaccaatgctgtctttggcccattatcatgacataattaatttctgaatactaaatagtaaagcttctctttcctgcaacattttgcagATATCGAAGGGTTTGTTAGACAAATATGGCCCTGATAGGGTTCTTGACACACCAATCACAGAG
|| |||   ||  ||  |  | | ||  | |  ||    | |    |  |   |  || ||| | | | | |  |||| |  | |   || ||| ||   |  |  |||| || || ||  | || || |||||||||||||| |||||||| || || ||||||||||||
gttagtggcatgctttatgaatccataattttctttttgcttggaaaccattcatatatttttttagttc-atctagtgat-cataatttgccttcattttcatatagATTTCTAAAGGGCTTTTGGAGAAATATGGCCCTGAGAGGGTTCTGGATACCCCAATCACAGAG

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|428335|gb|D24483.1|D24483
EST:     TGGGATGAAGAGGTTGGAGAATACCAAGGGGCATATAAG                         ATATCGAAGGGTTTGTTAGACAAATATGGCCCTGATAGGGTTCTTGACACA
genomic: TGGGA-GAAGAGGTTGGAGAATACCAAGGGGCATATAAGgtgagtaatt ... cattttgcagATATCGAAGGGTTTGTTAGACAAATATGGCCCTGATAGGGTTCTTGACACA
EST: gi|218484233|gb|FG953202.1|FG953202
EST:     GGGCATATAAG                         ATATCGAAGGGTTTGTTAGACAAATATGGCCCTGATAGGGTTCTTGACACA
genomic: GGGCATATAAGgtgagtaatt ... cattttgcagATATCGAAGGGTTTGTTAGACAAATATGGCCCTGATAGGGTTCTTGACACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattaatttctgaatactaaatagtaaagcttctctttcctgcaacattttgcagATATCGAAGGGTTTGTTAGACAAATATGGCCCTGATAGGGTTCTTGACACACCAATCACAGAG
              tactaaa  putative branch site (score: 1)
            aatactaaatagtaaa  TA-rich tract