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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctggtcatttaacacatttaccattttattgattattccaaatgatgtatataccagtctaattcccaaacatatatgccgccccattatggatttgcagAGACATTTGTACGAGCTGACGGTGCATTTATCCCATTTGCTGATGACTTTGACATTTCCACCGTCACGACTGTAGTTAGGGGAGTCGGTGACATTGGGGA

Basic information

species Oryza sativa
transcript LOC_Os04g52479.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g52479.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G102346_T01 (Zea mays), 3'ss of exon 4
ctggtcatttaacacatttaccattttattgattattccaaatg-atgtatataccagtctaattcccaaacatatatgccgccccattatggatttgcagAGACATTTGTACGAGCTGACGGTGCATTTATCCCATTTGCTGATGACTTTGACATTTCCACCGTCACGACTGTAGTTAGGGGAGTCGGTGACATTGGGGA
 || |     |  |  |  || || ||  | |||     | ||  ||| ||      |||| |||||||||||||  |||       | |||    |||||||||||||||||| || ||||| ||||| |||||||||||| | ||||| ||||| ||||| ||||| |||  ||||||||| || ||||||||||||||
atgattccaaatgatgtacacaatgtt-ctaattcccaaacatacatgcatgccatggtctgattcccaaacatacttgctatgttgtaatgagcctgcagAGACATTTGTACGCGCCGACGGGGCATTCATCCCATTTGCTCACGACTTCGACATCTCCACAGTCACAACTACAGTTAGGGGTGTTGGTGACATTGGGGA

upper sequence: LOC_Os04g52479.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G033724_T02 (Zea mays), 3'ss of exon 4
-ctggtcatttaacacatttaccattttattgattattccaaatgatgtatataccagtctaattcccaaacatatatgccgccccattatggatttgcagAGACATTTGTACGAGCTGACGGTGCATTTATCCCATTTGCTGATGACTTTGACATTTCCACCGTCACGACTGTAGTTAGGGGAGTCGGTGACATTGGGGA
 ||| | |||  | |   ||  ||   | ||  | ||||| ||  ||  ||       |||||||||||||||||  |||       | ||| || |||||||||||||||||| ||||| || ||||| |||||||||||| ||||||||||||| ||||| ||||| |||  ||||||||| || ||||| ||||||||
gctgatgattccaaatgatttacacaatgttc-taattcccaaacatacatgccatgttctaattcccaaacatacgtgctatgttctaatgaatctgcagAGACATTTGTACGTGCTGATGGGGCATTCATCCCATTTGCTCATGACTTTGACATCTCCACAGTCACAACTACAGTTAGGGGTGTTGGTGATATTGGGGA

upper sequence: LOC_Os04g52479.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G18300.1 (Glycine max), 3'ss of exon 4
-----------ctggtcatttaacacatttacc--attttattgattattccaaatgatgtatataccagtctaattcccaaacat-atatgccgccccattatggatttgcagAGACATTTGTACGAGCTGACGGTGCATTTATCCCATTTGCTGATGACTTTGACATTTCCACCGTCACGACTGTAGTTAGGGGAGTCGGTGACATTGGGGA
            | |   | |||   ||||||     ||  |||  | ||       | | ||   ||    || | | |   | | ||  | |      |  |   | ||||||||| |||||  ||||||| |||||||| || || |||||||||||||||||||| ||||| || || |||  ||| ||||| || || || ||||| ||
gtaacataaatttaggagtctaattgatttacttgggttacttgcattttgttccccacgcatgctcc---ttagtcctcgctcgtcatgagtcatgatgtgtttcttgtgcagAGACTTTTGTGAGAGCTGATGGTGCATTCATTCCTTTTGCTGATGACTTTGACATGTCCACTGTTACTACTTCAGTGAGGGGTGTTGGAGATATTGGTGA

upper sequence: LOC_Os04g52479.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA15G40700.1 (Glycine max), 3'ss of exon 4
---ctggtcatttaacacatttaccattttattgattattccaaatgatgtatataccagtctaattcccaaacat-atatgccgccccattatggatttgcagAGACATTTGTACGAGCTGACGGTGCATTTATCCCATTTGCTGATGACTTTGACATTTCCACCGTCACGACTGTAGTTAGGGGAGTCGGTGACATTGGGGA
        ||||| |  |  ||  || |||        || ||     |   || ||||  |  |  |  |  | | |  || |     || ||   | ||||||||| |||||  ||||||| |||||||| || || |||||||||||||||||||| ||||| || || |||  ||| ||||| || || || ||||| ||
aattcaaacatttcat-ctcttttcactttcacacccctttcattcctt---taaaccaaacatacccttagtcctcacttgtcatgatatgattcttgtgcagAGACTTTTGTGAGAGCTGATGGTGCATTCATTCCTTTTGCTGATGACTTTGACATGTCCACTGTTACTACTTCAGTGAGGGGTGTTGGAGATATTGGTGA

upper sequence: LOC_Os04g52479.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA20G02500.1 (Glycine max), 3'ss of exon 3
ctggtcatttaacacatttaccattttattgattattccaaatgatgtatataccagtctaattcccaa-acatatatgccgccccattatggatttgcagAGACATTTGTACGAGCTGACGGTGCATTTATCCCATTTGCTGATGACTTTGACATTTCCACCGTCACGACTGTAGTTAGGGGAGTCGGTGACATTGGGGA
 |  || | |  || ||||     || ||   ||   |  |    | | | |      || |  |   |  |||  |     |    || |    ||||||| |||||||| |||||||| || ||||| ||||||||||| || || ||  | ||   ||  || |  ||    || |  || || || || || || ||
gttttcttatttcaaatttgttggtt-atgattttggcttagaattttctgttgggtcctgacccatgacgcatgcacattacaattttgttatcttgcagAAACATTTGTGCGAGCTGATGGGGCATTCATCCCATTTGCAGAAGATTTCAATATGAACAATGTAATCACAACTGTAAAAGGTGTAGGGGAGATCGGTGA

upper sequence: LOC_Os04g52479.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA07G34800.1 (Glycine max), 3'ss of exon 4
--ctggtcatttaacacatttaccatttta-ttgattattccaaatgatgtatataccagtctaattcccaaacatatatgccgccccattatggatttgcagAGACATTTGTACGAGCTGACGGTGCATTTATCCCATTTGCTGATGACTTTGACATTTCCACCGTCACGACTGTAGTTAGGGGAGTCGGTGACATTGGGGA
  |   ||| ||       |||  |||||   | |  |||     ||  ||    |||    | | | |   ||||  |     |    || |    ||||||| |||||||| |||||||| || ||||| ||||||||||| || || ||  | ||   ||  || |  ||    || |  || || || || ||  | ||
ctcatttcaattttgttggttatgattttggcttagaattttctgtgg-gtcctgacc--cttgactgctgcacatgcacattacaattttgttatcttgcagAAACATTTGTGCGAGCTGATGGGGCATTCATCCCATTTGCAGAAGATTTCAATATGAACAATGTAATCACAACTGTAAAAGGTGTAGGGGAGATCAGTGA

upper sequence: LOC_Os04g52479.3 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv19s0027g00520.t01 (Vitis vinifera), 3'ss of exon 3
ctggtcatttaacacatttaccattttattgattatt--ccaaatgatgtatataccagtctaattcccaaacatatatgccgccccattatggatttgcagAGACATTTGTACGAGCTGACGGTGCATTTATCCCATTTGCTGATGACTTTGACATTTCCACCGTCACGACTGTAGTTAGGGGAGTCGGTGACATTGGGGA
      ||| |  |  || || | ||  ||    | |      || || |    | |     ||  ||  |  | | ||  ||      |    ||||||||||||||||||  |||| || || ||||| || |||||||||||||| ||||||||   |||  | || ||  | || |  || || || || || || ||
gataaaattgactattttgacaaattggtttcccagtaatttgataatcttgtcatctcctgaaccccatagtacaaattacggtttgctgc--atttgcagAGACATTTGTGAGAGCGGATGGGGCATTCATACCATTTGCTGATGATTTTGACATGAGCACAATAACAACATTGGTAAAAGGTGTAGGAGAGATAGGAGA

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|2428270|gb|C72733.1|C72733
EST:     TTTCATCACAGATGACGTTTGGTATGGAATCTATGCTGGAACAAACCCAG                         AGACATTTGTACGAGCTGACGGTGCATTTATCCCATTTGCTGATGACTTTG
genomic: TTTCATCACAGATGACGTTTGGTATGGAATCTATGCTGGAACAAACCCAGgtagagcagt ... ggatttgcagAGACATTTGTACGAGCTGACGGTGCATTTATCCCATTTGCTGATGACTTTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtatataccagtctaattcccaaacatatatgccgccccattatggatttgcagAGACATTTGTACGAGCTGACGGTGCATTTATCCCATTTGCTGATGACTTTGACATTTCCACCGTCACGACTGTAGTTAGGGGAGTCGGTGACATTGGGGA
           gtctaat  putative branch site (score: 3)
                      aaacatatat  TA-rich tract