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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaacaaaatgaaccatgctattgttgaatggaaaatggattactttacagtatttccaatatctcaaatattctgacagcactattatgttgtgttgcagCTGGCCAGGAGAGGTTTAGGACAATTACTAGTTCTTACTACAGAGGTGCTCAAGGCATTATTCTAG

Basic information

species Oryza sativa
transcript LOC_Os10g31830.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g31830.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G809265_T02 (Zea mays), 3'ss of exon 2
-aaacaaaatgaaccatgctattgt---tgaatggaaaatggattactttacagtatttccaatatctcaaatattctgacagcactattatgttgtgttgcagCTGGCCAGGAGAGGTTTAGGACAATTACTAGTTCTTACTACAGAGGTGCTCAAGGCATTATTCTAG
 ||||    |      |  |    |   | |||| ||    ||   | |  || | |    || |    |||||       |  |||  ||   ||   |||||||||||||||||||||||||||||| |||||||||||||||||||||||||| || |||||| |||
aaaaccttgtctctttttttcccttacttcaatgtaaggcagagctcctgccactttccttaaaaa--taaataaataataaatact--tacaatgctctgcagCTGGCCAGGAGAGGTTTAGGACAATAACTAGTTCTTACTACAGAGGTGCTCAGGGAATTATTTTAG

upper sequence: LOC_Os10g31830.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G075051_T01 (Zea mays), 3'ss of exon 2
-aaacaaaa---tgaaccatgctattgttgaatggaaaatggattactttacagtatttccaatatctcaaatattctgacagcactattatgttgtgttgcagCTGGCCAGGAGAGGTTTAGGACAATTACTAGTTCTTACTACAGAGGTGCTCAAGGCATTATTCTAG
 |  |||||   |   |  || | ||  | | |  ||        |  | |   |    |    || |||||||     | |  |    ||   ||  |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| || ||||||||||
gaggcaaaaccttctgctgtgttttttcttacttcaatgcaaggcagat-atcctgccactt-catttcaaataaataaataa-atacatacaatgc-ttgcagCTGGCCAGGAGAGGTTTAGGACAATTACTAGTTCTTACTACAGAGGTGCTCAGGGAATTATTCTAG

upper sequence: LOC_Os10g31830.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv08s0007g04740.t01 (Vitis vinifera), 3'ss of exon 2
aaacaaaatgaaccatgctattgttgaatggaaaa----tggattactttacagtatttccaat--atctcaaatattctgacagcactattatgttgtgttgcagCTGGCCAGGAGAGGTTTAGGACAATTACTAGTTCTTACTACAGAGGTGCTCAAGGCATTATTCTAG
  |    |  |   ||| | |  ||  |||         |    |  | || || | |    ||  ||    | || ||| |   || |||       || ||||||||| ||||||||||| || ||| | || || |||||||| |||||||| ||||| |||||||| |
--atgttactagttatgttgtcatttcatgcttgtctcttttgcttttctagagcaatgtggatggattctcattagtcttaactcattatggc----tgatgcagCTGGACAGGAGAGGTTCAGAACATTGACAAGCTCTTACTATAGAGGTGCCCAAGGGATTATTCTTG

upper sequence: LOC_Os10g31830.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv13s0019g05190.t01 (Vitis vinifera), 3'ss of exon 2
aaacaaaatgaaccatgctattgttgaatggaaaatggattactt-tacagtatttcca-atatctcaaatattctgacagcactattatgttgtg-ttgcagCTGGCCAGGAGAGGTTTAGGACAATTACTAGTTCTTACTACAGAGGTGCTCAAGGCATTATTCTAG
     |||   | |||   ||||   | | |  || |    | || | || | |||  | | |  |||| |  | ||||| || ||||   || || |||||||||| |||||||||||| | ||| | || |  ||||| || |||||||| || |||||||||||||
-gtagaaacatagcata--attgggaactagcgaaggtgacatttgtgcattttttaaagacaattcaatttgtttgacaacaatattcctttttggttgcagCTGGACAGGAGAGGTTTGGAACATTGACAAACTCTTATTATAGAGGTGCACATGGCATTATTCTAG

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|88399284|gb|CI618474.1|CI618474
EST:     GTTCCTTACGATTGGTGGAAAGAAATTGAAGCTGACAATATGGGATAGTG                         CTGGCCAGGAG
genomic: GTTCCTTACGATTGGTGGAAAGAAATTGAAGCTGACAATATGGGATACTGgtgagttcat ... tgtgttgcagCTGGCCAGGAG
EST: gi|58675259|gb|CK063946.1|CK063946
EST:     GTTCCTTACGATTGGTGGAAAGAAATTGAAGCTGACAATATGGGATACTG                         CTGGCCAGGAGAGGTTTAGGACAATTACTAGTTCTTACTACAGAGGTGCTC
genomic: GTTCCTTACGATTGGTGGAAAGAAATTGAAGCTGACAATATGGGATACTGgtgagttcat ... tgtgttgcagCTGGCCAGGAGAGGTTTAGGACAATTACTAGTTCTTACTACAGAGGTGCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacagtatttccaatatctcaaatattctgacagcactattatgttgtgttgcagCTGGCCAGGAGAGGTTTAGGACAATTACTAGTTCTTACTACAGAGGTGCTCAAGGCATTATTCTAG
                         ttctgac  putative branch site (score: 2)
            aatatctcaaatatt  TA-rich tract