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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggttgatttattatacaggtttggtttgcctgtgaaaagggagaaaaatgagaaccaaattgatagaatgttgtgttctgtgactatgaaaagggagaaaaatgataaccaaattgatggaatgtttgtgttctgtgaactgcagTTGCTCAGTACTGCGATAATGTGGAGATGTGTAGGCTCACAGAGCAAGTCGTGTTCTCAGACCCATACATGCTCGCCAAATACAATCGTTGCACATCACC

Basic information

species Oryza sativa
transcript LOC_Os04g57400.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g57400.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G464137_T03 (Zea mays), 3'ss of exon 2
gttggttgatttattatacaggtttggtttgcctgtgaaaagggagaaaaatgagaaccaaattgatagaatgttg---tgtt-ctgtgactatgaaaagggagaaaaatgataaccaaattga---tggaatgtttgtgttctgtgaactgcagTTGCTCAGTACTGCGATAATGTGGAGATGTGTAGGCTCACAGAGCAAGTCGTGTTCTCAGACCCATACATGCTCGCCAAATACAATCGTTGCACATCACC
||  | || || | |      |||||  |||| |||  |   ||     |||  |  || | | | | | | || |    ||  |  || || | ||| ||||||       ||||   |  |    || |||| | |||| ||||    |||||||||| ||||||  |  || |||||||||||||||||||| |||||||| |||||||| |||||||||    |  ||||||  ||||| || || || ||
gtgagctgcttcactgct---gtttgaattgcttgtcgacttggc----aattggctcccagtcgctggtacgtgggcacgtggccatgcctgt-aaaggggagatgcgcactaactggacgggatttgcaatggt-gtgtgctgttg-ttgcagTTGCTAAGTACTCTGCGAACGTGGAGATGTGTAGGCTCACGGAGCAAGTTGTGTTCTCGGACCCATACCGTGTTTCCAAATTTAATCGGTGGACCTCGCC
















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|428869|gb|D25025.1|D25025
EST:     CTTCTTCACCTCCCTTCTCTACAACTCCACCACTGATCACAAGAAAGGAG                         TTGCTCAGTACTGCGATAATGTGGAGATGTGTAGGCTCACAGAGCAAGTCG
genomic: CTTCTTCACCTCCCTTCTCTACAACTCCACCACTGATCACAAGAAAGGAGgttggttgat ... tgaactgcagTTGCTCAGTACTGCGATAATGTGGAGATGTGTAGGCTCACAGAGCAAGTCG
EST: gi|27576663|gb|CA999357.1|CA999357
EST:     CTTCTTCACCTCCCTTCTCTACAACTCCACCACTGATCACAAGAAAGGAG                         TTGCTCAGTACTGCGATAATGTGGAGATGTGTAGGCTCACAGAGCAAGTCG
genomic: CTTCTTCACCTCCCTTCTCTACAACTCCACCACTGATCACAAGAAAGGAGgttggttgat ... tgaactgcagTTGCTCAGTACTGCGATAATGTGGAGATGTGTAGGCTCACAGAGCAAGTCG
EST: gi|218504013|gb|FG946243.1|FG946243
EST:     CACAAGAAAGGAG                         TTGC-CAGTACTGCGATAATGTGGAGATGTGTA-GCTCACAGAGCAAGTCG
genomic: CACAAGAAAGGAGgttggttgat ... tgaactgcagTTGCTCAGTACTGCGATAATGTGGAGATGTGTAGGCTCACAGAGCAAGTCG
EST: gi|27578344|gb|CB001039.1|CB001039
EST:     CTTCTTCACCTCCCTTCTCTACAACTCCACCACTGATCACAAGAAAGGAG                         TTGCTCAGTACTGCGATAATGTG
genomic: CTTCTTCACCTCCCTTCTCTACAACTCCACCACTGATCACAAGAAAGGAGgttggttgat ... tgaactgcagTTGCTCAGTACTGCGATAATGTG
EST: gi|27576846|gb|CA999540.1|CA999540
EST:     CTTCTTCACCTCCCTTCTCTACAACTCCACCACTGATCACAAGAAAGGAG                         TTGCTCAGTACTGCGATAATGTGGAGATGTGTAGGCTCACAGAGCAAGTCG
genomic: CTTCTTCACCTCCCTTCTCTACAACTCCACCACTGATCACAAGAAAGGAGgttggttgat ... tgaactgcagTTGCTCAGTACTGCGATAATGTGGAGATGTGTAGGCTCACAGAGCAAGTCG
EST: gi|38473387|gb|CF957519.1|CF957519
EST:     CTTCTTCACCTCCCTTCTCTACAACTCCACCACTGATCACAAGAAAGGAG                         TTGCTCAGTACTGCGATTATGTGGAGATGTGTAGGCTCACAGAGCAAGTCG
genomic: CTTCTTCACCTCCCTTCTCTACAACTCCACCACTGATCACAAGAAAGGAGgttggttgat ... tgaactgcagTTGCTCAGTACTGCGATAATGTGGAGATGTGTAGGCTCACAGAGCAAGTCG
EST: gi|29626238|gb|CB631249.1|CB631249
EST:     CTTCTTCACCTCCCTTCTCTACAACTCCACCACTGATCACAAGAAAGGAG                         TTGCTCAGTACTGCGATAATGTGGAGATGTGTAGGCTCACAGAGCAAGTCG
genomic: CTTCTTCACCTCCCTTCTCTACAACTCCACCACTGATCACAAGAAAGGAGgttggttgat ... tgaactgcagTTGCTCAGTACTGCGATAATGTGGAGATGTGTAGGCTCACAGAGCAAGTCG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 74 (upstream exon), 67 (downstream exon)
Score: 27

GAGTACCCGCTGCTCGCCGAGCACATGGCGGATTACATGGCCAAGACGCTCTTCTTCACCTCCCTTCTCTACAACTCCACCACTGATCACAAGAAAGGAGgttggttgat ... tgaactgcagTTGCTCAGTACTGCGATAATGTGGAGATGTGTAGGCTCACAGAGCAAGTCGTGTTCTCAGACCCATACATGCTCGCCAAATACAATCGTTGCACATCACC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagggagaaaaatgataaccaaattgatggaatgtttgtgttctgtgaactgcagTTGCTCAGTACTGCGATAATGTGGAGATGTGTAGGCTCACAGAGCAAGTCGTGTTCTCAGACCCATACATGCTCGCCAAATACAATCGTTGCACATCACC
       aaaaatgataa  TA-rich tract