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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgttcctctaaggttctgactatccacatttactgttgaaaattgtcatgtaggattgaatagaatcactacttatttataatttaccagagacgtgtttctagtaactaattatgtctgccatggtaaaccacaaaacggaaaatgctgaccttccttttgtattgcagTTCTTATCGATGAAGCTTGCGACAGTAAACCCAAGGCTTGACCTCAACATAGAAGGGCTTCTTTCAAAAGAC

Basic information

species Oryza sativa
transcript LOC_Os09g29830.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g29830.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G818643_T02 (Zea mays), 3'ss of exon 3
gtactgttcctctaaggttctgactatccacatttactgttgaaaattgtcatgtaggattgaatagaatcactacttatttataatttaccagagacgtgtttctagtaactaattatgtctgccatggtaaaccacaaaacggaaaatgctgaccttccttttgtattgcagTTCTTATCGATGAAGCTTGCGACAGTAAACCCAAGGCTTGACCTCAACATAGAAGGGCTTCTTTCAAAAGAC
                                                                    | |   |||     || | |             |  ||  | ||     ||      ||||| || |  ||||||    |||  ||| |||  ||   |  ||||||||||||| |||||||| || || |||||||||||||| ||||||||||||||||||||||| || ||||| 
------------------------------------------------------------------ataccgagactagaacatgaatagaattctgtacatcccttattac-----atactgatcatggcaagcatcaaaacattgaat--tgatcttg-ttgcatcatgcagTTCTTATCAATGAAGCTCGCAACGGTAAACCCAAGGCTCGACCTCAACATAGAAGGGCTTCTATCGAAAGAT

upper sequence: LOC_Os09g29830.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G137541_T01 (Zea mays), 3'ss of exon 4
-------gtactgttcctctaaggttctgactatccacatttactgttgaaaattgtcatgtagga--ttgaatag--aatcactacttatttataatttaccagaga-cgtgtttctagtaactaattatgtctgccatggtaaaccacaaaacggaaaatgctgaccttc--cttttgtattgcagTTCTTATCGATGAAGCTTGCGACAGTAAACCCAAGGCTTGACCTCAACATAGAAGGGCTTCTTTCAAAAGAC
         |   | || |  |   | |    |  |     |   ||||  | |||  ||  ||||  | ||| ||  |  ||||       |  |  | | || ||  | | ||||||  ||    |  |  |   |||   | |||       || | ||    ||  |   |   | | ||||||||||| || |||||||| || || || ||||||||||||||||||||||||||||||||||| || ||||||
gtaataacaaacatcccccccaatatatactgagacctgaatcaagttgtcatttgcaatagaggaagtagaacagctagacactgagaccctgaatatgaacacagttcctctttctacaaaaccctcgttacatacata-cataccgatggcaggcacatcaaaacactgaacgaatctcttgcagTTCTTGTCAATGAAGCTCGCCACGGTGAACCCAAGGCTTGACCTCAACATAGAAGGGCTTCTATCGAAAGAC
















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|218493872|gb|FG957202.1|FG957202
EST:     TGCTTGACGAGATCATCAACTATGTTCAGTCCCTGCAAAGACAAGTTGAG                         TTCTTATCGATGAAGCTTGCGACAGTAAACCCAATGCTTGACCTCAACATA
genomic: TGCTTGACGAGATCATCAACTATGTTCAGTCCCTGCAAAGACAAGTTGAGgtactgttcc ... tgtattgcagTTCTTATCGATGAAGCTTGCGACAGTAAACCCAAGGCTTGACCTCAACATA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctgccatggtaaaccacaaaacggaaaatgctgaccttccttttgtattgcagTTCTTATCGATGAAGCTTGCGACAGTAAACCCAAGGCTTGACCTCAACATAGAAGGGCTTCTTTCAAAAGAC
                              tgctgac  putative branch site (score: 2)
                                    ccttccttttgtatt  CT-rich tract
                                          ttttgtatt  TA-rich tract