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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtaatacaaaataaagattatttcatgtacagtagacttccgaaattcatgtagatggattaaatggagatgaaatgaacatgaatctgattctctgcagATAGCACCTTATGATCAATTGGAAATGCTTGAGAGGCTTGTGGATGTTCCTCGTGCAACAACAGCAGCAGTCTCTTCATGATAGAGTAGAGATAATGTTC

Basic information

species Oryza sativa
transcript LOC_Os01g52170.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g52170.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G129208_T01 (Zea mays), 3'ss of exon 13
gtaatgtaatacaaaataaagattatttcatgtacagtagacttc-cgaaattcatgtagatggattaaatggagatgaaatgaacatgaatctgattct-ctgcagATAGCACCTTATGATCAATTGGAAATGCTTGAGAGGCTTGTGGATGTTCCTCGTGCAACAACAGC------AGCAGTCTCTTCATGATAGAGTAGAGATAATGTTC
                |||| || ||   |    | |||||  || |  ||    ||   ||  | |   || | |    ||      | | ||| | || |||||||||||||||||||| |||||||||||||| ||| || | ||||| | |||  || || || ||||      ||  | ||| |||||||| || ||| | |      
---------------gtaaatatgat--aaaaagctgtagaactcacttaacctgtg-gtatccactttctgaaaaatgcatacgttcgtacctggtgcttctgcagATAGCACCTTATGACCAATTGGAAATGCTGGAGCGGTTGGTGGAGGCTCCGAGTCCAGCAGCAGCGTCTGCAGTGGCCTCGTCATGATACAGCAGAAAGA------
















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|29683979|gb|CB680254.1|CB680254
EST:     CTATGGGAAACTACGCAGTTTCTATAACTTGGCCTGATGGTTTTTCTCAG                         ATAGCACCTTATGATCAATTGGAAATGCTTGAGAGGCTTGTGGATGTTCCT
genomic: CTATGGGAAACTACGCAGTTTCTATAACTTGGCCTGATGGTTTTTCTCAGgtaatgtaat ... ttctctgcagATAGCACCTTATGATCAATTGGAAATGCTTGAGAGGCTTGTGGATGTTCCT
EST: gi|38481133|gb|CF965222.1|CF965222
EST:     CTATGGGAAACTACGCAGTTTCTATAACTTGGCCTGATGGTTTTTCTCAG                         ATAGCACCTTATGATCAATTGGAAATGCTTGAGAGGCTTGTGGATGTTCCT
genomic: CTATGGGAAACTACGCAGTTTCTATAACTTGGCCTGATGGTTTTTCTCAGgtaatgtaat ... ttctctgcagATAGCACCTTATGATCAATTGGAAATGCTTGAGAGGCTTGTGGATGTTCCT
EST: gi|29641473|gb|CB646480.1|CB646480
EST:     CTATGGGAAACTACGCAGTTTCTATAACTTGGCCTGATGGTTTTTCTCAG                         ATAGCACCTTATGATCAATTGGAAATGCTTGAGAGGCTTGTGGATGTTCCT
genomic: CTATGGGAAACTACGCAGTTTCTATAACTTGGCCTGATGGTTTTTCTCAGgtaatgtaat ... ttctctgcagATAGCACCTTATGATCAATTGGAAATGCTTGAGAGGCTTGTGGATGTTCCT
EST: gi|29613739|gb|CB618752.1|CB618752
EST:     CTATGGGAAACTACGCAGTTTCTATAACTTGGCCTGATGGTTTTTCTCAG                         ATAGCACCTTATGATCAATTGGAAATGCTTGAGAGGCTTGTGGATGTTCCT
genomic: CTATGGGAAACTACGCAGTTTCTATAACTTGGCCTGATGGTTTTTCTCAGgtaatgtaat ... ttctctgcagATAGCACCTTATGATCAATTGGAAATGCTTGAGAGGCTTGTGGATGTTCCT
EST: gi|86874812|gb|CI325323.1|CI325323
EST:     CTATGGGAAAGTACGCAGTTTCTATAACTTCGCCTGATGGTTTTTCTCAG                         ATAGCACCTTATGATCAATT-GAAATGCTTGAGAGGCTTGTGGATGTTCCT
genomic: CTATGGGAAACTACGCAGTTTCTATAACTTGGCCTGATGGTTTTTCTCAGgtaatgtaat ... ttctctgcagATAGCACCTTATGATCAATTGGAAATGCTTGAGAGGCTTGTGGATGTTCCT

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: 72 (upstream exon), 60 (downstream exon)
Score: 24

AGTACAATATGGTGATATACCAGAAGACATTGAACCTGAAGAGATCCGTCCTATGGGAAACTACGCAGTTTCTATAACTTGGCCTGATGGTTTTTCTCAGgtaatgtaat ... ttctctgcagATAGCACCTTATGATCAATTGGAAATGCTTGAGAGGCTTGTGGATGTTCCTCGTGCAACAACAGCAGCAGTCTCTTCATGATAGAGTAGAGATAATGTTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatgtagatggattaaatggagatgaaatgaacatgaatctgattctctgcagATAGCACCTTATGATCAATTGGAAATGCTTGAGAGGCTTGTGGATGTTCCTCGTGCAACAACAGCAGCAGTCTCTTCATGATAGAGTAGAGATAATGTTC
                                       atctgat  putative branch site (score: 24)
                                             ttctctgc  CT-rich tract
             attaaat  TA-rich tract