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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatatctcatgtgttatcaaatgaatacaaatttgttttcaaatctgtgtgcttaaaaggagaaccatccttctgcagGCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACTATGGAAAATCACGAGTTGTTCTTCATTTTTGAAAACATG

Basic information

species Oryza sativa
transcript LOC_Os03g63020.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63020.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G045241_T01 (Zea mays), 3'ss of exon 5
--------------------gtaatatatctcatgtgttatcaaatgaatacaaatttgttttcaaatctgtgtgcttaaaaggagaaccatccttctgcagGCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACTATGGAAAATCACGAGTTGTTCTTCATTTTTGAAAACATG
                      || | | |  |   |   |||| |  |||| |   ||       || | | |    |||   ||||| ||  |||||||||| ||||| |||||   ||| || |||||||||||| | ||||| ||||| |||||||| || ||| |||||||||| |||||| |||||
ctaaattttagtctagtgactaaagaaaccaaacagggcctcaa-tagatactatcctgcagcttgattt-tcttaacaaagaaagaactatttttctgcagGCCCTTCAGAAACTATTTCACCCTAACATTGTGAAGCTGAAGGAAGTGACGATGGAAAACCATGAGCTGTTCTTCATCTTTGAACACATG
















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|29656191|gb|CB652466.1|CB652466
EST:     AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAG                         GCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
genomic: AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAGgtaatatatc ... ccttctgcagGCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
EST: gi|58694135|gb|CK082822.1|CK082822
EST:     AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAG                         GCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
genomic: AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAGgtaatatatc ... ccttctgcagGCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
EST: gi|29663526|gb|CB659801.1|CB659801
EST:     AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAG                         GCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
genomic: AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAGgtaatatatc ... ccttctgcagGCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
EST: gi|58656490|gb|CK045170.1|CK045170
EST:     AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAG                         GCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
genomic: AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAGgtaatatatc ... ccttctgcagGCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
EST: gi|88324687|gb|CI587656.1|CI587656
EST:     AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAG                         GCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
genomic: AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAGgtaatatatc ... ccttctgcagGCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
EST: gi|29644978|gb|CB649985.1|CB649985
EST:     AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAG                         GCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
genomic: AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAGgtaatatatc ... ccttctgcagGCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
EST: gi|58692426|gb|CK081113.1|CK081113
EST:     AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAG                         GCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
genomic: AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAGgtaatatatc ... ccttctgcagGCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
EST: gi|29613119|gb|CB618132.1|CB618132
EST:     AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAG                         GCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
genomic: AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAGgtaatatatc ... ccttctgcagGCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
EST: gi|29613394|gb|CB618407.1|CB618407
EST:     AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTACTCTGCGAGAGGTGAAG                         GCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT
genomic: AGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAGgtaatatatc ... ccttctgcagGCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACT

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: 69 (upstream exon), 64 (downstream exon)
Score: 38

GTTGCAGTTAAAAAAATGAAGAGGAAGTTTTTCCAATGGGAAGAGTGCATTAGTCTGCGAGAGGTGAAGgtaatatatc ... ccttctgcagGCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACTATGGAAAATCACGAGTTGTTCTTCATTTTTGAAAACATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatacaaatttgttttcaaatctgtgtgcttaaaaggagaaccatccttctgcagGCACTTCAAAAACTGAATCATCCCAACATTGTGAAGTTAAAGGAGGTGACTATGGAAAATCACGAGTTGTTCTTCATTTTTGAAAACATG
                                         ccatccttct  CT-rich tract
     aaatttgttttcaaat  TA-rich tract