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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgttgatggttttcatttgttgaatgtttcgctcacttgctctcccctaatacaattctcttctacatttcccagTGAAGTATCATTGCTCTTGGCATCAGAAACTGGAGATGGAAAGAGTAGCATTTACCCCCCTGTTATTGGAAATTCGTTTGCCTTTAAGCTTCAAGACCAA

Basic information

species Oryza sativa
transcript LOC_Os12g07190.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g07190.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G126656_T01 (Zea mays), 3'ss of exon 10
gtctgttgatggttttcatttgt-tgaatgtttcgctcacttgctctc---ccctaatacaattctcttc-----tacatttcccagTGAAGTATCATTGCTCTTGGCATCAGAAACTGGAGATGGAAAGAGTAGCATTTACCCCCCTGTTATTGGAAATTCGTTTGCCTTTAAGCTTCAAGACCAA
|| ||||||||  | |  |  |  | ||| ||   ||   || || |    |  |||||| | ||||||      |  |||   ||| || ||||| || ||| ||   |||||  |||||||||||||||||||  |||| ||||||||  |||| ||||||||| |||||||||| ||||||| |
gtttgttgatgaatcttttgaggattaattttcttctgttttcctatgaggctataatacgactctctttcttcttgtattgttcagCGAGGTATCCTTACTCCTGCAGTCAGAGGCTGGAGATGGAAAGAGTAGTGTTTATCCCCCTGTGGTTGGCAATTCGTTTTCCTTTAAGCTCCAAGACCGA
















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|29658205|gb|CB654480.1|CB654480
EST:     GATTCTACTCTTGCTTTGGAGTCTCCTGATGAGGAATGCGATAGCCGTAG                         TGAAGTATCATTGCTCTTGGCATCAGAAACTGGAGATGGAAAGAGTAGCAT
genomic: GATTCTACTCTTGCTTTGGAGTCTCCTGATGAGGAATGCGATAGCCGTAGgtctgttgat ... catttcccagTGAAGTATCATTGCTCTTGGCATCAGAAACTGGAGATGGAAAGAGTAGCAT
EST: gi|29683887|gb|CB680162.1|CB680162
EST:     GATTCTACTCTTGCTTTGGAGTCTCCTGATGAGGAATGCGATAGCCGTAG                         TGTAGTATCATTGCTCTTGGCAT
genomic: GATTCTACTCTTGCTTTGGAGTCTCCTGATGAGGAATGCGATAGCCGTAGgtctgttgat ... catttcccagTGAAGTATCATTGCTCTTGGCAT
EST: gi|29628515|gb|CB633526.1|CB633526
EST:     TGAGGAATGCGATAGCCGTAG                         TGAAGTATCATTGCTCTTGGCATCAGAAACTGGAGATGGAAAGAGTAGCAT
genomic: TGAGGAATGCGATAGCCGTAGgtctgttgat ... catttcccagTGAAGTATCATTGCTCTTGGCATCAGAAACTGGAGATGGAAAGAGTAGCAT
EST: gi|29620737|gb|CB625748.1|CB625748
EST:     GATTCTACTC-TGCTTTGGAGTCTCCAGATGAGGAATGCGATAGCCGTAG                         TGAAGTATCATTGCTCTTGGCATCAGAAACTGGAGATGGAAAGAGTAGCAT
genomic: GATTCTACTCTTGCTTTGGAGTCTCCTGATGAGGAATGCGATAGCCGTAGgtctgttgat ... catttcccagTGAAGTATCATTGCTCTTGGCATCAGAAACTGGAGATGGAAAGAGTAGCAT
EST: gi|29683888|gb|CB680163.1|CB680163
EST:     GAGGAATGCGATAGCCGTAG                         TGAAGTATCATTGCTCTTGGCATCAGAAACTGGAGATGGAAAGAGTAGCAT
genomic: GAGGAATGCGATAGCCGTAGgtctgttgat ... catttcccagTGAAGTATCATTGCTCTTGGCATCAGAAACTGGAGATGGAAAGAGTAGCAT
EST: gi|33799726|gb|CF325729.1|CF325729
EST:     GATTCTACTCTTGCTTTGGAGTCTCCTGATGAGGAATGCGATAGCCGTAG                         TGAAGTATCATTGCTCTTGGCATCAGAAACTGGAGATGGAAAGAGTAGCAT
genomic: GATTCTACTCTTGCTTTGGAGTCTCCTGATGAGGAATGCGATAGCCGTAGgtctgttgat ... catttcccagTGAAGTATCATTGCTCTTGGCATCAGAAACTGGAGATGGAAAGAGTAGCAT
EST: gi|29658285|gb|CB654560.1|CB654560
EST:     GCTTTGGAGTCTCCTGATGAGGAATGCGATAGCCGTAG                         TGAAGTATCATTGCTCTTGGCATCAGAAACTGGAGATGGAAAGAGTAGCAT
genomic: GCTTTGGAGTCTCCTGATGAGGAATGCGATAGCCGTAGgtctgttgat ... catttcccagTGAAGTATCATTGCTCTTGGCATCAGAAACTGGAGATGGAAAGAGTAGCAT

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: 58 (upstream exon), 60 (downstream exon)
Score: 18

GAAATGACACTGTAAATGATGTGGCAAATACAGTAATGCAGAGGTTTTGGGATTCTACTCTTGCTTTGGAGTCTCCTGATGAGGAATGCGATAGCCGTAGgtctgttgat ... catttcccagTGAAGTATCATTGCTCTTGGCATCAGAAACTGGAGATGGAAAGAGTAGCATTTACCCCCCTGTTATTGGAAATTCGTTTGCCTTTAAGCTTCAAGACCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaatgtttcgctcacttgctctcccctaatacaattctcttctacatttcccagTGAAGTATCATTGCTCTTGGCATCAGAAACTGGAGATGGAAAGAGTAGCATTTACCCCCCTGTTATTGGAAATTCGTTTGCCTTTAAGCTTCAAGACCAA
                        ccctaat  putative branch site (score: 18)
                                   ttctcttctacatttc  putative PPT
                           taatacaatt  TA-rich tract