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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgatccaagttaaaactgaacttggcctctcttatctctatttggttggtagacttcctttagttaaaactgaacttgtgccaacactctggtttttcgttaatttgtttgcttaaacatttggtagGATGGTAACACCCTTTACAATGAGCTTGAAGTTGTGGAAGGCATGAAACTTGACAGAGGCTACATCTCTCCTTACTTTGTTACCAACCCAAAGACCCAGA

Basic information

species Oryza sativa
transcript LOC_Os10g32550.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 5
gtaagttgatccaagttaaaactgaacttggcctctcttatctctatttggttggtagacttcctttagttaaaactgaacttgtgccaacactctggtttttcgttaatttgtttgcttaaacatttggtagGATGGTAACACCCTTTACAATGAGCTTGAAGTTGTGGAAGGCATGAAACTTGACAGAGGCTACATCTCTCCTTACTTTGTTACCAACCCAAAGACCCAGA
                           ||    |    |||   || ||  |   |   |   ||| |  | ||| ||  ||| |  |  || | || | ||||   | |||  |   |||||  ||   ||||| |||||||||||||| |||||||||||||||||||| || |||||||| |||||||| ||||||||||| |||||  |||||||| |||| |||||||
---------------------------ttatggtgctgtatgcttaattcttgtctttcccggcttca--tcaaattgctctttt-tctgcattgtgctgtttc---agtttactgatttaaatgttctttagGACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTAGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAACCCAGA

upper sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 5
gtaagttgatccaagttaaaactgaacttggcctctcttatctctatttggttggtagacttcctttagttaaaactgaacttgtgccaacactctggtttttcgttaatttgtttgcttaaacatttggtagGATGGTAACACCCTTTACAATGAGCTTGAAGTTGTGGAAGGCATGAAACTTGACAGAGGCTACATCTCTCCTTACTTTGTTACCAACCCAAAGACCCAGA
                            ||| ||  || ||   |      || |     ||||||   ||    ||    || ||| |    ||||  |||    | ||| | |   |||||  ||  ||||||||| ||||||||||| |||||||||||||||||||| || ||||||||||||||||| ||||||||||| |||||  |||||||| ||||  ||||||
--------------------------tgtggtcta-ctgataagtgcacattttgattgtttccttgtttttgctct---tttctgc-attgttctg--tttcaacttattggctgatttaaatgttctgtagGATGGCAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTTGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGA

upper sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G126878_T01 (Zea mays), 3'ss of exon 1
gtaagttgatccaagttaaaactgaacttggcctctcttatctctatttggttggtagacttcctttagttaaaactgaacttgtgccaacactctggtttttcgttaatttgtttgcttaaacatttggtagGATGGTAACACCCTTTACAATGAGCTTGAAGTTGTGGAAGGCATGAAACTTGACAGAGGCTACATCTCTCCTTACTTTGTTACCAACCCAAAGACCCAGA
                           |  |     || ||   |      || |     ||||||   ||    ||    || ||| |    ||||  |||    | ||| | |   |||||  ||  ||||||||| ||||||||||| |||||||||||||||||||| || ||||||||||||||||| ||||||||||| |||||  |||||||| |||| || ||  
---------------------------tgaggtctactgataagtgcgcattttgattgtttccttgtttttgctct---tttctgc-attgttctg--tttcaacttattggctgatttaaatgttctgtagGATGGCAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTTGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAACACATG

upper sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 6
gtaagttgatccaagttaaaactgaacttggcctctcttatctctatttggttggtagacttcctttagttaaaactgaacttgtgccaacactctggtttttcgttaatttgtttgcttaaacatttggtagGATGGTAACACCCTTTACAATGAGCTTGAAGTTGTGGAAGGCATGAAACTTGACAGAGGCTACATCTCTCCTTACTTTGTTACCAACCCAAAGACCCAGA
                            |   |    ||  |||         |||   | |  |||   | |  | |  | | |  ||| |   ||  | | |       |   |  |  ||  | |   |||||||||| ||  | ||||||||| | |||||||||||||| ||||| || ||||| || ||||| ||||| || ||  | || ||||  |||| |||||
----------------------------tcatcctcgttgcctcctccaaaggggt--ccgtggtttgaattatgccgtgcatttatcaata---tgaatatgctagggcctaacttttataaactgtttcagGATGGTAAGACATTGTACAATGAGTTGGAAGTTGTGGAAGGAATGAAGCTCGACAGGGGATACATTTCTCCATATTTCATAACAAACCAGAAGAACCAGA

upper sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 6
lower sequence: PP1S44_339V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------------------------------------------------gtaagttgatccaagtt--aaaactgaacttggcct-ctcttatctctatttggttggtagacttcctttagttaaaactgaacttgtgccaacactc--tggtttttcgttaatttgtttgcttaaacatttggtagGATGGTAACACCCTTTACAATGAGCTTGAAGTTGTGGAAGGCATGAAACTTGACAGAGGCTACATCTCTCCTTACTTTGTTACCAACCCAAAGACCCAGA
                                                           ||| | |  |     |  |||| || | ||   || | | | | ||        || | ||| |  || |   | || |    ||  | || ||     ||     || ||||    |      |||   ||  ||||||||||| || |||| ||||||  | |||||||||||||||||||| |||||||| || || ||||| ||||| ||  | ||||||   || || ||||
gtaagtgggaaatacatttgaacatgttggtctgcgatgtcattgtggttcattgtcattaaatgggcctggtatcaaaaattggagttaatctgcacatgtttcctcccttatgtttgacct--ttcacccataaatttctttaagtcagcatgagatgagaactcattaaaccatg-----aaattgtttttagGATGGTAAAACACTTTTCAATGAATTAGAAGTTGTGGAAGGCATGAAGCTTGACAGGGGTTATATCTCACCTTATTTCATCACCAACAACAAAACTCAGA

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|8528178|gb|AU092993.1|AU092993
EST:     TTGCAAAGGCTATGGAGAAGGTTGGCAAGGAGGGTGTAATCACCATTGCG                         GATGGTAACACCCTTTACAATGAGCTTGAAGTTTGTGGAANGCATGAAACT
genomic: TTGCAAAGGCTATGGAGAAGGTTGGCAAGGAGGGTGTAATCACCATTGCGgtaagttgat ... catttggtagGATGGTAACACCCTTTACAATGAGCTTGAAGTT-GTGGAAGGCATGAAACT
EST: gi|58663314|gb|CK052000.1|CK052000
EST:     TTGCAAAGGCTATGGAGAAGGTTGGCAAGGAGGGTGTAATCACCATTGCG                         GATGGTAACACCCTTTACAATGAGCTTGAAGTTGTGGAAGGCATGAAACTT
genomic: TTGCAAAGGCTATGGAGAAGGTTGGCAAGGAGGGTGTAATCACCATTGCGgtaagttgat ... catttggtagGATGGTAACACCCTTTACAATGAGCTTGAAGTTGTGGAAGGCATGAAACTT
EST: gi|86851054|gb|CI311272.1|CI311272
EST:     TTGCAAAGGCTATGGAGAAGGTTGGCAAGGAGGGTGTAATCACCATTGCG                         GATGGTAACACCCTTTACAATGAGCTTGAAGTTGTGGAAGGCATGAAACTT
genomic: TTGCAAAGGCTATGGAGAAGGTTGGCAAGGAGGGTGTAATCACCATTGCGgtaagttgat ... catttggtagGATGGTAACACCCTTTACAATGAGCTTGAAGTTGTGGAAGGCATGAAACTT
EST: gi|29627179|gb|CB632190.1|CB632190
EST:     TTGCAAAGGCTATGGAGAAGGTTGGCAAGGAGGGTGTAATCACCATTGCG                         GATGGTAACACCCTTTACAATGAGCTTGAAGTTGTGGAAGGCATGAAACTT
genomic: TTGCAAAGGCTATGGAGAAGGTTGGCAAGGAGGGTGTAATCACCATTGCGgtaagttgat ... catttggtagGATGGTAACACCCTTTACAATGAGCTTGAAGTTGTGGAAGGCATGAAACTT
EST: gi|58691748|gb|CK080435.1|CK080435
EST:     TTGCAAAGGCTATGGAGAAGGTTGGCAAGGAGGGTGTAATCACCATTGCG                         GATGGTAACACCCTTTACAATGAG
genomic: TTGCAAAGGCTATGGAGAAGGTTGGCAAGGAGGGTGTAATCACCATTGCGgtaagttgat ... catttggtagGATGGTAACACCCTTTACAATGAG

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: 75 (upstream exon), 70 (downstream exon)
Score: 62

GTGGGCACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCAAAGGCTATGGAGAAGGTTGGCAAGGAGGGTGTAATCACCATTGCGgtaagttgat ... catttggtagGATGGTAACACCCTTTACAATGAGCTTGAAGTTGTGGAAGGCATGAAACTTGACAGAGGCTACATCTCTCCTTACTTTGTTACCAACCCAAAGACCCAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacttgtgccaacactctggtttttcgttaatttgtttgcttaaacatttggtagGATGGTAACACCCTTTACAATGAGCTTGAAGTTGTGGAAGGCATGAAACTTGACAGAGGCTACATCTCTCCTTACTTTGTTACCAACCCAAAGACCCAGA
                         cgttaat  putative branch site (score: 62)
                    tttttcgttaattt  TA-rich tract