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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcaacatatttttctctcatcatttcaggaattactttttgtatttcgacacttattacatcgacgcccataaccttctacttttgctcttaatgctgtaattctatgtcaattatttggattactttaaataagctgcagtgacaattgtggttcttcattttcagAGTTTTTCCAGAACAAGTTAGTAGAGACCATACAGTTCATGGAAGTTCTTAACTTAAAGGACAGTGTTGAGAAAGATAGCTTTTTCCGTAAACTACCGAA

Basic information

species Oryza sativa
transcript LOC_Os01g60440.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60440.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G098078_T02 (Zea mays), 3'ss of exon 8
gtaagttcaacatatttttctctcatcatttcaggaattactttttgtatttcgacacttattacatcgacgcccataaccttctacttttgctcttaatgctgtaattctatgtcaattatttggattactttaaataagctgcagtgacaattgtggttcttcattttcagAGTTTTTCCAGAACAAGTTAGTAGAGACCATACAGTTCATGGAAGTTCTTAACTTAAAGGACAGTGTTGAGAAAGATAGCTTTTTCCGTAAACTACCGAA
||||| ||||||||||||||     || ||     | | |  |||||   |  |||| |||| ||||       | | |     || | ||      | |  |||   || ||||     | ||| |||  ||  || |||||| | ||     | ||| |||   |||||||||||||||||||| |||||||||||||| || |||||||||||| ||||||| || || ||||   |||||||||| ||||||||||| || || || ||
gtaagctcaacatatttttcat--gtcgttc----agtcaacttttggggt--gacatttatcacatt-----tcttcagtgcatagtcttatcacaattattgtc-ctccatgtggg--aattgcatttgttcgaa-aagctgaaatggtgtctttggctctctgttttcagAGTTTTTCCAGAATAAGTTAGTAGAGACTATCCAGTTCATGGAAATTCTTAATTTGAAAGACACCTTTGAGAAAGACAGCTTTTTCCGGAAGCTTCCCAA

upper sequence: LOC_Os01g60440.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AC218972.3_FGT001 (Zea mays), 3'ss of exon 8
gtaagttcaacatatttttctctcatcatttcaggaattactttttgtatttcgacacttattacatcgacgcccataaccttctacttttgctcttaatgctgtaattctatgtcaatt---atttggattactttaaataagctgcagtgacaattgtggttcttcattttcagAGTTTTTCCAGAACAAGTTAGTAGAGACCATACAGTTCATGGAAGTTCTTAACTTAAAGGACAGTGTTGAGAAAGATAGCTTTTTCCGTAAACTACCGAA
||||| ||||||||||||       || || |||  |  |||||| |  | ||     ||||   ||       |||   |||| |   ||  |||||   |  | ||| |    ||  |   | ||| |||  || ||| |||||| | ||     | ||| |||   ||| |||||||||||||||||||||||||||||||||| |||||||||||| ||||||| || || ||||   |||||||||| || ||||| |||||||| || ||
gtaagctcaacatattttctg--tgtcgtt-cagcca--acttttggggtgtcat--tttatctaattataatacatt-tcttcaatgcttagtcttaccacaattattgtcctccatgtgggaattgcatttgttcaaa-aagctgaaatggtgtctttggctctctgttt-cagAGTTTTTCCAGAACAAGTTAGTAGAGACCATCCAGTTCATGGAAATTCTTAATTTGAAAGACACCTTTGAGAAAGACAGTTTTTTTCGTAAACTCCCCAA

upper sequence: LOC_Os01g60440.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv13s0067g03110.t01 (Vitis vinifera), 3'ss of exon 8
gtaagttcaacatatttttctctcatcatttcaggaattactttttgtatttcgacacttattacatcgacgcccataaccttctacttttgctcttaatgctgtaattctatgtcaattatttggattactttaaataagctgcagtgacaattgtggttcttcattttcagAGTTTTTCCAGAACAAGTTAGTAGAGACCATACAGTTCATGGAAGTTCTTAACTTAAAGGACAGTGTTGAGAAAGATAGCTTTTTCCGTAAACTACCGAA
                                                                     |   |  |  |    |   |||  ||||| |  |    |||| | |   || |     ||  |||   |       | | |     |  | | | ||||  |||| | |||||| || |||||||| || || ||||| ||||||||  ||||||| || |||||||||||||| || |||| ||| |||||||| || || ||
---------------------------------------------------------------------atttctttgcctcagtctctttcttcttagtattccc-ttctttcttccttttcctttttttttttggtg---cctactaatttcagaagatatgcattggcagAATATTTCCAAAATAAGTTAGTGGATACTATACATTTCATGGACATTCTTAATTTGAAGGACAGTGTTGAAAAGGATACCTTCTTCCGTAAGCTTCCAAA

upper sequence: LOC_Os01g60440.1 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S47_172V6.1 (Physcomitrella patens), 3'ss of exon 8
gtaagttcaacatatttttctctcatcatttcaggaattactttttgtatttcgacacttattacatcgacgcccataaccttctacttttgctcttaatgctgtaattctatgtcaattatttggattactttaaataagctgcagtgacaattgtggttcttcattttcagAGTTTTTCCAGAACAAGTTAGTAGAGACCATACAGTTCATGGAAGTTCTTAACTTAAAGGACAGTGTTGAGAAAGATAGCTTTTTCCGTAAACTACCGAA
                                                           || ||  | |  ||  ||       |||||||  | |  | | |     |   || | || |     | ||    ||| ||  || | |||  | |||   | || | |  ||||||||||||| || ||| | || || || ||||| || |||||| |||| ||||||||||||||||| |||||||||  ||| || || || || || | 
----------------------------------------------------------atactaggttgg-gcagatggtagaatacttttcttttctaggtt-----ttgttgccgatga---aaactag--caaagaaagtg-actgatgactgt---tattgactagcagAGTTTTTCCACAATAAGCTGGTGGAAACTATACAATTTATGGAAATTCTGAACTTAAAGGACAGTGTAGAGAAAGATGTCTTCTTTCGCAAGCTTCCTAC

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|29623603|gb|CB628614.1|CB628614
EST:     TTCTGCCCCTTCTCGTAGAATGAACCCTTCTAAACTTATTGACAACAGTG                         AGTTTTTCCAGAACAAGTTAGTAGAGACCATACAGTTCATGGAAGTTCTTA
genomic: TTCTGCCCCTTCTCGTAGAATGAACCCTTCTAAACTTATTGACAACAGTGgtaagttcaa ... tcattttcagAGTTTTTCCAGAACAAGTTAGTAGAGACCATACAGTTCATGGAAGTTCTTA
EST: gi|58662163|gb|CK050843.1|CK050843
EST:     TTCTGCCCCTTCTCGTAGAATGAACCCTTCTAAACTTATTGACAACAGTG                         AGTTTTTCCAGAACAAGTTAGTAGAGACCATACAGTTCATGGAAGTTCTTA
genomic: TTCTGCCCCTTCTCGTAGAATGAACCCTTCTAAACTTATTGACAACAGTGgtaagttcaa ... tcattttcagAGTTTTTCCAGAACAAGTTAGTAGAGACCATACAGTTCATGGAAGTTCTTA
EST: gi|88397102|gb|CI593314.1|CI593314
EST:     TTCTGCCCCTTCTCGTAGAATGAACCCTTCTAAACTTATTGACAACAGTG                         AGTTTTTCCAGAACAAGTTAGTAGAGACCATACAGTTCATGGAAGTTCTTA
genomic: TTCTGCCCCTTCTCGTAGAATGAACCCTTCTAAACTTATTGACAACAGTGgtaagttcaa ... tcattttcagAGTTTTTCCAGAACAAGTTAGTAGAGACCATACAGTTCATGGAAGTTCTTA
EST: gi|58684299|gb|CK072986.1|CK072986
EST:     TTCTGGCCCTTCTCGTAGAATGAACCCTTCTAAACTTATTGACAACAGTG                         AGTTTTTCCAGAACAAGTTAGTAGAGACCATACAGTTCATGGAAGTTC
genomic: TTCTGCCCCTTCTCGTAGAATGAACCCTTCTAAACTTATTGACAACAGTGgtaagttcaa ... tcattttcagAGTTTTTCCAGAACAAGTTAGTAGAGACCATACAGTTCATGGAAGTTC

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: 70 (upstream exon), 61 (downstream exon)
Score: 38

TCTTTACTTCCAGATTACCAGAGGCTCTTGAGTTCTGCCCCTTCTCGTAGAATGAACCCTTCTAAACTTATTGACAACAGTGgtaagttcaa ... tcattttcagAGTTTTTCCAGAACAAGTTAGTAGAGACCATACAGTTCATGGAAGTTCTTAACTTAAAGGACAGTGTTGAGAAAGATAGCTTTTTCCGTAAACTACCGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatttggattactttaaataagctgcagtgacaattgtggttcttcattttcagAGTTTTTCCAGAACAAGTTAGTAGAGACCATACAGTTCATGGAAGTTCTTAACTTAAAGGACAGTGTTGAGAAAGATAGCTTTTTCCGTAAACTACCGAA
                                         ttcttcattttc  CT-rich tract
        attactttaaataa  TA-rich tract