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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtttgcacgatcatggtcctgaatctgtctctatttagctattgattttttttgttggtaatttttgtattgcttctccactgtttgaagtctgtaatgtagagcattatgctgactaatctatacattgttcatgcgtatcataaagttgttggtttccttctattttgctgcagTCTTTACTTCCAGATTACCAGAGGCTCTTGAGTTCTGCCCCTTCTCGTAGAATGAACCCTTCTAAACTTATTGACAACAGTG

Basic information

species Oryza sativa
transcript LOC_Os01g60440.1
intron # 7
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 7
lower sequence: GRMZM2G098078_T01 (Zea mays), 3'ss of exon 7
gttagtttgcacgatcatggtcctgaatctgtctctatttagctattgattttttttgttggtaatttttgtattgcttctccactgtttgaagtctgtaatgtagagcattatgctgactaatctatacattgttcatgcgtatcataaagttgttggtttccttctattttgctgcagTCTTTACTTCCAGATTACCAGAGGCTCTTGAGTTCTGCCCCTTCTCGTAGAATGAACCCTTCTAAACTTATTGACAACAGTG
||||| |  || |||       |   |||  |   | |  | |     |||   ||| |||||    |||| |  | |||| |||||||  || |       |||||   || |            || ||||     || || |  |   ||| |||  | | ||||   |  ||| ||||| ||||||||||||||||||||||||||| |||  | ||| |||||||| | || ||||| ||||||||||||||||| |
gttagctcacatgatttcacctc---atcacttattttgcaccatgcaattacatttattggt----tttgga--gtttcttcactgttctaact-------gtagaagtttgt------------atgcatt-----tgtgtctt-tttggttattgactactttct---tccctgtagTCTCTACTTCCAGATTACCAGAGGCTCTTGAATTCCACACCTACTCGTAGACTAAATCCTTCAAAACTTATTGACAACAGCG

upper sequence: LOC_Os01g60440.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AC218972.3_FGT001 (Zea mays), 3'ss of exon 7
gttagtttgcacgatcatggtcctgaatctgtctctatttagctattgattttttttgttggtaatttttgtattgcttctccactgtttgaagtctgtaatgtagagcattatgctgactaatctatacattgttcatgcgtatcataa-agttgttggtttccttctattttgctgcagTCTTTACTTCCAGATTACCAGAGGCTCTTGAGTTCTGCCCCTTCTCGTAGAATGAACCCTTCTAAACTTATTGACAACAGTG
                       | |       |   || ||||| | | || |||||      | | |   ||| | |        |||| ||| |           || | | || |||     |     | | |||  || || |    ||| |||  |   ||||   |  ||| ||||| ||||||||||||||||||||||||||| |||  | |||||||||||| | || ||||| ||||||||||||||||| |
----------------------gtcagctcacatgatttcagctagtcacttattttgc-----actgtgcaattaccttcattgcttttggagtttccc--------cactgttctaactgcagaagtttgtatgcatttgtgtctttttggttattgactattttct---tccctgtagTCTCTACTTCCAGATTACCAGAGGCTCTTGAATTCCACACCTTCTCGTAGACTAAATCCTTCAAAACTTATTGACAACAGCG

upper sequence: LOC_Os01g60440.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv13s0067g03110.t01 (Vitis vinifera), 3'ss of exon 7
gttagtttgcacgatcatggtcctgaatctgtctctatttagctattgattttttttgttggtaatt---tttgtattgcttctccactgtttgaa--gtctgtaatgtagagcattatgctgactaatctatacattgttcatgcgtatcataaagtt--gttggtttccttctattttgctg-----cagTCTTTACTTCCAGATTACCAGAGGCTCTTGAGTTCTGCCCCTTCTCGTAGAATGAACCCTTCTAAACTTATTGACAACAGTG
|| |||||  |     || ||   | ||   ||  |  || || ||||    ||| |   | |   |   ||||  || ||| ||| ||  | ||   | || | |||||      | ||     |  | ||    |    | |  | |  ||  | ||   || |  ||  ||||||||  ||     |||||| ||||||||||||| ||| |||||||||||||    ||| |||| ||  ||||| | || || ||||| || || ||||
gtcagttttta-----attgtttgggatggatcattgatt-gcaattggccctttctccggttctatcactttgctttacttttcctctcatggagttgccttttatgtatgtgcatgtgtgtcatggtttacttctcaagcttttgaaaaattcattttcatttgcatctgtctattttcttgtctcacagTCTCTACTTCCAGATTATCAGCGGCTCTTGAGTTCCATGCCTGCTCGCAGGTTGAACACATCGAAGCTTATAGAAAATAGTG

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:     CAAAGCTAACCAGGACAGAGGACCTTCGGAACACTGCTTCAATCCCAAAG                         TCTTTACTTCCAGATTACCAGAGGCTCTTGAGTTCTGCCCCTTCTCGTAGA
genomic: CAAAGCTAACCAGGACAGAGGACCTTCGGAACACTGCTTCAATCCCAAAGgttagtttgc ... tttgctgcagTCTTTACTTCCAGATTACCAGAGGCTCTTGAGTTCTGCCCCTTCTCGTAGA
EST: gi|58662163|gb|CK050843.1|CK050843
EST:     CAAAGCTAACCAGGACAGAGGACCTTCGGAACACTGCTTCAATCCCAAAG                         TCTTTACTTCCAGATTACCAGAGGCTCTTGAGTTCTGCCCCTTCTCGTAGA
genomic: CAAAGCTAACCAGGACAGAGGACCTTCGGAACACTGCTTCAATCCCAAAGgttagtttgc ... tttgctgcagTCTTTACTTCCAGATTACCAGAGGCTCTTGAGTTCTGCCCCTTCTCGTAGA
EST: gi|88397102|gb|CI593314.1|CI593314
EST:     CAAAGATAACCAGGACAGAGGACCTTCGGAACACTGCTTCAATCCCAAAG                         TCTTTACTTCCAGATTACCAGAGGCTCTTGAGTTCTGCCCCTTCTCGTAGA
genomic: CAAAGCTAACCAGGACAGAGGACCTTCGGAACACTGCTTCAATCCCAAAGgttagtttgc ... tttgctgcagTCTTTACTTCCAGATTACCAGAGGCTCTTGAGTTCTGCCCCTTCTCGTAGA
EST: gi|58684299|gb|CK072986.1|CK072986
EST:     CAAAGCTAACCAGGACAGAGGACCTTCGGAACACTGCTTCAATCCCAAAG                         TCTTTACTTCCAGATTACCAGAGGCTCTTGAGTTCTGGCCCTTCTCGTAGA
genomic: CAAAGCTAACCAGGACAGAGGACCTTCGGAACACTGCTTCAATCCCAAAGgttagtttgc ... tttgctgcagTCTTTACTTCCAGATTACCAGAGGCTCTTGAGTTCTGCCCCTTCTCGTAGA

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: 37

GGTGTTTAATTTATGAGCTCTTTTCTGGTGCAAAGCTAACCAGGACAGAGGACCTTCGGAACACTGCTTCAATCCCAAAGgttagtttgc ... tttgctgcagTCTTTACTTCCAGATTACCAGAGGCTCTTGAGTTCTGCCCCTTCTCGTAGAATGAACCCTTCTAAACTTATTGACAACAGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatacattgttcatgcgtatcataaagttgttggtttccttctattttgctgcagTCTTTACTTCCAGATTACCAGAGGCTCTTGAGTTCTGCCCCTTCTCGTAGAATGAACCCTTCTAAACTTATTGACAACAGTG
                                  tttccttctattttgc  CT-rich tract
                 tatcataaa  TA-rich tract