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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtgcctcttctggttctccattttgcatcgtttcatttgggatgtttgaaattttaactaacaatgcaatttttggttgttaattagATCACCCGTGGATCAAGGAAGATGGAGAAGCACCTGACACGCCGCTTGACAACGCTGTCATGAACAGGCTCAAGCAGTTCAGGGCTATGAACCAATTCAA

Basic information

species Oryza sativa
transcript LOC_Os01g59360.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g59360.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G167276_T01 (Zea mays), 3'ss of exon 2
gtacgtgcctcttctggttctccattttgcatcgtttcatttgggatgtttgaaattttaa-ctaacaatgcaatttttggttgttaattagATCACCCGTGGATCAAGGAAGATGGAGAAGCACCTGACACGCCGCTTGACAACGCTGTCATGAACAGGCTCAAGCAGTTCAGGGCTATGAACCAATTCAA
||| |||    |   |   |  ||  ||    |  ||  | |  ||  | ||||      | || | |  |       ||  ||      ||| || || ||||||||||||||||| ||||| ||||||||||| || ||||||||||||||||||||||| |||||||||| ||| |||||||| |||||
gtatgtggtcgtcaagaagcagcagcttattactctttttcttcgagttctgaatcgccgagctgaaacggaggcacctgtctgccctgcagACCATCCTTGGATCAAGGAAGATGGCGAAGCGCCTGACACGCCACTGGACAACGCTGTCATGAACAGGCTGAAGCAGTTCAAGGCGATGAACCAGTTCAA

upper sequence: LOC_Os01g59360.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AC203294.3_FGT001 (Zea mays), 3'ss of exon 1
gtacgtgcctcttctggttctccattttgcatcgtttcatttgggatgtttgaaattttaactaacaatgcaatttttggttgttaattagATCACCCGTGGATCAAGGAAGATGGAGAAGCACCTGACACGCCGCTTGACAACGCTGTCATGAACAGGCTCAAGCAGTTCAGGGCTATGAACCAATTCAA----------------
                                                           |  |   ||  || ||  | |   |     ||| || || |||||||||||||| || ||||| ||||||||||| || |||||||||||||||||||||||||||||||||| ||| |||||||| |||||                
----------------------------------------------------------gagttcctaaaccacttggttgaaatgtgccagaccatccttggatcaaggaagacggtgaagcgcctgacacgccactggacaacgctgtcatgaacagGCTCAAGCAGTTCACGGCAATGAACCAGTTCAAGAAGGCCGCGCTGAGG

upper sequence: LOC_Os01g59360.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA20G08140.1 (Glycine max), 3'ss of exon 3
---------------------------------------------------gtacgtgcctcttctggttctccattttgcatcgtttcatttgggatgtttga-aattttaactaacaatgcaatttttggttgttaattagATCACCCGTGGATCAAGGAAGATGGAGAAGCACCTGACACGCCGCTTGACAACGCTGTCATGAACAGGCTCAAGCAGTTCAGGGCTATGAACCAATTCAA
                                                    |||  | | |||          ||  |     | || | | ||||  ||    || | |||  | ||||| | || ||   |   ||  |||||| || ||||||||||| || || |||||||| || | ||| |||||||| |||||  |||| |||||||| || || || || ||||||||||||||
gtaagcactcattattcttcgctgtttttgtttcaccttcaattctttgtcttactagtcgcttgaatcctcttataatttcatgatttactggggaaattaatcaactctaataatcaatgaacttgttatgttaaaaacagATCATCCTTGGATCAAGGAGGACGGCGAAGCACCAGATAAGCCTCTTGACAATGCTGTACTGAATAGGCTCAAACAATTTAGAGCAATGAACCAATTCAA

upper sequence: LOC_Os01g59360.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA02G44720.1 (Glycine max), 3'ss of exon 3
--------------------------------------gtacgtgcctcttctggttctccattttgcatcgtttcatttgggatgtttgaaattttaactaacaatgcaatttttggttgtt-----aattagATCACCCGTGGATCAAGGAAGATGGAGAAGCACCTGACACGCCGCTTGACAACGCTGTCATGAACAGGCTCAAGCAGTTCAGGGCTATGAACCAATTCAA
                                        | || | |  | |   | |  ||||| |       |     |  || || ||       |||| || |||  ||||  ||  |     ||  |||||| || ||||||||||| |||||||||||||| || || || ||||||||||| ||  |||| |||||||| |||||||| || |||||| |||||||
gtacgtataatattgacttcctttctatgaattcgactacatgttcttgatttacatattaattttactatagcccgggcagattggttcaatgcaattctaataaagcacattttactttatgtgaaaaacagATCATCCATGGATCAAGGAGGATGGAGAAGCACCAGATACACCTCTTGACAACGCAGTACTGAATAGGCTCAAACAGTTCAGAGCAATGAACGAATTCAA

upper sequence: LOC_Os01g59360.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA07G36000.1 (Glycine max), 3'ss of exon 3
----------------------------------------------------gtacgtgcctcttctggttctccattttgcatcgtttcatttgggatgtttgaaattttaactaacaatgcaatttttggttgttaattagATCACCCGTGGATCAAGGAAGATGGAGAAGCACCTGACACGCCGCTTGACAACGCTGTCATGAACAGGCTCAAGCAGTTCAGGGCTATGAACCAATTCAA
                                                     |||   || |||    |     |   |     | || | |   ||  ||    ||| |||  | |   | |  | ||   |   ||  |||||| || ||||||||||| ||||| |||||||| || |  || |||||||| |||||  |||| ||||| || || ||||| || ||||||||||||||
gtaagcatatatcctccactgtttttgtttcaccttcaatcaattattttttttacaaaccgcttgaattcacttacaatttcatgatttactaacgaaatt---gattataataatcggcgaacgtgttatgttaaaaacagATCATCCATGGATCAAGGAGGATGGCGAAGCACCAGATAAACCACTTGACAATGCTGTACTGAATAGGCTGAAACAATTCAGAGCAATGAACCAATTCAA

upper sequence: LOC_Os01g59360.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA14G04010.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------gtacgtgcctcttctggttctccattttgcatcgtttcatttgggatgtttgaaattttaactaacaatgcaatttttggttgttaatt-----------agATCACCCGTGGATCAAGGAAGATGGAGAAGCACCTGACACGCCGCTTGACAACGCTGTCATGAACAGGCTCAAGCAGTTCAGGGCTATGAACCAATTCAA
                                                    | | |  | ||    |  ||||| | |     ||       || || ||       |||| || |   |||||  || || |||           |||||| || ||||||||||| |||||||||||||| || || || |||||||| || ||  |||| |||||||| |||||||| || ||||||||||||||
gtgcgtataatattgacttcctttctatgaacatcttgaattcaactaggaattcttgatttgcaaattaattttactttagcccagacaaattggttcaatgcaattctaataaagtcttttttatttttttattttgtgaaaaacagATCATCCATGGATCAAGGAGGATGGAGAAGCACCAGATACACCTCTTGACAATGCAGTACTGAATAGGCTCAAACAGTTCAGAGCAATGAACCAATTCAA

upper sequence: LOC_Os01g59360.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv06s0009g03150.t01 (Vitis vinifera), 3'ss of exon 3
-----gtacgtgcctcttctggtt--ctccattttgcatcgt-ttcatttgggatgtttgaaattttaactaacaatg-caatttttggttgttaattagATCACCCGTGGATCAAGGAAGATGGAGAAGCACCTGACACGCCGCTTGACAACGCTGTCATGAACAGGCTCAAGCAGTTCAGGGCTATGAACCAATTCAA
     ||  |    | ||  ||    ||   |||    || |  | | ||  |||||| |  |||  |  |     ||  ||  ||   || ||  |||||||| || ||||| ||||| ||||||||||||||||| || || |||||||| || ||  |  | ||| |||| ||||| || || |||||| | |||||
actgagtttggagatatttaggaaaactttgtttgaagtcatacttaattatgatgttagccattgcacatttttctgataaaattcaattttttcttagATCATCCATGGATTAAGGAGGATGGAGAAGCACCTGATACTCCTCTTGACAATGCAGTTTTTGAAAGGTTCAAACAGTTTAGAGCAATGAACAAGTTCAA

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), 74 (downstream exon)
Score: 111

AGTGACCCATGGCCACGCATTTCAGCTAGCGCCAAGGACCTTGTCAGGAAGATGCTCAACTCCGACCCCAAGAAGAGAATTTCAGCCTACGAAGTCCTCAgtacgtgcct ... tgttaattagATCACCCGTGGATCAAGGAAGATGGAGAAGCACCTGACACGCCGCTTGACAACGCTGTCATGAACAGGCTCAAGCAGTTCAGGGCTATGAACCAATTCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatttgggatgtttgaaattttaactaacaatgcaatttttggttgttaattagATCACCCGTGGATCAAGGAAGATGGAGAAGCACCTGACACGCCGCTTGACAACGCTGTCATGAACAGGCTCAAGCAGTTCAGGGCTATGAACCAATTCAA
                       aactaac  putative branch site (score: 111)
            tttgaaattttaacta  TA-rich tract