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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgaattattgtcactctcataaatactgatgatcatgaaaactgtattagcatctgctattcaacttcctacccatcttattaccactgtttgcatatgaagtctagaagttctgtttcttctgaacatattataagctgccttacagcaacatgaagctacctatttgtcctaattgtttgctcaatgtgcagTAAATGGGTTATGATGCACAAGCTTACAAGGAGGCTAGCAAGAATTCCTGATGAAGTACGTACTGAAATAGAGCCATACTTTTTTGAGCATGCTTCTATT

Basic information

species Oryza sativa
transcript LOC_Os06g39520.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g39520.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G700221_T01 (Zea mays), 3'ss of exon 6
gtttgaattattgtcactctcataaatactgatgatcatgaaaactgtattag-catctgctattcaacttcctacccatcttattaccactgtttgcatatgaagtctagaagttctgtttcttctgaacatattataagctgccttacagcaacatgaagctacctatttgtcctaattgtttgctcaatgtgcagTAAATGGGTTATGATGCACAAGCTTACAAGGAGGCTAGCAAGAATTCCTGATGAAGTACGTACTGAAATAGAGCCATACTTTTTTGAGCATGCTTCTATT-
||| ||||   || ||| |||||| ||    || || |    || | |||||| ||| |  |  || ||   || || || |||| |        ||||| |  ||| |      |||| |      |||     | |||     |||||||  | ||   | | | | ||  |    | | | || ||  ||||||||||||||||||||||| |||| || || |||| ||| ||||||||||  ||| |||| || ||||||||||||||||||||| ||| |  | || || || 
gttcgaatctctgccacactcatatatctatatcatta-atcaattttattagtcatttatt--tctaccaactgcc-atgttatgattgac-cctgcatttatagttt-----ctctgctc-----gaagtccgtgtaa-----cttacag--atatcttgttgcattttattttctaatctgtg-tctttgtgcagTAAATGGGTTATGATGAACAAACTCACTAGGAAGCTTGCAAGAATTCTAGAT-AAGTGCGGACTGAAATAGAGCCATACTTTGTTGGGTGTTCTGCTGTTG

upper sequence: LOC_Os06g39520.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G140298_T01 (Zea mays), 3'ss of exon 7
gtttgaattattgtcactctcataaatactgatgatcatgaaaactgtattagcatctgctattcaacttcctacccatcttattaccactgtttgcatatgaagtctagaagttctgtttcttctgaacatattataagctgccttacagcaacatgaagctacctatttgtcctaattgtttgctcaatgtgcagTAAATGGGTTATGATGCACAAGCTTACAAGGAGGCTAGCAAGAATTCCTGATGAAGTACGTACTGAAATAGAGCCATACTTTTTTGAGCATGCTTCTATT
|||  |||   || ||| |||||| ||    || || |    || | |||||||   |  ||||     | | | |   | | |||| | ||      |||            || |  ||  | ||  || | |||  |   | |      | | ||  ||    ||||  | ||||||  |  ||   ||||||||||||||||||||||| |||| || || |||| ||| ||||||||||| |||||||| | |||||| ||||||||||||||| ||| || | || |||||
gttcaaatctctgccacactcatatatctatatcatta-atcaattttattagccatt--tattt---ctaccaactgccatgttacaattgaccctgtat------------ttatagtttctttgctcaaagtatgtgtaacttatagatatcttgttgcattttatt--ttctaatttgtgtctt--tgtgcagTAAATGGGTTATGATGAACAAACTCACTAGGAAGCTTGCAAGAATTCCAGATGAAGTGCATACTGATATAGAGCCATACTTTGTTGGGCGTTCTGCTATT

upper sequence: LOC_Os06g39520.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G079308_T01 (Zea mays), 3'ss of exon 11
gtttgaattattgtcactctcataaatactgatgatcatgaaaactgtattagcatctgctattcaacttcctacccatcttattaccactg--tttgcatatgaagtctagaagttctgtttcttctgaacatattataagctgccttacagcaacatgaagctacctatttgtcctaattgtttgctcaatgtgcagTAAATGGGTTATGATGCACAAGCTTACAAGGAGGCTAGCAAGAATTCCTGATGAAGTACGTACTGAAATAGAGCCATACTTTTTTGAGCATGCTTCTATT
||| ||||   || ||| ||||| | ||    | ||||     | | |||||||   |  ||||     | | | |   | | |||| | ||    ||||| |  ||| ||     |||| |       ||     | |||  | || |   |||             | | | | ||||||  |  ||   ||||||||||||||||||||||| |||| || || |||| ||| ||||||||||| |||||||| || ||||||||||||||||||||| ||| || | || |||||
gttcgaatctctgccacactcatta-tatcattaatca-----attttattagccatt--tattt---ctaccaactgccatgttacgattgaccctgcatttatagttta-----tctgctc-----aaagtccgtgtaacttaccctgttgca------------ttttattttctaatttgtgtctt--tgtgcagTAAATGGGTTATGATGAACAAACTCACTAGGAAGCTTGCAAGAATTCCAGATGAAGTGCGGACTGAAATAGAGCCATACTTTGTTGGGCGTTCTGCTATT

upper sequence: LOC_Os06g39520.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G025211_T01 (Zea mays), 3'ss of exon 8
gtttgaattattgtcactctcataaatactgatgatcatgaaaactgtattagcatctgctattcaacttcctacccatcttattaccactgtttgcatatgaagtctagaagttctgtttcttctgaacatattataagctgccttacagcaacatgaagctacctatt-tgtcctaattgtttgctcaatgtgcagTAAATGGGTTATGATGCACAAGCTTACAAGGAGGCTAGCAAGAATTCCTGATGAAGTACGTACTGAAATAGAGCCATACTTTTTTGAGCATGCTTCTATT-
||| ||||   || ||| |||||| ||    || || |    || | |||||||       ||| |  || ||||| |      |   ||  ||  |         |  | | || |  ||  ||||  || | |    | |  |||||||  | ||   | | | | || | | ||||||  |  ||   |||| |||||||||||||||||| |||| || || |||| ||| ||||||||||  ||| |||| || ||||||||||||||||||||| ||| || | || ||||| 
gttcgaatatctgccacactcatatatctatatcatta-atcaattttattagc------cattta--tttctaccaactgccatgttacgattgac---------cctgcatttatagtttctctgctcaaagtccgtg-taacttacag--atatcttgttgcattttattttctaatttgtgtctt--tgtgtagTAAATGGGTTATGATGAACAAACTCACTAGGAAGCTTGCAAGAATTCTAGAT-AAGTGCGGACTGAAATAGAGCCATACTTTGTTGGGCGTTCTGCTATTG

upper sequence: LOC_Os06g39520.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G406603_T02 (Zea mays), 3'ss of exon 4
gtttgaattattgtcactctcataaatactgatgatcatgaaaactgtattagcatctgctattcaacttcctacccatcttattaccactgtttgcatatgaagtctagaagttctgtttcttctgaacatattataagctgccttacagcaacatgaagctacctatttgtcctaattgtttgctcaatgtgcagTAAATGGGTTATGATGCACAAGCTTACAAGGAGGCTAGCAAGAATTCCTGATGAAGTACGTACTGAAATAGAGCCATACTTTTTTGAGCATGCTTCTATT
|||  |||   || ||| || ||| ||    || ||     || | || |||  ||| | |  |     | ||| |   | |||||| |   ||| ||  || | ||   |  || | | |  |   |  | ||  |||| |       | || | ||   | |  | ||| | ||||||  |  ||   ||||||||||||||||||||||| |||| || || |||| ||| ||||||||||| |||||||| || |||||||||||||||||||||||||||||| || |||||
gttgaaatctctgccacactgatatatctatatcatt----aatcagttttattatcagtttatt--tctgctaactgccatattacga---tttacac-tgcattc---atattttctctgcttgaagtacat-gtaagttatacgg-aacaccctgtcac-attttttttttctaatttatgtctt--tgtgcagTAAATGGGTTATGATGAACAAACTCACTAGGAAGCTTGCAAGAATTCCAGATGAAGTGCGGACTGAAATAGAGCCATACTTTTTTGAGCATTCTGCTATT

upper sequence: LOC_Os06g39520.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G330609_T01 (Zea mays), 3'ss of exon 2
gtttgaattattgtcactctcataaatactgatgatcatgaaaactgtattagcatctgctattcaacttcctacccatcttattaccactgtttgcatatgaagtctagaagttctgtttcttctgaacatattataagctgccttacagcaacatgaagctacctatt-tgtcctaattgtttgctcaatgtgcagTAAATGGGTTATGATGCACAAGCTTACAAGGAGGCTAGCAAGAATTCCTGATGAAGTACGTACTGAAATAGAGCCATACTTTTTTGAGCATGCTTCTATT
||| ||||   || ||| |||||| ||    || || |    || | |||||||   |  ||||     | | | |   | | |||| | ||      |||            || |  ||  ||||  || | |    | |  |||||||  | ||   | | | | || | | ||||||  |  ||   ||||||||||||||||||||||| |||| || || |||| ||| ||||||||||| |||||||| |  ||||| ||||||||||||||| ||| || | || |||||
gttcgaatctctgccacactcatatatctatatcatta-atcaattttattagccatt--tattt---ctaccaactgccatgttacgattgaccctgtat------------ttatagtttctctgctcaaagtccgtg-taacttacag--atatcttgttgcattttattttctaatttgtgtctt--tgtgcagTAAATGGGTTATGATGAACAAACTCACTAGGAAGCTTGCAAGAATTCCAGATGAAGTGCAGACTGATATAGAGCCATACTTTGTTGGGCGTTCTGCTATT

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), 67 (downstream exon)
Score: 37

AAGTAGATACATGGGTTGGTGCTCATGGTAAAAATGGAATGCGCAGAGACTGGCATATACGTGATTCTGTAACAGGCCATACAATATTGAAGGCTACAAGgtttgaatta ... caatgtgcagTAAATGGGTTATGATGCACAAGCTTACAAGGAGGCTAGCAAGAATTCCTGATGAAGTACGTACTGAAATAGAGCCATACTTTTTTGAGCATGCTTCTATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccttacagcaacatgaagctacctatttgtcctaattgtttgctcaatgtgcagTAAATGGGTTATGATGCACAAGCTTACAAGGAGGCTAGCAAGAATTCCTGATGAAGTACGTACTGAAATAGAGCCATACTTTTTTGAGCATGCTTCTATT
                              tcctaat  putative branch site (score: 37)
                                       tttgctc  putative PPT
                                 taattgttt  TA-rich tract