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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaccttttttttaacacttctttttaacatacatgtgctcattagattatttgcaattggactccatgtgtttatcatgaattttgtgatgcagTATCTAGTTCAATCGGCCGTTGATGGATATAATGTTTGTATATTTGCTTATGGGCAAACTGGTTCTGGAAAAACTTTTACAATTTATGGATCTGAAAACA

Basic information

species Oryza sativa
transcript LOC_Os04g57140.2
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g57140.2 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 17
----------------------------------------gtgaccttttttttaacacttc--tttttaacat-acatgtgctcattagattatttgcaatt-ggactccatgtgtttatcatgaattt-tgtgatgcagTATCTAGTTCAATCGGCCGTTGATGGATATAATGTTTGTATATTTGCTTATGGGCAAACTGGTTCTGGAAAAACTTTTACAATTTATGGATCTGAAAACA
                                        || |      |||||   ||    || ||  | | | |||  ||  | |  |||| | || || ||  | ||| || |  |  ||||||| ||||||||||||||| || ||||| || ||||||||||||||||| ||||||||||| ||||| ||||||||||||||||| ||||| || |||||||| || |||||||
gtgaatatttcaaatgctatcttttgtgttgatgccgtcggtaatacaaattttatttctaagattgttggcttcatatgatctgttgaatttatgttcattttgggtttcatatgatc-tgttgaatttatgtgatgcagTATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTATGGCCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGAAAACA

upper sequence: LOC_Os04g57140.2 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G423861_T02 (Zea mays), 3'ss of exon 17
---------------gtgaccttttttttaacacttctttttaacatacatgtgctcattag-attatttgcaattggactccatgtgtttatcatgaattt-tgtgatgcagTATCTAGTTCAATCGGCCGTTGATGGATATAATGTTTGTATATTTGCTTATGGGCAAACTGGTTCTGGAAAAACTTTTACAATTTATGGATCTGAAAACA
               |  | ||||| | |        |   ||| ||| || |  |   ||| | | ||  |    ||  | ||| || |  |  ||||||| |||||||||||| || || ||||| || |||||||||||||| ||||| |||||||| ||||| ||||||||||||||||| ||||| || |||||||| || || ||||
gtgaatatttcaaatgctatcttttgtgttgatgccatcagtaatataaattttatttctaggactgttcactga-gggtttcatatgat-gtgttgaatttatgtgatgcagTACCTGGTACAATCAGCTGTTGATGGATATAACGTTTGCATATTTGCATATGGTCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGATAACA

upper sequence: LOC_Os04g57140.2 (Oryza sativa), 3'ss of exon 18
lower sequence: GLYMA01G35950.1 (Glycine max), 3'ss of exon 19
-------------------------gtgaccttttttttaacacttctttttaacatacatgtgctcattagattatttgcaattggactccatgtgtttatcatg-aattttgtgatgcagTATCTAGTTCAATCGGCCGTTGATGGATATAATGTTTGTATATTTGCTTATGGGCAAACTGGTTCTGGAAAAACTTTTACAATTTATGGATCTGAAAACA-------
                          |    ||||  || | |   | | |  ||||  |  ||    | | ||| |||  | |      | |||| ||| |  || || ||||  ||||||||  |||| ||||| || || ||||| ||||||||||| |||||||||||||| ||||||||||||||||| ||||||||||| ||||||  ||||||||       
gtcttagtataacaaattatagatcatagttttttgctttagatagcatat--acattgaaatggatttaatattttttatactcattaccaatgtttttcttttggaaatttgcaatgcagtacttagTGCAATCTGCTGTGGATGGTTATAATGTTTGCATATTTGCTTATGGTCAAACTGGTTCTGGAAAGACTTTTACAATCTATGGAGTTGAAAACAATCCTGG

upper sequence: LOC_Os04g57140.2 (Oryza sativa), 3'ss of exon 18
lower sequence: GLYMA11G09480.1 (Glycine max), 3'ss of exon 19
-----------------------------gtgaccttttttttaacacttctttttaacatacatgtgctcattagattatttgcaattggactccatgtgtttatcatgaat-tttgtgatgcagTATCTAGTTCAATCGGCCGTTGATGGATATAATGTTTGTATATTTGCTTATGGGCAAACTGGTTCTGGAAAAACTTTTACAATTTATGGATCTGAAAACA
                              |    ||||  || | |     | |  |   | ||    | | ||  || | |  | |        |||| ||| |  || |  ||||  ||||||||  |||| ||||| || || ||||| ||||||||||| ||||||||||| || |||||||||||||| || ||||||||||| |||||| |||||||||
gcaagtcttagtataacaaattaaagatcctagttttttgctttagataatatgtacattgaaatagatttaatat-ttttctatactcattactaatgtttttcttttggacatttgcaatgcagTACTTAGTGCAATCTGCTGTAGATGGTTATAATGTTTGCATATTTGCTTACGGTCAAACTGGTTCTGGGAAGACTTTTACAATCTATGGAGCTGAAAACA

upper sequence: LOC_Os04g57140.2 (Oryza sativa), 3'ss of exon 18
lower sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 19
---------------gtgaccttttttttaacacttctttttaacatacatgtgctcattagattatttgcaattggactccatgtgtttatcatgaattttgtgatgcagTATCTAGTTCAATCGGCCGTTGATGGATATAATGTTTGTATATTTGCTTATGGGCAAACTGGTTCTGGAAAAACTTTTACAATTTATGGATCTGAAAACA
                 | |   |  |||| ||  | | |||    |  ||| |  ||| | || | || || |        ||   ||| || || |||| |  ||||||||| | || || || || || ||||| ||||||||||| |||||||| ||||| |||||||| |||||||| || |||||||| ||||||||||| ||||
gtatttgaggatacaaaggcaagtcatttatcatatttatttcttgtttatgggaacat-atataacttacactca----ttatcaatttctcgtggattt-gcaatgcagTATTTGGTGCAGTCTGCTGTAGATGGTTATAATGTTTGCATATTTGCCTATGGTCAAACTGGCTCTGGAAAGACATTTACAATCTATGGATCTGACAACA

upper sequence: LOC_Os04g57140.2 (Oryza sativa), 3'ss of exon 18
lower sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 22
gtgaccttttttttaacacttctttttaacatacatgtgctcattagattatttgcaattggactccatgtgtttatcatgaattttgtgatgcagTATCTAGTTCAATCGGCCGTTGATGGATATAATGTTTGTATATTTGCTTATGGGCAAACTGGTTCTGGAAAAACTTTTACAATTTATGGATCTGAAAACA
|  |    |   ||   | || ||| |  | ||      |  ||   || | || || |        |    ||| || || |||| |  ||||||||| | || ||||| || || ||||| ||||||||||| |||||||||||||| |||||||| |||||||| || |||||||| |||||||| || | ||
gcaagtcataaattg-tatttatttcttgcttatggaaacatat---ataacttacactca----ttaccaatttctcgtgtattt-gcaatgcagTATTTGGTGCAATCTGCTGTAGATGGTTATAATGTTTGCATATTTGCTTATGGTCAAACTGGATCTGGAAAGACATTTACAATCTATGGATCGGACATCA

upper sequence: LOC_Os04g57140.2 (Oryza sativa), 3'ss of exon 18
lower sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 16
gtgaccttttttttaacacttctttttaac-atacatgtgctcattagattatttgcaattggactccatgtgtttatcatgaattttgtgatgcagTATCTAGTTCAATCGGCCGTTGATGGATATAATGTTTGTATATTTGCTTATGGGCAAACTGGTTCTGGAAAAACTTTTACAATTTATGGATCTGAAAACA
             ||  | |  | | ||||  |     |   | ||  ||  ||||  |||    |     |  | |    |  ||   |    |||||| | || || ||||| || ||||| ||||| ||||| || ||||| ||||| ||||||||||||||||||||||| || || |||||   ||| | ||
------------gtattattgatatgtaactgtgttcatttacctttcatcctttgttattttcttgtggttactaacatcgttttccttttaacagTATTTGGTACAGTCGGCTGTAGATGGGTATAACGTTTGCATCTTTGCATATGGTCAAACTGGTTCTGGAAAAACTTTCACTATATATGGGCATGAGAGCA

upper sequence: LOC_Os04g57140.2 (Oryza sativa), 3'ss of exon 18
lower sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 18
gtgaccttttttttaacacttctttttaacatacatgtgctcattagattatttgcaattggactccatgtgtttatcatgaattttgtgat-gcagTATCTAGTTCAATCGGCCGTTGATGGATATAATGTTTGTATATTTGCTTATGGGCAAACTGGTTCTGGAAAAACTTTTACAATTTATGGATCTGAAAACA
|  |  |     | |  | |  || ||| || || |||  | |||| |||| ||   | |  |     |||| |  |    |  ||| |||| ||||||| | ||||||||||| || |||||||||||||| || |||||||| ||||| || |||||||||||||| || || ||||||||||| |||||    |
gcaag-tcaacatcatgaatgtttgttagca-acttgt-ttgattacattaattagtagttcaagttgtgtgatattttctatgtttatgattgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATATGGTCAGACTGGTTCTGGAAAGACATTCACAATTTATGGTTCTGATGGTA

upper sequence: LOC_Os04g57140.2 (Oryza sativa), 3'ss of exon 18
lower sequence: PP1S199_47V6.1 (Physcomitrella patens), 3'ss of exon 20
--------------------------------------------------------------------------------------gtgaccttttttttaacacttctttttaacatacatgtgctcattagattatttgcaa--ttggactccatgtgtttatcatgaattttgtgatgcagTATCTAGTTCAATCGGCCGTTGATGGATATAATGTTTGTATATTTGCTTATGGGCAAACTGGTTCTGGAAAAACTTTTACAATTTATGGATCTGAAAACA
                                                                                       | |       |  || || |   ||  |   || |||     |   || |||    |  |||   ||   | || || | ||  ||      |||||||| | || ||||| ||  |||| ||||| ||||| ||||||||||| || ||||||||||| || || ||||| ||||| ||||| || ||||| ||||
gtatagttggtcagagtaattgagtcaatccgtgcaatctttttatcatggaatggctttggttgtaactactgatcccgatgagaataaaaccaactaaaagaccttgattagatcgacttgtttatttggtatcattgaatactttgtcttctgcgcgtctaacgtgctttaatgtgtgcagTATTTGGTCCAATCAGCAATTGACGGATACAATGTCTGTATATTTGCATACGGGCAAACTGGGTCAGGCAAAACGTTTACGATTTACGGTTCTGACAACA

upper sequence: LOC_Os04g57140.2 (Oryza sativa), 3'ss of exon 18
lower sequence: PP1S83_25V6.1 (Physcomitrella patens), 3'ss of exon 19
gtgaccttttttttaacacttctttttaacatacatgtgctcattagattatttgcaat-----tggactccatgtgtttatcatgaattttgtg-atgcagTATCTAGTTCAATCGGCCGTTGATGGATATAATGTTTGTATATTTGCTTATGGGCAAACTGGTTCTGGAAAAACTTTTACAATTTATGGATCTGAAAACA
     | |  || |    ||  |||     || ||    ||   | | |  |    |||     || | ||   |    || ||||||| |   |  |||||||| | || ||||| ||  ||||||| || ||||| ||||| ||||| || || |||||||| || || ||||||||||| |||||||| |||||||| |
--acacctagttgtcctgctgttttagggtattcaaaaacttcattgttattcaataatgattctgtattctgcgcagctaacatgaatgtaacgtgtgcagTATTTGGTCCAATCAGCGATTGATGGGTACAATGTCTGTATTTTTGCATACGGACAAACTGGATCAGGGAAAACTTTTACTATTTATGGTTCTGAAAATA

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: 61 (upstream exon), 72 (downstream exon)
Score: 8

AGTTGCACATCCATGGAAAGATGACAAGTCAAAACAACATATATATGACCGTGTTTTTGATGCTAACACTACCCAAGAAGAAGTATTTGAGGACACGAAGgtgacctttt ... tgtgatgcagTATCTAGTTCAATCGGCCGTTGATGGATATAATGTTTGTATATTTGCTTATGGGCAAACTGGTTCTGGAAAAACTTTTACAATTTATGGATCTGAAAACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattagattatttgcaattggactccatgtgtttatcatgaattttgtgatgcagTATCTAGTTCAATCGGCCGTTGATGGATATAATGTTTGTATATTTGCTTATGGGCAAACTGGTTCTGGAAAAACTTTTACAATTTATGGATCTGAAAACA
                               tttatcatgaatttt  TA-rich tract