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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAACCTGATCTCCCTCGATTGCATGAGTGGCATTTCCGATCTGGACTGGATCGCTACATATGGATTGTGGGGATGATTTATGCTTATTACCATCCAACTgtatgtttcctgccaactgtgctatacttttacatagtgttcagttatagatgttctatttctttagttttatcaaatttcataaatcgcataaaagttg...

Basic information

species Oryza sativa
transcript LOC_Os03g19970.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g19970.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G020721_T01 (Zea mays), 5'ss of exon 9
TAAACCTGATCTCCCTCGATTGCATGAGTGGCATTTCCGATCTGGACTGGATCGCTACATATGGATTGTGGGGATGATTTATGCTTATTACCATCCAACTgtatgtttcctgccaactgtgctatacttttacatagtgttcagttatagatgttctatttctttagttttatcaa-------atttcataaatcgcataaaagttg--------------------------------
|||||| ||||| || || |||||||| ||||| || ||||||||||||||||||||||| ||||| ||||||||||| ||||| |||||||||||||||||||||||    |||  | |  | || || ||  |  | |     | |||||         | || |    | | |        ||||| | | || |   ||||||                                
TAAACCAGATCTTCCCCGGTTGCATGAATGGCAATTTCGATCTGGACTGGATCGCTACATTTGGATCGTGGGGATGATATATGCATATTACCATCCAACTgtatgtttttgaccatatatttttta-ttgtagttgttctgtttctttagattcatagaccccttggaggcaaccacatgattgtttcaaagagcgtaaggaagttgtattttggcattgatgaaatatcctgtctcag

upper sequence: LOC_Os03g19970.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA17G04070.1 (Glycine max), 5'ss of exon 9
TAAACCTGATCTCCCTCGATTGCATGAGTGGCATTTCCGATCTGGACTGGATCGCTACATATGGATTGTGGGGATGATTTATGCTTATTACCATCCAACTgtatgtttcctgccaactgtgctatacttttacatagtgttcagttatagatgttctatttctttagttttatcaaatttcataaatcgcataaaagttg-----------------------------------------------------------------------------
 ||| |  ||||  |||| |||||||| |||||||| || || || || || ||||||||||||||  | || ||||||||||||||||| |||||||||||| |||||             |||  ||||  |   |||  |  | |||||      | |||||  |    | |   |||  ||   | | || |  |                                                                              
CAAATCACATCTTTCTCGCTTGCATGAATGGCATTTTCGTTCAGGGCTTGACCGCTACATATGGATAATTGGAATGATTTATGCTTATTATCATCCAACTgtaagtttctcatt-------ttatgtttttgaaatatgtcaacatttagatccatcctctctttgatcgagtgatgattctgaagcaggaaaatatctctgatttctgtctcctcttttctttgctttcattttcctgagttgagtaccttattgtctgtcacatggtattataag

upper sequence: LOC_Os03g19970.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA07G36550.1 (Glycine max), 5'ss of exon 9
TAAACCTGATCTCCCTCGATTGCATGAGTGGCATTTCCGATCTGGACTGGATCGCTACATATGGATTGTGGGGATGATTTATGCTTATTACCATCCAACTgtatgtttcctgccaactgtgctatacttttacatagtgt-tcagttatagatgttctatttctttagttttatcaaatttcataaatcgcataaaagttg-----------------------------------------------------------------------------
 ||| |  ||||  |||| ||||||||||||||||| || || || || |||||||||||||||||  | || ||||||||||||||||| |||||||||||| |||||        |||  |  |  |      |     ||    ||  |  | |  | ||| |  ||   | ||  |||  ||   | | || |  |                                                                              
CAAATCACATCTTTCTCGCTTGCATGAGTGGCATTTTCGTTCAGGGCTTGATCGCTACATATGGATAATTGGAATGATTTATGCTTATTATCATCCAACTgtaagtttctcattttatgtttttgaaataagtgaaacaaatctaacatttagatccattctctctgattgagtgaagattctgaagcagaaaaacatctctgatttctgtctcctcctttttttgcttcaatttccctgatttgagtaccttattgtctgtcacatggcattacaag

upper sequence: LOC_Os03g19970.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AT3G06550.2 (Arabidopsis thaliana), 5'ss of exon 9
TAAACCTGATCTCCCTCGATTGCATGAGTGGCATTTCCGATCTGGACTGGATCGCTACATATGGATTGTGGGGATGATTTATGCTTATTACCATCCAACTgtatgtttcctgccaactgtgctatacttttacatagtgttcagttatagatgttctatttctttagttttatcaa---atttcataaatcgcataaaagttg-
 |||||| | || || |  |||||||||||||||||||| |||||||| ||||| |||||||||||  | |||||| | ||||| || ||||| ||||||||| ||| ||    |   |  ||  || |  ||    ||||||   || | |     | |  |  ||  ||| |     ||||| |  ||    ||     |  
AAAACCTCAGCTTCCCCTCTTGCATGAGTGGCATTTCCGCTCTGGACTTGATCGGTACATATGGATAATCGGGATGCTATATGCATACTACCACCCAACTgtaagttcccaat-actagaacttcacatcaactc--tgttcacaaatggttagctcagtgataaagacttaccgtttcatttccttgattatgtatcttatag

upper sequence: LOC_Os03g19970.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv05s0077g00620.t01 (Vitis vinifera), 5'ss of exon 9
TAAACCTGATCTCCCTCGATTGCATGAGTGGCATTTCCGATCTGGACTGGATCGCTACATATGGATTGTGGGGATGATTTATGCTTATTACCATCCAACTgtatgtttcctgccaactgtgctatacttttacatagtgttcagttatagatgttctatttctttagttttat---caaatttcataaatcg-cataaaagttg-----------------
 ||||   |  |  | || |||||||||||||||||||| || || || ||||| |||||||||||  | || ||||| ||||||||||| ||||| |||||| | ||||   |   | |||  |  |||   ||| | |  |||   |  | ||   ||| | ||  |  |    ||    | || |   |  || ||   ||                 
AAAACAAAAGTTTTCCCGTTTGCATGAGTGGCATTTCCGCTCAGGTCTTGATCGTTACATATGGATAATTGGAATGATATATGCTTATTATCATCCTACTgtaagcttccatgcccttttgccttgttttccaatattttcaagtacaacttatttcttttatctacatggagatacagtccttatgaggtgatattaataatgggcatttgttgatgtag

upper sequence: LOC_Os03g19970.1 (Oryza sativa), 5'ss of exon 9
lower sequence: PP1S5_239V6.1 (Physcomitrella patens), 5'ss of exon 9
-TAAACCTGATCTCCCTCGATTGCATGAGTGGCATTTCCGATCTGGACTGGATCGCTACATATGGATTGTGGGGATGATTTATGCTTATTACCATCCAACTgtatgtt--tcctgccaactg-tgctatactt-----------ttacatagtgttcagttatagatgttc-tatttctttagttttatcaaatttcataaat-cgca-taaaagttg--------------------------------------------------------------------------------
    |||      |||| | || ||||| ||||||||  |||| ||||||||||| || || ||||| || || ||| | |||||||||| ||||||||| |||||||  |   | || ||  | ||||   |           ||||  | |||||    ||| ||||   |  |  |||  ||||  ||  |   | | || |||| | |  | |                                                                                 
TGCGACCCCGCAGCCCTTGCTT-CATGAATGGCATTTTAGATCAGGACTGGATCGATATATTTGGATCGTCGGCATGCTCTATGCTTATTTCCATCCAACGgtatgttgatttggtcacctaattctatcggtagaagggcgatttacgca-tgttcctgaataaatgtgagtggtcttttcattttgacacgtagtacagatacgcagttatggctacggcgcgttaatttttcgaaattacagagggctcacttccacatatttgacaatgcttttcatgaacttcatgttggcag

upper sequence: LOC_Os03g19970.1 (Oryza sativa), 5'ss of exon 9
lower sequence: PP1S357_34V6.1 (Physcomitrella patens), 5'ss of exon 9
TAAACCTGATCTCCCTCGATTGCATGAGTGGCATTTCCGATCTGGACTGGATCGCTACATATGGATTGTGGGGATGATTTATGCTTATTACCATCCAACTgtatgtttcctgccaactgtgctatacttttacatagtgttcagttatagat---gttctatttctttagttttatcaaatttcataaatcgcataaaagttg
 || |        ||     ||||||| ||||| ||| |||| ||||||||||| ||||| ||||||||||| ||| | ||||| ||||  ||||| || |||| |  | |    ||| |  | |      | |    ||  |||||| | |   ||||      | | || |  | |  ||     | ||   | |      
AAAGCACCCCACTCCCTTGCTGCATGAATGGCACTTCAGATCAGGACTGGATCGATACATCTGGATTGTGGGCATGCTCTATGCGTATTTTCATCCTACGgtat-taacatttggacttttgtttcgaaagaaaagacgtatagttatcgtttgagttcgcagcatgttgtgtactaagtttctggcattcttgtcatgac--

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|88335711|gb|CI647067.1|CI647067
EST:     ATCGCTACATATGGATTGTGGGGATGATTTATGCTTATTACCATCCAACT                         GTTGAGAAGTGGATGGAGAAGCTTGAAGAAGCTGAAACGAAAACTAAACTC
genomic: ATCGCTACATATGGATTGTGGGGATGATTTATGCTTATTACCATCCAACTgtatgtttcc ... tgtgttgcagGTTGAGAAGTGGATGGAGAAGCTTGAAGAAGCTGAAACGAAAACTAAACTC
EST: gi|38475137|gb|CF959270.1|CF959270
EST:     ATCGCTATATATGGATTGTGGGGATGATTTATGCTTATTACCATCCAACT                         GTTGAGAAGTGGATGGAGAAGCTTGAAGAAGCTGAAACGAAAACTAAACTC
genomic: ATCGCTACATATGGATTGTGGGGATGATTTATGCTTATTACCATCCAACTgtatgtttcc ... tgtgttgcagGTTGAGAAGTGGATGGAGAAGCTTGAAGAAGCTGAAACGAAAACTAAACTC

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), 75 (downstream exon)
Score: 14

TAAACCTGATCTCCCTCGATTGCATGAGTGGCATTTCCGATCTGGACTGGATCGCTACATATGGATTGTGGGGATGATTTATGCTTATTACCATCCAACTgtatgtttcc ... tgtgttgcagGTTGAGAAGTGGATGGAGAAGCTTGAAGAAGCTGAAACGAAAACTAAACTCTATATTAAGGCCTTGATAGTTTCAATTGCTTTAACG




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