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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGGCAATAGCAAAAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTACATGGGTACCTgtaagttgatctcattcacgaagtgtatcattatagatgttctggtggaaacacttaattctcattctcatcttcag

Basic information

species Oryza sativa
transcript LOC_Os09g10600.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g10600.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G079256_T01 (Zea mays), 5'ss of exon 3
ATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGGCAATAGCAAAAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTACATGGGTACCTgtaagttgatctcattcacgaagtgtatcattatagatgttctggtggaaa--cacttaattctcattctcatctt-cag
|||||| ||||||||||||||||||||||| ||||| |||||||| || || ||||||||||| |||||||| ||||||||||||||||||||||| |||||||||||||||||||   | | | |||| |  | |||||||||| | |||   | |      | ||    || ||  ||
ATTTATAGCTGGAGTTGCTGATGATAATGGTTATGGTTGGGCAATTGCTAAGGCTCTTGCTGCTGCTGGTGCTGAGATTCTTGTTGGTACATGGGTGCCTgtaagttgatctcatttgtgtaatttatcgtactggatgttctggcgtaaaattattctggagttatcaaaattttgtag

upper sequence: LOC_Os09g10600.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA18G31780.1 (Glycine max), 5'ss of exon 2
ATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGGCAATAGCAAAAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTACATGGGTACCTgtaagttgatctcattcac------gaagtgtat-----cattatagatgttctggtggaaacacttaattctcattctcatcttcag-----------------------------------
 || |||||||| || |||||||| ||||| ||||||||||||||||||||| |||| || ||||| || || || |||||||| || ||||||||||||||||||  || | | | |       | ||||| |     |||| |  |  ||      ||||   |    ||||  |   || | ||                                    
TTTCATTGCTGGTGTGGCTGATGACAATGGATATGGCTGGGCAATAGCAAAATCTCTCGCAGCAGCAGGAGCTGAAATTCTTGTCGGCACATGGGTACCTgtaagtaaatattactgattctggtgtagtgtgtttgtacattgtttacttttaccctgaaatgatggcatctctgtgaaatatacaagtggtcaggtactaactttgaacattttcatgcag

upper sequence: LOC_Os09g10600.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA08G45990.1 (Glycine max), 5'ss of exon 3
ATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGGCAATAGCAAAAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTACATGGGTACCTgtaagttgatctcattcac------gaagtgtat-----cattatagatgttctggtggaaacacttaattctcattctcatcttcag-----------------------------------
 || |||||||| || |||||||| ||||| ||||||||||||||||||||| ||||||| ||||| || || || |||||||| || ||||||||||||||||||  || ||| | |       | ||||| |     |||| |  |  ||      ||||   |    ||||  | | || | ||                                    
TTTCATTGCTGGTGTGGCTGATGACAATGGATATGGCTGGGCAATAGCAAAATCTCTTGCAGCAGCAGGAGCTGAAATTCTTGTCGGCACATGGGTACCTgtaagtaaatatcactgattctggtgtagtgtgtttgcacattgtttacttttaccctgaaatcatgttatctctgtgtaatatacaagtggtcaggttctaacttcgaacattttcatgcag

upper sequence: LOC_Os09g10600.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA11G10770.1 (Glycine max), 5'ss of exon 3
ATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGGCAATAGCAAAAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTACATGGGTACCTgtaagttg-------atctcattcacgaagtgtatcattatagatgttctggtggaaacacttaattctcatt-ctcatcttcag----------------------------------------------------------------------------------
 ||||||||||| ||||||||||| ||||| ||||| |||||||| |||||| ||||||||||||| || || || ||||||||||| |||||||||||||||||||        || |     |  || ||  |   |||   |          |  |||    ||||   | || |  ||  |                                                                                  
TTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGGCAATTGCAAAATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCACATGGGTACCTgtaagttatttgtttattttggataaaaaatgggtacctatcagttgatatacaaattcacgaggttctgtctgctgacttttggaacaacacctcccccctccagtgcatatgttttccagtccttttacggtgatacatttactaactgtgaactatttctatag

upper sequence: LOC_Os09g10600.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA12G03060.1 (Glycine max), 5'ss of exon 4
ATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGGCAATAGCAAAAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTACATGGGTACCTgtaagttg-------atctcattcacgaagtgtatcattatagatgttctggtggaaacacttaattctcatt-ctcatcttcag------------------------------------------------------------------------------------
 ||||||||||| ||||||||||| ||||| ||||| |||||||| |||||||||||||||||||| || || ||||| |||||||| |||||||||||||||||||        || |     |  || ||  |   |||   |        | |  |||    ||||   | || |  ||  |                                                                                    
TTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGGCAATTGCAAAAGCTCTTGCTGCAGCAGGAGCTGAGATCCTTGTTGGCACATGGGTACCTgtaagttatttgtttattttggataaaaaatgggtatctatcagttgatatacgaattcacgaggttctgtctgctgacttttggaacaacacctcccccctccagtgcatatgttttttccagtccttttgtgctgatacatttactaactgtgaaccatttctatag

upper sequence: LOC_Os09g10600.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT2G05990.2 (Arabidopsis thaliana), 5'ss of exon 3
ATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGGCAATAGCAAAAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTACATGGGTACCTgtaagttgatctcattcacgaagtgtatcattatagatgttctggtggaaacacttaattctcattc--tcatcttcag-
 || ||||||||  | |||||||||||||||||||| ||||| ||||||||| |||||||||| ||||| || || ||  | ||||| || ||||| |||||||||   | |   |   |  |  | |  ||       ||         | ||| |  | | | |   |  ||| |   
TTTCATTGCTGGTATAGCTGATGATAATGGCTATGGTTGGGCCATAGCAAAATCTCTTGCTGCTGCTGGAGCTGAAATATTGGTTGGGACTTGGGTTCCTgtaagtcatttttggttcagctgcttttagtttccttcattgcta-aattatactaacctatgaatggatggtctactag

upper sequence: LOC_Os09g10600.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv08s0007g06390.t01 (Vitis vinifera), 5'ss of exon 3
ATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGGCAATAGCAAAAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTACATGGGTACCTgta----agttgatctca-ttcacgaagtgtatcatt-atagat----------gttctggtggaaacacttaattctcattctcatcttcag------------------------------------
||||||||| || || |||||||||||||| ||||| ||||||||||||||| | |||||||| || || || || |||||| |||| |||||||| ||||||    | ||  ||| | |||   || ||  |  |  |||||           |||||||    ||   ||  |||    |   || ||                                       
ATTTATTGCGGGTGTAGCTGATGATAATGGATATGGTTGGGCAATAGCAAAATCGCTTGCTGCTGCAGGAGCTGAAATTCTTATTGGCACATGGGTGCCTgtatgtaaattattctaacttctttaattgacttgtggatagactgattcatgagttctggcaacaatgttttgttccttgtaaaatattttattttttaatgataataataattttttattttcatag

upper sequence: LOC_Os09g10600.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv06s0004g01310.t01 (Vitis vinifera), 5'ss of exon 3
ATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGGCAATAGCAAAAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTACATGGGTACCTgtaagttgatctcattcacgaagtgtatcattatagatgttc-tggtggaaacacttaattctcattctcatcttcag----------------------------
 ||||||||||| ||||||||||| ||||| ||||| ||||||||||| ||| ||||||| || || ||||| || ||||||||||| |||||||| |||||||||  ||   | | |  |  | ||||||| |     ||  |    ||   |  | |  |   | |  | | |  |                            
CTTTATTGCTGGTGTTGCTGATGACAATGGATATGGTTGGGCAATAGCCAAATCTCTTGCAGCTGCAGGTGCTGAAATTCTTGTTGGCACATGGGTTCCTgtaagtaaat--taatgatcacatatatcattctctgctttaatcacagagtaatctgagccatgt-caaaccattggattactaactgggaagctccttgtgtag

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|58660187|gb|CK048867.1|CK048867
EST:     AAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTACATGGGTACCT                         GCACTGAACATATTTGAGAC
genomic: AAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTACATGGGTACCTgtaagttgat ... tcatcttcagGCACTGAACATATTTGAGAC
EST: gi|58658677|gb|CK047357.1|CK047357
EST:     AAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTACATGGGTACCT                         GCACTGAACATATTTGAGACAAGCTTGAGGCGTGGGAAGTTTGACGAATCA
genomic: AAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTACATGGGTACCTgtaagttgat ... tcatcttcagGCACTGAACATATTTGAGACAAGCTTGAGGCGTGGGAAGTTTGACGAATCA
EST: gi|29670466|gb|CB666741.1|CB666741
EST:     AAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTACATGGGTACCT                         GCACTGAACATATTTGAGACAAGCTTGAGGCGTGGGAAGTTTGACGAATCA
genomic: AAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTACATGGGTACCTgtaagttgat ... tcatcttcagGCACTGAACATATTTGAGACAAGCTTGAGGCGTGGGAAGTTTGACGAATCA
EST: gi|58655118|gb|CK043798.1|CK043798
EST:     AAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTACATGGGTACCT                         GCACTGAACATATTTGAGACAAGCTTGAGGCGTGGGAAGTTT
genomic: AAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTACATGGGTACCTgtaagttgat ... tcatcttcagGCACTGAACATATTTGAGACAAGCTTGAGGCGTGGGAAGTTT
EST: gi|29640101|gb|CB645110.1|CB645110
EST:     AAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTACATGGGTACCT                         GCACTGAACATATTTGAGACAAGCTTGAGGCGTGGGAAGTTTGACGAATCA
genomic: AAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTACATGGGTACCTgtaagttgat ... tcatcttcagGCACTGAACATATTTGAGACAAGCTTGAGGCGTGGGAAGTTTGACGAATCA

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: 67 (upstream exon), 56 (downstream exon)
Score: 38

ATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGGCAATAGCAAAAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTACATGGGTACCTgtaagttgat ... tcatcttcagGCACTGAACATATTTGAGACAAGCTTGAGGCGTGGGAAGTTTGACGAATCACGAAA




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGGCAATAGCAAAAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTACATGGGTACCTgtaagttgatctcattcacgaagtgtatcattatagatgttctggtggaaacacttaattctcattctcatcttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG