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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGTAAAGCATGAGCAAAAGCTTGACTGTGGTGGTGGATATGTCAAGTTGCTTGGTGGTGATGTTGACCAGAAGAAATTTGGTGGGGACACACCGTACAGgtaatgattttcttctattgtagctctgattctcacttttctcaagattagtactagttatctaacttggtacttttgaatgcag

Basic information

species Oryza sativa
transcript LOC_Os07g14270.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g14270.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G358059_T01 (Zea mays), 5'ss of exon 3
CTGTAAAGCATGAGCAAAAGCTTGACTGTGGTGGTGGATATGTCAAGTTGCT---TGGTGGTGATGTTGACCAGAAGAAATTTGGTGGGGACACACCGTACAGgtaatgattttcttctattgtagctctgattctcacttttctcaagattagtactagttatctaacttggtacttttgaa-tgcag
   | ||||| ||||| ||||||||||| |||||||| || |||||||||||   |||||||||||| |||||||||||||||||||| |||||| | ||||||||    ||      |||||| || ||  ||||| || |   ||    |  |  |     | |||| |  | ||| || | |||||
---TGAAGCACGAGCAGAAGCTTGACTGCGGTGGTGGCTACGTCAAGTTGCTGGGTGGTGGTGATGTAGACCAGAAGAAATTTGGTGGAGACACATCTTACAGgtagactttgaacaatattgttgcgctccttctccctat---catatctcatcttgtacttgtaacctcattcttctgtactgcag

upper sequence: LOC_Os07g14270.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G074687_T01 (Zea mays), 5'ss of exon 3
CTGTAAAGCATGAGCAAAAGCTTGACTGTGGTGGTGGATATGTCAAGTTGCTTGGTGGTGATGTTGACCAGAAGAAATTTGGTGGGGACACACCGTACAGgtaatgattttcttctattgtagctctgattctcacttt--tctcaagattagtactagttatctaacttggtacttttgaatgcag
|||| ||||| ||||| |||||||||||||||||||| || ||||||||||| ||||||||||| |||||||| ||||| |||||||||||| | ||||||||    | |   | |||| | |  ||  ||||| || |  | ||     | ||| ||||  | ||||||  | ||| || ||||||
CTGTGAAGCACGAGCAGAAGCTTGACTGTGGTGGTGGTTACGTCAAGTTGCTGGGTGGTGATGTAGACCAGAAAAAATTCGGTGGGGACACAACTTACAGgtagcc-tatggatatattcttgtactttttctccctatcatatctgatcttgtagtagtagt-taacttcattcttctgtatgcag

upper sequence: LOC_Os07g14270.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA10G28890.1 (Glycine max), 5'ss of exon 3
CTGTAAAGCATGAGCAAAAGCTTGACTGTGGTGGTGGATATGTCAAGTTGCTTGGTGGTGATGTTGACCAGAAGAAATTTGGTGGGGACACACCGTACAGgtaatgattttcttctattgtagctctgattctcacttttctcaagattagtactagttatctaac--ttggtacttttgaatgcag-------------
|||| ||||| || || |||||||||||||||||||| ||  | ||||||||  |||| |||||||| |||||||||||||| ||||| || || ||||||| ||   | | | |  || | | | || | |||  |  |     |     |    ||| |  |||   || |  |||   ||                 
CTGTTAAGCACGAACAGAAGCTTGACTGTGGTGGTGGCTACATGAAGTTGCTCAGTGGGGATGTTGATCAGAAGAAATTTGGCGGGGATACTCCTTACAGgtgatttatatatcccctt-ttgatttgctgctctttcctgatgggtgcctttgatgttgtaaaacagctgatcttttgacatttgttgttctgttgcag

upper sequence: LOC_Os07g14270.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA20G23080.2 (Glycine max), 5'ss of exon 3
CTGTAAAGCATGAGCAAAAGCTTGACTGTGGTGGTGGATATGTCAAGTTGCTTGGTGGTGATGTTGACCAGAAGAAATTTGGTGGGGACACACCGTACAGgtaatg-----attttcttcta--ttgtagctctgattctcacttttctcaagattagtactagttatctaacttggtacttttgaatgcag--------
|||| |||||||| || ||||||||||| |||||||| ||  | ||||||||  ||||||||||||| |||||||||||||||||||| || || ||||||| ||      ||   ||| |   |||| |||||  | || |    |  |     ||   | |   | || || |  ||   ||   ||           
CTGTCAAGCATGAACAGAAGCTTGACTGCGGTGGTGGCTACATGAAGTTGCTCAGTGGTGATGTTGATCAGAAGAAATTTGGTGGGGATACTCCTTACAGgtgatttatatatccccttttgatttgttgctctt-tcctgatgggtgcctctcatatcgcaaaacacctgaccttttaacatttgttgttctgttgcag

upper sequence: LOC_Os07g14270.3 (Oryza sativa), 5'ss of exon 3
lower sequence: AT1G56340.1 (Arabidopsis thaliana), 5'ss of exon 3
CTGTAAAGCATGAGCAAAAGCTTGACTGTGGTGGTGGATATGTCAAGTTGCTTGGTGGTGATGTTGACCAGAAGAAATTTGGTGGGGACACACCGTACAGgtaatgattttcttctattgtagctctgattctcacttttctcaagattagtactagttatctaacttggtacttttgaatgcag
|||| ||||||||||| |||||||||||||||||||| ||  | ||||||||  ||| |||||||||||||| |||||| || || ||||| || |||||||  || |||||   || | |       |   |||    |   || |  ||      ||||||  |||     ||||   |||||
CTGTCAAGCATGAGCAGAAGCTTGACTGTGGTGGTGGCTACATGAAGTTGCTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAGgtg-tgtttttcggttactttcatatcaaacttcaaacattcaaacaccag----gcttatctttctt----tttttatctgcag

upper sequence: LOC_Os07g14270.3 (Oryza sativa), 5'ss of exon 3
lower sequence: AT1G09210.1 (Arabidopsis thaliana), 5'ss of exon 3
CTGTAAAGCATGAGCAAAAGCTTGACTGTGGTGGTGGATATGTCAAGTTGCTTGGTGGTGATGTTGACCAGAAGAAATTTGGTGGGGACACACCGTACAGgtaatgattttcttctattgtagctctgat--tctcacttttctcaagattagtactagttatctaacttggta-----------cttttgaatgcag
| || ||||| ||||||||||||||||| |||||||| ||  | ||| | ||  |||||||||||||||| |||||||||||||| |||||||| ||||||||   ||  | |   ||  |  |||| ||  |||||   |  |    ||||  |  | |  |  ||  |   |            ||||   |||||
CAGTCAAGCACGAGCAAAAGCTTGACTGCGGTGGTGGCTACATGAAGCTACTAAGTGGTGATGTTGACCAAAAGAAATTTGGTGGAGACACACCATACAGgtacaaatcctatctcatc-tcactcttatcatctcaacctattatcaattaacatcaatgtttaaaaataacaacccatctgcttttttacctgcag

upper sequence: LOC_Os07g14270.3 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv07s0005g01390.t01 (Vitis vinifera), 5'ss of exon 3
CTGTAAAGCATGAGCAAAAGCTTGACTGTGGTGGTGGATATGTCAAGTTGCTTGGTGGTGATGTTGACCAGAAGAAATTTGGTGGGGACACACCGTACAGgtaatgattttcttctattgtagctctgattctcacttttctcaagattagtac-tagtta---tctaacttggtac-ttttgaatgcag----------
|||| ||||| || |||||||| || ||||||||||| ||  | ||||||||  ||||||| ||||| || |||||||||||||| || || || || |||| |  || | | |||  || | |  |  || |  ||  | ||||  ||  | | |||||    |||||| ||  |  ||||| || | |          
CTGTTAAGCACGAACAAAAGCTAGATTGTGGTGGTGGCTACATGAAGTTGCTCAGTGGTGAAGTTGATCAAAAGAAATTTGGTGGTGATACCCCTTATAGgtgac-atgtgcctctgctg-aacaatcctttttgctcctttcaattttctttcctagttgggttctaacctgacaaattttgtattctgtggactgcag

upper sequence: LOC_Os07g14270.3 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv14s0060g01290.t01 (Vitis vinifera), 5'ss of exon 3
CTGTAAAGCATGAGCAAAAGCTTGACTGTGGTGGTGGATATGTCAAGTTGCTTGGTGGTGATGTTGACCAGAAGAAATTTGGTGGGGACACACCGTACAGgtaatgattttcttctattgtagctctgattctcacttttctcaagatta-gtactagttatctaacttggtacttttgaat-gcag----------------
|||| || ||||| || |||||||||||||||||||||||  | ||||||||  ||||||| ||||| || |||||||||||||| || || || ||||||| |   || | ||   ||   | | || || || ||||    | || |    |||  |||||    ||     | |||| | |                   
CTGTTAAACATGAACAGAAGCTTGACTGTGGTGGTGGATACATGAAGTTGCTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAGgtcagtgttatttttgcttactg-tttgtttgtccctttgtctatgactccaaacttcttatcccttttaaagttgttgatttgttataaaacatgattgcag

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|33796309|gb|CF324022.1|CF324022
EST:     CTTGGTGGTGATGTTGACCAGAAGAAATTTGGTGGGGACACACCGTACAG                         CATTATGTTTGGACCAGACATCTGTGGGTACAGCACCAAGAAGGTCCATAC
genomic: CTTGGTGGTGATGTTGACCAGAAGAAATTTGGTGGGGACACACCGTACAGgtaatgattt ... ttgaatgcagCATTATGTTTGGACCAGACATCTGTGGGTACAGCACCAAGAAGGTCCATAC
EST: gi|58660986|gb|CK049666.1|CK049666
EST:     CTTGGTGGTGATGTTGACCAGAAGAAATTTGGTGGGGACACACCGTACAG                         CATTATGTTTGGACCAGACATCTGTGGGTACAGCACCAAGAAGGTCCATAC
genomic: CTTGGTGGTGATGTTGACCAGAAGAAATTTGGTGGGGACACACCGTACAGgtaatgattt ... ttgaatgcagCATTATGTTTGGACCAGACATCTGTGGGTACAGCACCAAGAAGGTCCATAC
EST: gi|29675378|gb|CB671653.1|CB671653
EST:     CTTGGTGGTGATGTTGACCAGAAGAAATTTGGTGGGGACACACCGTACAG                         CATTATGTTTGGACCAGACATCTGTGGGTACAGCACCAAGAAGGTCCATAC
genomic: CTTGGTGGTGATGTTGACCAGAAGAAATTTGGTGGGGACACACCGTACAGgtaatgattt ... ttgaatgcagCATTATGTTTGGACCAGACATCTGTGGGTACAGCACCAAGAAGGTCCATAC
EST: gi|58659500|gb|CK048180.1|CK048180
EST:     CTTGGTGGTGATGTTGACCAGAAGAAATTTGGTGGGGACACACCGTACAG                         CATTATGTTTGGACCAGACATCTGTGGGTACAGCACCAAGAAGGTCCATAC
genomic: CTTGGTGGTGATGTTGACCAGAAGAAATTTGGTGGGGACACACCGTACAGgtaatgattt ... ttgaatgcagCATTATGTTTGGACCAGACATCTGTGGGTACAGCACCAAGAAGGTCCATAC
EST: gi|58656433|gb|CK045113.1|CK045113
EST:     CTTGGTGGTGATGTTGACCAGAAGAAATTTGGTGGGGACACACCGTACAG                         CATTATGTTTGGACCAGACATCTGTGGGTACAGCACCAAGAAGGTCCATAC
genomic: CTTGGTGGTGATGTTGACCAGAAGAAATTTGGTGGGGACACACCGTACAGgtaatgattt ... ttgaatgcagCATTATGTTTGGACCAGACATCTGTGGGTACAGCACCAAGAAGGTCCATAC
EST: gi|29675242|gb|CB671517.1|CB671517
EST:     CTTGGTGGTGATGTTGACCAGAAGAAATTTGGTGGGGACACACCGTACAG                         CATTATGTTTGGACCAGACATCTGTGGGTACAGCACCAAGAAGGTCCATAC
genomic: CTTGGTGGTGATGTTGACCAGAAGAAATTTGGTGGGGACACACCGTACAGgtaatgattt ... ttgaatgcagCATTATGTTTGGACCAGACATCTGTGGGTACAGCACCAAGAAGGTCCATAC
EST: gi|88688874|gb|CI732450.1|CI732450
EST:     CTTGGTGGTGATGTTGACCAGAAGAAATTTGGTGGGGACACACCGTACAG                         CATTATGTTTGGACCAGACATCTGTGGGTACAGCACCAAGAAGGTCCATAC
genomic: CTTGGTGGTGATGTTGACCAGAAGAAATTTGGTGGGGACACACCGTACAGgtaatgattt ... ttgaatgcagCATTATGTTTGGACCAGACATCTGTGGGTACAGCACCAAGAAGGTCCATAC
EST: gi|66915891|gb|CX102739.1|CX102739
EST:     CTTGGTGGTGATGTTGACCAGAAGAAATTTGGTGGGGACACACCGTACAG                         CATTATGTTTGGACCAGACATCTGTGGGTACAGCACCAAGAAGGTCCATAC
genomic: CTTGGTGGTGATGTTGACCAGAAGAAATTTGGTGGGGACACACCGTACAGgtaatgattt ... ttgaatgcagCATTATGTTTGGACCAGACATCTGTGGGTACAGCACCAAGAAGGTCCATAC
EST: gi|88689333|gb|CI732909.1|CI732909
EST:     CTTGGTGGTGATGTTGACCAGAAGAAATTTGGTGGGGACACACCGTACAG                         CATTATGTTTGGACCAGACATCTGTGGGTACAGCACCAAGAAGGTCCATAC
genomic: CTTGGTGGTGATGTTGACCAGAAGAAATTTGGTGGGGACACACCGTACAGgtaatgattt ... ttgaatgcagCATTATGTTTGGACCAGACATCTGTGGGTACAGCACCAAGAAGGTCCATAC
EST: gi|88688533|gb|CI732109.1|CI732109
EST:     CTTGGTGGTGATGTTGACCAGAAGAAATTTGGTGGGGACACACCGTACAG                         CATTATGTTTGGACCAGACATCTGTGGGTACAGCACCAAGAAGGTCCATAC
genomic: CTTGGTGGTGATGTTGACCAGAAGAAATTTGGTGGGGACACACCGTACAGgtaatgattt ... ttgaatgcagCATTATGTTTGGACCAGACATCTGTGGGTACAGCACCAAGAAGGTCCATAC

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), 75 (downstream exon)
Score: 285

CTGTAAAGCATGAGCAAAAGCTTGACTGTGGTGGTGGATATGTCAAGTTGCTTGGTGGTGATGTTGACCAGAAGAAATTTGGTGGGGACACACCGTACAGgtaatgattt ... ttgaatgcagCATTATGTTTGGACCAGACATCTGTGGGTACAGCACCAAGAAGGTCCATACTATCTTTACTAAGAATGACAAGAACCATTTGATCAAGAAGGATGTCCCC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGTAAAGCATGAGCAAAAGCTTGACTGTGGTGGTGGATATGTCAAGTTGCTTGGTGGTGATGTTGACCAGAAGAAATTTGGTGGGGACACACCGTACAGgtaatgattttcttctattgtagctctgattctcacttttctcaagattagtactagttatctaacttggtacttttgaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG