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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTCATTCCACGCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAGgtaactgatggatgtgtgtgtgttttttaaaagaaaatatacaaaccttctctaacattgcttctttttctctcctgatag

Basic information

species Oryza sativa
transcript LOC_Os02g47600.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47600.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G046587_T03 (Zea mays), 5'ss of exon 2
TGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTCATTCCACGCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAGgtaactgatggatgtgtgtgtgttttttaaaagaaaatat-acaaacctt-ctctaacattgcttctttttctctcctgatag
||||||||| || ||||||||||||||||| |||||||| ||||||||||||||||| ||||||||    |||||| |||| |||||| | ||||||||||||  | |   |||| ||     |||    |      ||| |  | | ||  ||||||||||  |  | || |   |||  ||
TGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTCATTCCACGCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtatttta---atgtatgcagcgtttcggtagccttttattatcagctttattctaacattgtgtgctcttttt--ctggaag

upper sequence: LOC_Os02g47600.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA01G37790.1 (Glycine max), 5'ss of exon 5
TGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTCATTCCACGCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAGgta-----actgatggatgt-gtgtgtgttttttaaaagaaaatata----------caaaccttctctaacattgcttctt---tttctctcctgatag-
| ||||||||||||| ||||| |||||||||||||||||||| || ||| | ||  ||||||| ||| |||| || |||||||| || || || |||||||||      || |    ||| || | || |  |||| ||||||| |           ||||  |||      |||     ||    || | | |||| |  
TATTCTTTACTCATCAGTTGTCTACCCACACAACTATGGTTTTATCCCAAGAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTCTAATGCAGgtaccaatgcttaaaattgttgtttctgatacttaagagaaaatgtttgtttccagccaaaatttcaactgtattaaaatttgaacttttgttctgagaag

upper sequence: LOC_Os02g47600.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA11G07530.1 (Glycine max), 5'ss of exon 5
TGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTCATTCCACGCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAGgtaac------tgatggatg--tgtgtgtgttttttaaaagaaaatata----------caaaccttctctaacattgcttctt---tttctctcctgatag-
| ||||||||||||| || || |||||||||||||||||||| || ||| | ||  ||||||| ||| |||| || |||||||| || || || ||||||||| |      | |   ||   ||| | || | || ||  |||||| |           ||||  |||      |||      |    || | | |||| |  
TATTCTTTACTCATCAGTAGTCTACCCACACAACTATGGTTTTATCCCAAGAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTCTAATGCAGgtagcaatgcttaaaaaattattgtttctgatgttgaaccgaaaatgtttgtttccagccaaaatttcaactgtattaaaatgtgaacttttattctgagaag

upper sequence: LOC_Os02g47600.2 (Oryza sativa), 5'ss of exon 5
lower sequence: AT2G18230.1 (Arabidopsis thaliana), 5'ss of exon 5
TGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTCATTCCACGCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAGgtaact------gatggatgtgtgtgtgttttttaaaagaaaat--atacaaaccttctctaacattgcttcttt----ttctctcctg-atag
 ||||| ||||||||  |||| ||||| |||||||| |||||||| || || ||  | ||||| ||| |||| || ||||| ||||| || |||||||||||   |      |    || |  |  |   | || | | ||| |  ||  ||||   |  | | ||  |    ||    |    | |||   ||
CGTTCTCTACTCATCCATTGTGTACCCCCACAACTACGGTTTCATCCCTCGAACTATCTGTGAAGACAGTGATCCAATGGATGTCCTGGTACTGATGCAGgtgctttctctcgcctcatcttagctttcatgttcatacaaacttgatgtaaacaggcagtgaaataacagacttgagataaaatactgtgcag

upper sequence: LOC_Os02g47600.2 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv04s0023g02050.t01 (Vitis vinifera), 5'ss of exon 4
TGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTCATTCCACGCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAGgtaac--tgatggatgtgtgtgtgttttttaaaagaaaatatacaaaccttctctaacattgcttctttttctctcctgatag-------------------------
||||||||||||||| |||||||| ||||| |||||||||||||| || || ||  | ||||| ||| | || || ||||| |||||  | || |||||||||       | ||  |     | ||     ||  |  ||| |  |    | | | |  ||   |  ||   |||  | | |                          
TGTTCTTTACTCATCAGTTGTTTATCCACATAACTATGGTTTCATCCCTCGAACCATCTGTGAAGACAGCGATCCTATGGATGTCCTGATTCTAATGCAGgtagtgtcatttgacatac-catcttaccacaatcatgatacattacatcttttttat-ttttctaattaaatcttataaaaattcatcaattcgccctctcgtgtag

upper sequence: LOC_Os02g47600.2 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S315_67V6.1 (Physcomitrella patens), 5'ss of exon 2
TGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTCATTCCACGCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAGgta-actgatggatgtgtgtgtgttttttaaaagaaaa-tatacaaaccttctctaacattgcttctttttctctcctgatag--------------------
| | || ||||| ||||| || ||||| ||||| |||||||||||||||||||| ||||| |||||||  || ||||| || || || ||| | ||||||||| | |  |   || |||  ||   ||      |  | | | |  |    | |||   |||  |   ||     |   | ||                    
TATCCTATACTCGTCTGTGGTGTACCCGCACAATTATGGTTTCATTCCACGCACCCTTTGCGAGGACGAGGATCCCATCGATGTTCTGGTCATCATGCAGgtagagtcctttgtgcgtgaatgaagttagtggcacgactgtgcgtaatcccgcta---ttggatgagttgagagcagaagaggcgtgtttgaatggagtgtg

upper sequence: LOC_Os02g47600.2 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S552_1V6.1 (Physcomitrella patens), 5'ss of exon 5
TGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTCATTCCACGCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAGgtaac-tgatggatgtgtgtgtgttttttaaaagaaaa-tatacaaaccttctctaacattgcttctttttctctcctgatag--------------------
| | || ||||| ||||| || ||||| ||||| |||||||||||||||||||| ||||| |||||||  || ||||| || || || ||| | ||||||||| | |  |   || |||  ||   ||      |  | | | |  |    | |||   |||  |   ||     |   | ||                    
TATCCTATACTCGTCTGTGGTGTACCCGCACAATTATGGTTTCATTCCACGCACCCTTTGCGAGGACGAGGATCCCATCGATGTTCTGGTCATCATGCAGgtagcgtcctttgtgcgtgaatgaagttagtggcacgactgtgcgtaatcccgcta---ttggatgagttgagagcagaagaggcgtgtttgaatggagtgtg

upper sequence: LOC_Os02g47600.2 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S46_53V6.1 (Physcomitrella patens), 5'ss of exon 6
TGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTCATTCCACGCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAGgta--actgatggatgtgtgtgtgtttt-ttaaaagaaaatatacaaaccttctc--taacattg-cttctttttctctcctgatag-------------
| |  | |||||||| ||||| || |||||||| ||||| ||||||||||| || ||||||||||| |  || ||||| || || |||||| | |||||||||  | | | |  | | | | |   ||  ||||    || ||    |  || |   | | || | ||    ||| | |    |  |             
TATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCATTATGCAGgtactattcaagacttttttttttccttactaaatttcaacatttgtattttgtgaatgagatagactgagatttttatagcaaaggtaaatgcacgtaa

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|163918159|gb|EG715273.1|EG715273
EST:     GCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAG                         GAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAGgtaactgatg ... ctcctgatagGAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|163925750|gb|EG714586.1|EG714586
EST:     TGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAG                         GAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: TGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAGgtaactgatg ... ctcctgatagGAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|163926919|gb|EG715144.1|EG715144
EST:     GCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAG                         GAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAGgtaactgatg ... ctcctgatagGAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|58601442|gb|CK011970.1|CK011970
EST:     GCACACTCTGTGAGGACGGTGACCCCATGGACGTCCTTGTCCTGATGCAG                         GAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAGgtaactgatg ... ctcctgatagGAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|8404630|gb|AU091984.1|AU091984
EST:     GCACACTTTGTGAGGNCGGTGACCCCATGGACGTCCTCGTCCTGATGCAG                         GAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAGgtaactgatg ... ctcctgatagGAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|15852955|gb|BI805751.1|BI805751
EST:     CACTTTGTGAGGACGGTTGACCCCCAGTGGACGTCCTCGTCCTGATGCAGG                         GAACAAGTTGTCCCGT-GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCA
genomic: CACTTTGTGAGGACGG-TGA-CCCCA-TGGACGTCCTCGTCCTGATGCA-Ggtaactgatg ... ctcctgatagGAACAAGTTGTCCC-TGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCA
EST: gi|33823829|gb|CF337721.1|CF337721
EST:     CACACTTTGTGAGGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAG                         GAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: CACACTTTGTGAGG-ACGGTGACCCCATGGACGTCCTCGTCCTGATGCAGgtaactgatg ... ctcctgatagGAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|58689221|gb|CK077908.1|CK077908
EST:     GCACACTCTGTGAGGACGGTGACCCCATGGACGTCCTTGTCCTGATGCAG                         GAACAAGTTGTCCCTNGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCAT
genomic: GCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAGgtaactgatg ... ctcctgatagGAACAAGTTGTCCCT-GGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCAT
EST: gi|163928605|gb|EG710890.1|EG710890
EST:     GAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAG                         GAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAGgtaactgatg ... ctcctgatagGAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|58688425|gb|CK077112.1|CK077112
EST:     GCACACTCTGTGAGGACGGTGACCCCATGGACGTCCTTGTCCTGATGCAG                         GAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAGgtaactgatg ... ctcctgatagGAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|58596788|gb|CK007316.1|CK007316
EST:     GGACGTCCTTGTCCTGATGCAG                         GAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GGACGTCCTCGTCCTGATGCAGgtaactgatg ... ctcctgatagGAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|58667772|gb|CK056458.1|CK056458
EST:     GCACACTCTGTGAGGACGGTGACCCCATGGACGTCCTTGTCCTGATGCAG                         GAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAGgtaactgatg ... ctcctgatagGAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|58676589|gb|CK065276.1|CK065276
EST:     GCACACTCTGTGAGGACGGTGACCCCATGGACGTCCTTGTCCTGATGCAG                         GAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAGgtaactgatg ... ctcctgatagGAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG

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), 66 (downstream exon)
Score: 105

TGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTCATTCCACGCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAGgtaactgatg ... ctcctgatagGAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTCATTCCACGCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAGgtaactgatggatgtgtgtgtgttttttaaaagaaaatatacaaaccttctctaacattgcttctttttctctcctgatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA