Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtccagctaaccataaccaaatcccattgtttcttatgactatgttgttgtagggttacaggtgcttgccagctaacataaataggattgcagGTTTTGTCTGATGATGAGAAGCGATCAATCTATGATAAATATGGAGAAGCTGGTTTGAAGGGTGCTGGAATGGGAACAGGA

Basic information

species Oryza sativa
transcript LOC_Os05g26914.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g26914.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G091811_T01 (Zea mays), 3'ss of exon 6
gttagtccagctaaccataaccaaatcccattgtttcttatgactatgttgttgtagggttacaggtgcttgc-cagctaacataaataggattgcagGTTTTGTCTGATGATGAGAAGCGATCAATCTATGATAAATATGGAGAAGCTGGTTTGAAGGGTGCTGGAATGGGAACAGGA
||| | ||| ||   ||||   |  ||| | |   | || ||    |   | || |   |||    ||||| |  ||| |  ||  ||    ||| |||||||||||||||||||||||||||||||||||||||||||||||||||| ||| |||| |||||||| ||||| ||||||
gttgggccaactgttcatacttagctccaaattccttttttggtagtag-gatgcacatttatttatgcttacatagcaaggatgtatg---ttgtagGTTTTGTCTGATGATGAGAAGCGATCAATCTATGATAAATATGGAGAAGCAGGTCTGAAAGGTGCTGGCATGGGCACAGGA

upper sequence: LOC_Os05g26914.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G856084_T01 (Zea mays), 3'ss of exon 6
gttagtccagctaaccataaccaaatcccattgtttcttatgactatgttgttgtagggttacaggtgcttgccagctaacataaataggat---tgcagGTTTTGTCTGATGATGAGAAGCGATCAATCTATGATAAATATGGAGAAGCTGGTTTGAAGGGTGCTGGAATGGGAACAGGA
||| | ||  ||   ||||  ||| ||| |        |   | | |   || ||||| |||||  |   |    ||| || || | |||||   || ||||| |||||||||||||||||||||| ||||||||||||||||||||||| ||| ||||||||||||| ||||| ||||||
gttgggcccactgttcatactcaactccaaaatccaaattccatt-ttcggtagtaggattacacatttatttatgcttacgtagaaaggatgtctgtagGTTCTGTCTGATGATGAGAAGCGATCGATCTATGATAAATATGGAGAAGCAGGTCTGAAGGGTGCTGGCATGGGCACAGGA

upper sequence: LOC_Os05g26914.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA11G38040.1 (Glycine max), 3'ss of exon 6
gttagtccagctaaccataaccaaatcccattgtttctta-tgactatgttgt-tgtagggttacaggtgcttgccagctaacataaataggattgcagGTTTTGTCTGATGATGAGAAGCGATCAATCTATGATAAATATGGAGAAGCTGGTTTGAAGGGTGCTGGAATGGGAACAGGA
                |  || | | |   |||        || | ||  ||  |||    | | |  || |   | | |||   ||||    |||||||| ||||| ||||||||||| ||||| || ||||||| ||||||||| |||||  | |||||| | |||||||| |  || 
--------------gtaatactacagcttgttgaacgcagctggccattatgcatgtctactcataattgatcttctg-taattcaaattcttttgcagGTCTTGTCAGATGATGAGAAACGATCCATATATGATACATATGGAGAGGCTGGACTTAAGGGTTCAGGAATGGGCATGGGG

upper sequence: LOC_Os05g26914.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA18G01960.1 (Glycine max), 3'ss of exon 6
gttagtccagctaaccataaccaaatcccattgtttcttatgactatgttgttgtagggttacaggtgcttgccagctaacataaataggattgcagGTTTTGTCTGATGATGAGAAGCGATCAATCTATGATAAATATGGAGAAGCTGGTTTGAAGGGTGCTGGAATGGGAACAGGA
    ||  | |||    |     ||  |   ||    |||||  | | |  | |||          || |   | | |||   ||||    |||||||| ||||| ||||||||||| ||||| || ||||| | ||||||||| |||||  | |||||| | |||||||| |  || 
----gtaaatctacagcttgttgaacacagctggccattatgcatgtctactcgtaat--------tgatcttctg-taattcaaattcttttgcagGTCTTGTCAGATGATGAGAAACGATCCATATATGACACATATGGAGAGGCTGGACTTAAGGGTTCAGGAATGGGCATGGGG

upper sequence: LOC_Os05g26914.1 (Oryza sativa), 3'ss of exon 6
lower sequence: PP1S386_29V6.1 (Physcomitrella patens), 3'ss of exon 5
gttagtccagctaaccataaccaaatcccattgtttcttatgactatgttgttgtagggttacaggtgcttgcc----agctaacataaatag--------gattgcagGTTTTGTCTGATGATGAGAAGCGATCAATCTATGATAAATATGGAGAAGCTGGTTTGAAGGGTGCTGGAATGGGAACAGGA------
            || | | |   |      | || |||||  | | | ||||  | |  ||    ||||   |     |||| ||   ||| |          ||||||||| | ||||||||||||||||||||||| ||||| | || ||| ||||||||| | || |||||||||   | |  |||       
--------gatcaatcttgaagtagggatttcgtctctta-aaatgtattgtatttgaattgtgtgtgcactcttcaaagctgacgctaattgtctttattatttgcagGTTCTCTCTGATGATGAGAAGCGATCAATTTATGACAGATTTGGTGAAGCTGGTCTTAAAGGTGCTGGAGGTGCAGGAGGGACTGGG

upper sequence: LOC_Os05g26914.1 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ07566 (Selaginella moellendorffii), 3'ss of exon 3
gttagtccagctaaccataaccaaatcccattgtttcttatgactatgttgttg-tagggttacaggtgcttgccagctaacataaataggattgcagGTTTTGTCTGATGATGAGAAGCGATCAATCTATGATAAATATGGAGAAGCTGGTTTGAAGGGTGCTGGAATGGGAACAGGA
                                      || |   |  ||  || |  ||| |  ||   |  | |    |      | ||     ||||| |||||||||| || || ||||| ||||| ||||||||||| |||||||||||||| || ||||||   ||| ||   
-------------------------------------gtaagctcacatttctgctttggtgatgggctttgtctaa--gatgctttttggtggatagGTTCTGTCTGATGACGATAAACGATCCATCTACGATAAATATGGTGAAGCTGGTTTGAAAGGAGCTGGAGCTGGAGCA---

upper sequence: LOC_Os05g26914.1 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ10769 (Selaginella moellendorffii), 3'ss of exon 4
gttagtccagctaaccataaccaaatcccattgtttcttatgactatgttgttgtagggttacaggtgcttgccagctaacataaataggattgcagGTTTTGTCTGATGATGAGAAGCGATCAATCTATGATAAATATGGAGAAGCTGGTTTGAAGGGTGCTGGAATGGGAACAGGA
                      |  || |||| |||  | ||   |||   ||     ||   || |||||    |          | ||||   ||||| ||||||||||||| || ||||| ||||| ||||||||||| |||||||||||||| || ||||||   ||| ||   
-------------------gtaagctcacattttttgctttggtgatgggcttt----gtctaagatgctttttgg----------tgggat---agGTTCTGTCTGATGATGATAAACGATCCATCTACGATAAATATGGTGAAGCTGGTTTGAAAGGAGCTGGAGCTGGAGCA---

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|58608089|gb|CK036122.1|CK036122
EST:     AGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG                         GTTTTGTCTGATGATGAGAAGCGATCAATCTATGATAAATATGGAGAAGCT
genomic: AGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAGgttagtccag ... aggattgcagGTTTTGTCTGATGATGAGAAGCGATCAATCTATGATAAATATGGAGAAGCT
EST: gi|29685207|gb|CB681482.1|CB681482
EST:     AGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG                         GTTTTGTCTGATGATGAGAAGCGATCAATCTATGATATATATGGAGAAGCT
genomic: AGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAGgttagtccag ... aggattgcagGTTTTGTCTGATGATGAGAAGCGATCAATCTATGATAAATATGGAGAAGCT
EST: gi|58656403|gb|CK045083.1|CK045083
EST:     GTTCAAGGATATTAGCAATGCTTATGAG                         G-TTTGTCTGATGATGAGAAGCGATCAATCTATGATAAATATGGAGAAGCT
genomic: GTTCAAGGATATTAGCAATGCTTATGAGgttagtccag ... aggattgcagGTTTTGTCTGATGATGAGAAGCGATCAATCTATGATAAATATGGAGAAGCT
EST: gi|29620923|gb|CB625934.1|CB625934
EST:     AGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG                         GTTTTGTCTGATGATGAGAAGCGATCAATCTATGATAAATATGGAGAAGCT
genomic: AGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAGgttagtccag ... aggattgcagGTTTTGTCTGATGATGAGAAGCGATCAATCTATGATAAATATGGAGAAGCT
EST: gi|58673732|gb|CK062418.1|CK062418
EST:     AGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG                         GTTTTGTCTGATGATGAGAAGCGATCAATCTATGATAAATATGGAGAAGCT
genomic: AGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAGgttagtccag ... aggattgcagGTTTTGTCTGATGATGAGAAGCGATCAATCTATGATAAATATGGAGAAGCT
EST: gi|29680449|gb|CB676724.1|CB676724
EST:     AGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG                         GTTTTGTCTGATGATGAGAAGCGATCAATCTATGA
genomic: AGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAGgttagtccag ... aggattgcagGTTTTGTCTGATGATGAGAAGCGATCAATCTATGA
EST: gi|29681007|gb|CB677282.1|CB677282
EST:     AGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG                         GTTTTGTCTGATGATGAGAAGCGATCAATCTATGATANATATGGAGAAGCT
genomic: AGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAGgttagtccag ... aggattgcagGTTTTGTCTGATGATGAGAAGCGATCAATCTATGATAAATATGGAGAAGCT
EST: gi|58660788|gb|CK049468.1|CK049468
EST:     AGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG                         GTTTTGTCTGATGATGAGAAGCGATCAATCTATGATAAATATGGAGAAGCT
genomic: AGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAGgttagtccag ... aggattgcagGTTTTGTCTGATGATGAGAAGCGATCAATCTATGATAAATATGGAGAAGCT
EST: gi|29680374|gb|CB676649.1|CB676649
EST:     AGATCCTGGTGCTGAACAAAAGTTCAAGGATATTACCAATGCTTATGAA                         GTTTTGTCTGATGATGAGAAGCGATCCATCTATGATAAATATGG
genomic: AGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAGgttagtccag ... aggattgcagGTTTTGTCTGATGATGAGAAGCGATCAATCTATGATAAATATGG
EST: gi|58676612|gb|CK065299.1|CK065299
EST:     AGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG                         GTTTTGTCTGATGATGAGAAGCGATCAATCTATGATAAATATGGAGAAGCT
genomic: AGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAGgttagtccag ... aggattgcagGTTTTGTCTGATGATGAGAAGCGATCAATCTATGATAAATATGGAGAAGCT

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), 73 (downstream exon)
Score: 23

AGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAGgttagtccag ... aggattgcagGTTTTGTCTGATGATGAGAAGCGATCAATCTATGATAAATATGGAGAAGCTGGTTTGAAGGGTGCTGGAATGGGAACAGGA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actatgttgttgtagggttacaggtgcttgccagctaacataaataggattgcagGTTTTGTCTGATGATGAGAAGCGATCAATCTATGATAAATATGGAGAAGCTGGTTTGAAGGGTGCTGGAATGGGAACAGGA
                                agctaac  putative branch site (score: 23)
                                   taacataaata  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtccagctaaccataaccaaatcccattgtttcttatgactatgttgttgtagggttacaggtgcttgccagctaacataaataggattgcagGTTTTGTCTGATGATGAGAAGCGATCAATCTATGATAAATATGGAGAAGCTGGTTTGAAGGGTGCTGGAATGGGAACAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA