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'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcgctacttatgttttcagaatagtgtacttcctgaagaacctgagctaaaatctacaacaatcatttacagGTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTTGAGATACATTGGAAG

Basic information

species Oryza sativa
transcript LOC_Os01g64660.4
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g64660.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G836250_T02 (Zea mays), 3'ss of exon 7
------------------------------------------------gtacgcgctacttatgttttcagaatagtgtacttcctgaagaacctgagctaaaatctaca--acaatcatttacagGTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTTGAGATACATTGGAAG
                                                | || | |  | | |  |||     | |      |       | |   ||||  |   ||||  | ||| |   |||||||||||||||||||||||| ||| || ||||| ||  |||| | ||| |||||||||||||||||
gtacgtttcgtcgtctgtgactgactcctgtccatagcacttgctcaagaactccccgcctcttcttttgtttttgaaacgattaaacgaagctccagctgtagcttacaccataataaaccacagGTTTGTGGAGAAGTGCAAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAG

upper sequence: LOC_Os01g64660.3 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv18s0072g00770.t01 (Vitis vinifera), 3'ss of exon 8
gtacgcgctacttatg-ttttcagaatagtgtacttcctgaagaacctgagctaaaatctacaacaatcatttacagGTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTTGAGATACATTGGAAG
||| |    |||  |  | || |  ||  | |   | |||  |  |     |   | | |       | | ||| |||| |||||| || ||||||||||| || |||||||||||||| |||||  |  |||||||||||||
gtatgtttaactagtaatctttatcatgctattaattctgttgtgcaattccctgacttttttttttttactta-agGTATGTGGAAAAATGCAAGTTCCCCAAAGATGGTTCATCACCAAAATCTCTACGATACATTGGAAG
















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|38470545|gb|CF954676.1|CF954676
EST:     AGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAA                         GTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
genomic: AGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAAgtacgcgcta ... tcatttacagGTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
EST: gi|29686739|gb|CB683014.1|CB683014
EST:     TATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAA                         GTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
genomic: TATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAAgtacgcgcta ... tcatttacagGTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
EST: gi|29621610|gb|CB626621.1|CB626621
EST:     TATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAA                         GTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
genomic: TATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAAgtacgcgcta ... tcatttacagGTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
EST: gi|58588683|gb|CF986991.1|CF986991
EST:     TATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAA                         G-TTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
genomic: TATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAAgtacgcgcta ... tcatttacagGTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
EST: gi|29613014|gb|CB618027.1|CB618027
EST:     TATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAA                         GTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
genomic: TATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAAgtacgcgcta ... tcatttacagGTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
EST: gi|29617760|gb|CB622772.1|CB622772
EST:     TATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAA                         GTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
genomic: TATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAAgtacgcgcta ... tcatttacagGTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
EST: gi|38473796|gb|CF957928.1|CF957928
EST:     TATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAA                         GTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
genomic: TATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAAgtacgcgcta ... tcatttacagGTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
EST: gi|33820806|gb|CF336207.1|CF336207
EST:     TATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAA                         GTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
genomic: TATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAAgtacgcgcta ... tcatttacagGTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
EST: gi|27546650|gb|CA764792.2|CA764792
EST:     TATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAA                         GTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
genomic: TATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAAgtacgcgcta ... tcatttacagGTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
EST: gi|89198621|gb|CI016706.1|CI016706
EST:     ACGAGCCTACCGCAAA                         GTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
genomic: ACGAGCCTACCGCAAAgtacgcgcta ... tcatttacagGTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
EST: gi|29682614|gb|CB678889.1|CB678889
EST:     TATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAA                         GTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT
genomic: TATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAAgtacgcgcta ... tcatttacagGTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTT

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: 71 (upstream exon), 66 (downstream exon)
Score: 44

ATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAAgtacgcgcta ... tcatttacagGTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTTGAGATACATTGGAAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaatagtgtacttcctgaagaacctgagctaaaatctacaacaatcatttacagGTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTTGAGATACATTGGAAG
                           agctaaa  putative branch site (score: 44)
                              taaaatcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgcgctacttatgttttcagaatagtgtacttcctgaagaacctgagctaaaatctacaacaatcatttacagGTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTTGAGATACATTGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG