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'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCGgtacacattaagcctactctcggcatctcacttcgcttatggtacttccaatttcatattgataaacaattctgaattcaccaaatcttggaattacag

Basic information

species Oryza sativa
transcript LOC_Os01g64660.3
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g64660.4 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM5G836250_T03 (Zea mays), 5'ss of exon 9
TATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCGgtacacattaagcctactctcggcatctcacttcgcttatggt----acttccaatttcatattga--------taaacaattctgaattcaccaaatcttggaattacag
|||||||||||| || |||||||| |||||||| || || || |||||||||||||| ||| |||||| |||||| ||||| ||||||||   ||||||| | |  |   | ||     |||||    ||     || |   |  || |            | |||   |||   ||         ||||  ||  ||
TATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCGgta---attaagcttccgttacccctccagactcgctctcagtctcagctgctcgtaacacaccaccccggccctgaacctgtctcggttggtttg-ctttggttttgtag

upper sequence: LOC_Os01g64660.4 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA16G28310.1 (Glycine max), 5'ss of exon 11
TATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCGgtacacattaagcctactctcggcatctcacttcgcttatggtacttccaatttcatattgataaacaattctgaattcaccaaatcttggaattacag------------
 ||||| |||||||| || ||||||||||| ||||||||  | |||||||||||||| ||||| || || |||||||||||||| |||||    | | |   |  ||| |||| ||||||      ||  |   |  ||   | ||||| ||| | ||   || | |     |    |||||  |             
CATGGTAGCTGATGTTCATCGTACGTTGCTTTATGGAGGCATCTTTTTGTACCCTGCTGACAAAAAAAGTCCAAATGGAAAACTTCGgtat--gtcatgttcaacctctgcat-tcactttaggcctga-agagcatatccaagattgacaaa-actttgaaaattaattgttggctgaattgaactgttttgtgtag

upper sequence: LOC_Os01g64660.4 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv18s0072g00770.t01 (Vitis vinifera), 5'ss of exon 10
TATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCGgtacacattaag-------cctactctcggcatctca-cttcgcttatggtacttccaatttcatattgataa--acaatt-----------ctgaattcaccaaatcttgga-attacag
 ||||| |||||||||||||| || || || || || ||  | |||||||||||||| || ||||||||||| || |||||||| |||||   | | |        | | |||||     |||| |||| |  |    | || ||| | || ||| | ||  ||||||           |||||||      | |||| |    ||||
CATGGTAGCTGATGTCCACCGCACATTACTTTACGGTGGTATCTTTTTGTACCCTGCTGATAAGAAGAGCCCCAACGGAAAACTGCGgtaagtactgatgtttcaccttcctctctctccctcaacttctcaaaacaaatttgcaaatgcagatttacaacaacaattaatttttgtgactgaatttggtttaacttgtatggaacag

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:     GGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCG                         TGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
genomic: GGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCGgtacacatta ... ggaattacagTGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
EST: gi|29686739|gb|CB683014.1|CB683014
EST:     GGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCG                         TGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
genomic: GGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCGgtacacatta ... ggaattacagTGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
EST: gi|29621610|gb|CB626621.1|CB626621
EST:     GGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCG                         TGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
genomic: GGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCGgtacacatta ... ggaattacagTGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
EST: gi|86524631|gb|CI164837.1|CI164837
EST:     TTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCG                         TGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
genomic: TTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCGgtacacatta ... ggaattacagTGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
EST: gi|88251080|gb|CI349310.1|CI349310
EST:     GACAAGAAGAGCCCAAATGGAAAACTCCG                         TGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
genomic: GACAAGAAGAGCCCAAATGGAAAACTCCGgtacacatta ... ggaattacagTGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
EST: gi|313079819|gb|HO213258.1|HO213258
EST:     ACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCG                         TGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
genomic: ACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCGgtacacatta ... ggaattacagTGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
EST: gi|86844563|gb|CI338579.1|CI338579
EST:     TATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCG                         TGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
genomic: TATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCGgtacacatta ... ggaattacagTGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
EST: gi|86834851|gb|CI345935.1|CI345935
EST:     GACAAGAAGAGCCCAAATGGAAAACTCCG                         TGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
genomic: GACAAGAAGAGCCCAAATGGAAAACTCCGgtacacatta ... ggaattacagTGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
EST: gi|58588683|gb|CF986991.1|CF986991
EST:     GGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCG                         TGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
genomic: GGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCGgtacacatta ... ggaattacagTGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
EST: gi|88519728|gb|CI447382.1|CI447382
EST:     TGGAAAGCTCCG                         TGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
genomic: TGGAAAACTCCGgtacacatta ... ggaattacagTGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
EST: gi|86413542|gb|CI019127.1|CI019127
EST:     GGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCG                         TGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
genomic: GGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCGgtacacatta ... ggaattacagTGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
EST: gi|38476059|gb|CF960192.1|CF960192
EST:     AGAGCCCAAATGGAAAACTCCG                         TGTTCTGTATGAAGTTTTCCCCATGTCAGTCCTGATGGAGCAGGCTGGAGG
genomic: AGAGCCCAAATGGAAAACTCCGgtacacatta ... ggaattacagTGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
EST: gi|88283280|gb|CI404726.1|CI404726
EST:     CCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCG                         TGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
genomic: CCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCGgtacacatta ... ggaattacagTGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
EST: gi|88506218|gb|CI433724.1|CI433724
EST:     GGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCG                         TGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
genomic: GGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCGgtacacatta ... ggaattacagTGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
EST: gi|89184643|gb|CI007068.1|CI007068
EST:     GGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCG                         TGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
genomic: GGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCGgtacacatta ... ggaattacagTGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
EST: gi|33663176|gb|CF294143.1|CF294143
EST:     AGACAAGAAGAGCCCAAATGGAAAACTCCG                         TGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
genomic: AGACAAGAAGAGCCCAAATGGAAAACTCCGgtacacatta ... ggaattacagTGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
EST: gi|88478802|gb|CI416073.1|CI416073
EST:     CTGCAGACAAGAAGAGCCCAAATGGAAAACTCCG                         TGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
genomic: CTGCAGACAAGAAGAGCCCAAATGGAAAACTCCGgtacacatta ... ggaattacagTGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
EST: gi|29613014|gb|CB618027.1|CB618027
EST:     GGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCG                         TGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
genomic: GGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCGgtacacatta ... ggaattacagTGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
EST: gi|86833721|gb|CI337295.1|CI337295
EST:     GAGCCCAAATGGAAAACTCCG                         TGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
genomic: GAGCCCAAATGGAAAACTCCGgtacacatta ... ggaattacagTGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
EST: gi|88967746|gb|CI016261.1|CI016261
EST:     GGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCG                         TGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
genomic: GGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCGgtacacatta ... ggaattacagTGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
EST: gi|88533107|gb|CI460643.1|CI460643
EST:     CAGACAAGAAGAGCCCAAATGGAAAACTCCG                         TGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
genomic: CAGACAAGAAGAGCCCAAATGGAAAACTCCGgtacacatta ... ggaattacagTGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
EST: gi|88476483|gb|CI413754.1|CI413754
EST:     AGCCCAAATGGAAAACTCCG                         TGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
genomic: AGCCCAAATGGAAAACTCCGgtacacatta ... ggaattacagTGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
EST: gi|29617760|gb|CB622772.1|CB622772
EST:     GGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCG                         TGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
genomic: GGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCGgtacacatta ... ggaattacagTGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
EST: gi|33820806|gb|CF336207.1|CF336207
EST:     GGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCG                         TGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
genomic: GGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCGgtacacatta ... ggaattacagTGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
EST: gi|27546650|gb|CA764792.2|CA764792
EST:     GGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCG                         TGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
genomic: GGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCGgtacacatta ... ggaattacagTGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
EST: gi|88473302|gb|CI410573.1|CI410573
EST:     GGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCG                         TGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
genomic: GGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCGgtacacatta ... ggaattacagTGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
EST: gi|89198621|gb|CI016706.1|CI016706
EST:     GGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCG                         TGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
genomic: GGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCGgtacacatta ... ggaattacagTGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
EST: gi|86874736|gb|CI318295.1|CI318295
EST:     GGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCG                         TGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
genomic: GGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCGgtacacatta ... ggaattacagTGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
EST: gi|29682614|gb|CB678889.1|CB678889
EST:     GGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCG                         TGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
genomic: GGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCGgtacacatta ... ggaattacagTGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
EST: gi|88543369|gb|CI473372.1|CI473372
EST:     ACCCGGCAGACAAGAAGAGCCCAAATGGAAAACTCCG                         TGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
genomic: ACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCGgtacacatta ... ggaattacagTGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
EST: gi|38476585|gb|CF960718.1|CF960718
EST:     GGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCG                         TGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
genomic: GGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCGgtacacatta ... ggaattacagTGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
EST: gi|88481285|gb|CI418556.1|CI418556
EST:     GGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCG                         TGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG
genomic: GGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCGgtacacatta ... ggaattacagTGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCGgtacacattaagcctactctcggcatctcacttcgcttatggtacttccaatttcatattgataaacaattctgaattcaccaaatcttggaattacag

- - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG