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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagatagacctcatgtaggatattgagatattcatatgccatcattcaatacttaattaatgatttttattatctccgtagGCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACATCAACAGCCTGGTGACTGGTAGAGAAATAACTGGGATCGCAAGCTTCAAAC

Basic information

species Oryza sativa
transcript LOC_Os01g06600.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g06600.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM5G862219_T03 (Zea mays), 3'ss of exon 11
------------------------------------------------------------------------------------------gtagata--gacctcatgtaggatattgagatattcatatgc----catcattcaatacttaat-taatgatttttattatctccgtagGCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACATCAACAGCCTGGTGACTGGTAGAGAAATAACTGGGATCGCAAGCTTCAAAC
                                                                                            || ||    || ||       | ||   ||     ||||     || ||   || |   ||| |  |||| | | || |      |||| ||||| ||||||||||| || ||||| ||||| ||||| ||||||||||||||||||||||| || || ||  | || |||||||| |||||||  |
gtatgcggtagcgatctagtaggagtcgtcttttcccggtggtggttttacacctcgaccagccactcgtagtataggagcctttagctatcagttaccacccccacccccttttttttaatccatgtatgtttaacaacaacaaacaacaaatgtggtgatctctgtt-tacatacagGCGTTCTGCGACCTGGAGCCCATCTACTCGTACGAGGGCACGTACGACATCAACAGCCTGGTGACCGGCAGGGAGGTCACCGGGATCGCGAGCTTCAGGC
















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|29658082|gb|CB654357.1|CB654357
EST:     GAGAATTGTTGGGTGGAAATGGAATTTTGGCTGATTTTCTAGTTGCAAAG                         GCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACATC
genomic: GAGAATTGTTGGGTGGAAATGGAATTTTGGCTGATTTTCTAGTTGCAAAGgtagatagac ... atctccgtagGCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACATC
EST: gi|88227372|gb|CI226852.1|CI226852
EST:     TTTCTAGTTGCAAAG                         GCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACATC
genomic: TTTCTAGTTGCAAAGgtagatagac ... atctccgtagGCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACATC
EST: gi|86504925|gb|CI147558.1|CI147558
EST:     GAGAATTGTTGGGTGGAAATGGAATTTTGGCTGATTTTCTAGTTGCAAAG                         GCATTCTGTGACCTGGAGCCTAGATACTCATACGAAGGCACATACGACATC
genomic: GAGAATTGTTGGGTGGAAATGGAATTTTGGCTGATTTTCTAGTTGCAAAGgtagatagac ... atctccgtagGCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACATC
EST: gi|33683999|gb|CF312238.1|CF312238
EST:     GAGAATTGTTGGGTGGAAATGGAATTTTGGCTGATTTTCTAGTTGCAAAG                         GCATTTTGTGACCTGGAGCCTATATACCCATACGAAGGCACATACGAGCAT
genomic: GAGAATTGTTGGGTGGAAATGGAATTTTGGCTGATTTTCTAGTTGCAAAGgtagatagac ... atctccgtagGCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGA-CAT
EST: gi|18386375|gb|BM419573.1|BM419573
EST:     AGAATT-TTGGGT-GAAATGGAATTTT-GCTGGATTTTCTAGTTGCAAAG                         GCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACATC
genomic: AGAATTGTTGGGTGGAAATGGAATTTTGGCT-GATTTTCTAGTTGCAAAGgtagatagac ... atctccgtagGCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACATC
EST: gi|18385617|gb|BM418816.1|BM418816
EST:     GAATTGTTTGGTGGAAATGGAATTTTGGCTGATTTTCTAGTTGCCACAA-                         GCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACAT
genomic: GAATTGTTGGGTGGAAATGGAATTTTGGCTGATTTTCTAGTTG-CA-AAGgtagatagac ... atctccgtagGCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACAT
EST: gi|59930157|gb|AB178699.1|AB178699
EST:     TGGAAATGGAATTTTGGCTGATTTTCTAGTTGCAAAG                         GCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACATC
genomic: TGGAAATGGAATTTTGGCTGATTTTCTAGTTGCAAAGgtagatagac ... atctccgtagGCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACATC
EST: gi|44666104|gb|CR279538.1|CR279538
EST:     GAGAATTGTTGGGTGGAAATGGAATTTTGGCTGATTTTCTAGTTGCAAAG                         GCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACATC
genomic: GAGAATTGTTGGGTGGAAATGGAATTTTGGCTGATTTTCTAGTTGCAAAGgtagatagac ... atctccgtagGCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACATC
EST: gi|4715706|gb|AU056822.1|AU056822
EST:     GAGAATTGTTGGGTGGAAATGGAATTTTGGCTGATTTTCTAGTTGCAAAG                         GCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACATC
genomic: GAGAATTGTTGGGTGGAAATGGAATTTTGGCTGATTTTCTAGTTGCAAAGgtagatagac ... atctccgtagGCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACATC
EST: gi|86537166|gb|CI177372.1|CI177372
EST:     GAGAATTGTTGGGTGGAAATGGAATTTTGGCTGATTTTCTAGTTGCAAAG                         GCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACATC
genomic: GAGAATTGTTGGGTGGAAATGGAATTTTGGCTGATTTTCTAGTTGCAAAGgtagatagac ... atctccgtagGCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACATC
EST: gi|88903725|gb|CI089263.1|CI089263
EST:     TGGAAATGGAATTTTGGCTGATTTTCTAGTTGCAAAG                         GCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACATC
genomic: TGGAAATGGAATTTTGGCTGATTTTCTAGTTGCAAAGgtagatagac ... atctccgtagGCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACATC
EST: gi|7839222|gb|AU090633.1|AU090633
EST:     GAGAATTGTTGGGTGGAAATGGAATTTTGGCTGATTTTCTAGTTGCAAAG                         GCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACATC
genomic: GAGAATTGTTGGGTGGAAATGGAATTTTGGCTGATTTTCTAGTTGCAAAGgtagatagac ... atctccgtagGCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACATC
EST: gi|29668419|gb|CB664694.1|CB664694
EST:     GAGAATTGTTGGGTGGAAATGGAATTTTGGCTGATTTTCTAGTTGCAAAG                         GCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACATC
genomic: GAGAATTGTTGGGTGGAAATGGAATTTTGGCTGATTTTCTAGTTGCAAAGgtagatagac ... atctccgtagGCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACATC
EST: gi|87015276|gb|CI275466.1|CI275466
EST:     GAGAATTGTTGGGTGGAAATGGAATTTTGGCTGATTTTCTAGTTGCAAAG                         GCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACATC
genomic: GAGAATTGTTGGGTGGAAATGGAATTTTGGCTGATTTTCTAGTTGCAAAGgtagatagac ... atctccgtagGCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACATC
EST: gi|86425749|gb|CI070846.1|CI070846
EST:     ATTTTCTAGTTGCAAAG                         ACATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACATC
genomic: ATTTTCTAGTTGCAAAGgtagatagac ... atctccgtagGCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACATC
EST: gi|29660317|gb|CB656592.1|CB656592
EST:     GAGAATTGTTGGGTGGAAATGGAATTTTGGCTGATTTTCTAGTTGCAAAG                         GCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACATC
genomic: GAGAATTGTTGGGTGGAAATGGAATTTTGGCTGATTTTCTAGTTGCAAAGgtagatagac ... atctccgtagGCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACATC
EST: gi|29660291|gb|CB656566.1|CB656566
EST:     GAGAATTGTTGGGTGGAAATGGAATTTTGGCTGATTTTCTAGTTGCAAAG                         GCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACATC
genomic: GAGAATTGTTGGGTGGAAATGGAATTTTGGCTGATTTTCTAGTTGCAAAGgtagatagac ... atctccgtagGCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACATC
EST: gi|58593876|gb|CF992184.1|CF992184
EST:     GAGAATCGTGGGGTGGAAATGGAATTTTGGCTGATTTTCTAGTTGCAAAG                         GCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACATC
genomic: GAGAATTGTTGGGTGGAAATGGAATTTTGGCTGATTTTCTAGTTGCAAAGgtagatagac ... atctccgtagGCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACATC

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: 69 (upstream exon), 47 (downstream exon)
Score: 18

GGTTGGACTTCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATTGTTGGGTGGAAATGGAATTTTGGCTGATTTTCTAGTTGCAAAGgtagatagac ... atctccgtagGCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACATCAACAGCCTGGTGACTGGTAGAGAAATAACTGGGATCGCAAGCTTCAAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatattcatatgccatcattcaatacttaattaatgatttttattatctccgtagGCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACATCAACAGCCTGGTGACTGGTAGAGAAATAACTGGGATCGCAAGCTTCAAAC
                            aattaat  putative branch site (score: 18)
                                     tttttattatctcc  putative PPT
              atcattcaatacttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagatagacctcatgtaggatattgagatattcatatgccatcattcaatacttaattaatgatttttattatctccgtagGCATTCTGTGACCTGGAGCCTATATACTCATACGAAGGCACATACGACATCAACAGCCTGGTGACTGGTAGAGAAATAACTGGGATCGCAAGCTTCAAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT