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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acgtggcccaatttggtttgacctgttctgtcttgtatttgaaatgttttctgtttcacattggttttaagaagctaactgaattctctgctttgaccagTCATTCAAAGAAGCACTCTCTGAAGTCCGATTCTGCTCTAGAATGGAAGAGCTTTTACTGAAGAAAAAAACATCTACTGCCGGAGACTCCCTTGAGATTC

Basic information

species Oryza sativa
transcript LOC_Os01g06270.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g06270.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G102196_T01 (Zea mays), 3'ss of exon 3
acgtggcccaatttggtttgacctgttctgtcttgt-atttgaaatgtt-ttctgt-ttcacattggtttta-------agaagctaactgaattctctgctttgaccagTCATTCAAAGAAGCACTCTCTGAAGTCCGATTCTGCTCTAGAATGGAAGAGCTTTTACTGAAGAAAAAAACATCTACTGCCGGAGACTCCCTTGAGATTC
           |||| ||||| |||||   |||| | ||  | ||| || || ||  || | | || |||||       | |||||||||  ||| |   | |||  ||||| |||||||||||||||   ||||||||||| |||||||||||||| || ||| || ||||||| ||||||  || | | || || ||| | ||||| |
----------gtttgctttgatctgttgcatctttttataagtaattttattatgcctttatagtgcttttagtttggaacaagctaactctatttttcaccttgctcagTCTTTCAAAGAAGCACTCAACGAAGTCCGATTTTGCTCTAGAATGGAGGAACTTCTATTGAAGAAGAAAACAATTAATACTGGGGATTCCTTAGAGATCC
















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|88666765|gb|CI718901.1|CI718901
EST:     AAGAAGACCATGCAAAAACTACGGAAAGGACTTCTGCTACAACTGTTGAG                         TCATTCAAAGAAGCACTCTCTGAAGTCCGA
genomic: AAGAAGACCATGCAAAAACTACGGAAAGGACTTCTGCTACAACTGTTGAGgtgttgcctc ... ctttgaccagTCATTCAAAGAAGCACTCTCTGAAGTCCGA
EST: gi|88593663|gb|CI713617.1|CI713617
EST:     AAGAAGACCATGCAAAAACTACGGAAAGGACTTCTGCTACAACTGTTGAG                         TCATTCAAAGAAGCACTCTCTGAAGTTCGATTCTGCT
genomic: AAGAAGACCATGCAAAAACTACGGAAAGGACTTCTGCTACAACTGTTGAGgtgttgcctc ... ctttgaccagTCATTCAAAGAAGCACTCTCTGAAGTCCGATTCTGCT
EST: gi|88675253|gb|CI727368.1|CI727368
EST:     AAGAAGACCATGCAAAAACTACGGAAAGGACTTCTGCTACAACTGTTGAG                         TCATTCAAAGAAGCACTCTCTGAAGTCCGATTCTGCTCTAGAATGGAAGAG
genomic: AAGAAGACCATGCAAAAACTACGGAAAGGACTTCTGCTACAACTGTTGAGgtgttgcctc ... ctttgaccagTCATTCAAAGAAGCACTCTCTGAAGTCCGATTCTGCTCTAGAATGGAAGAG
EST: gi|88972621|gb|CI717347.1|CI717347
EST:     AAGAAGACCATGCAAAAACTACGGAAAGGACTTCTGCTACAACTGTTGAG                         TCATTCAAAGAA
genomic: AAGAAGACCATGCAAAAACTACGGAAAGGACTTCTGCTACAACTGTTGAGgtgttgcctc ... ctttgaccagTCATTCAAAGAA
EST: gi|88670454|gb|CI724570.1|CI724570
EST:     AAGAAGACCATGCAAAAACTACGGAAAGGACTTCTGCTACAACTGTTGAG                         TCATTCAAAGAAGCACTCTCTGAAGTCCGATTCTGCTCTAGAATGGAAGAG
genomic: AAGAAGACCATGCAAAAACTACGGAAAGGACTTCTGCTACAACTGTTGAGgtgttgcctc ... ctttgaccagTCATTCAAAGAAGCACTCTCTGAAGTCCGATTCTGCTCTAGAATGGAAGAG
EST: gi|88595334|gb|CI714155.1|CI714155
EST:     AAGAAGACCATGCAAAAACTACGGAAAGGACTTCTGCTACAACTGTTGAG                         TCATTCAAAGAAGCACTCTCTGAAGTCCGATTCTGC
genomic: AAGAAGACCATGCAAAAACTACGGAAAGGACTTCTGCTACAACTGTTGAGgtgttgcctc ... ctttgaccagTCATTCAAAGAAGCACTCTCTGAAGTCCGATTCTGC
EST: gi|88670097|gb|CI724213.1|CI724213
EST:     AAGAAGACCATGCAAAAACTACGGAAAGGACTTCTGCTACAACTGTTGAG                         TCATTCAAAGAAGCACTCCTCTGAAGTCCGATTCTGCTCTAGAATGGAAGA
genomic: AAGAAGACCATGCAAAAACTACGGAAAGGACTTCTGCTACAACTGTTGAGgtgttgcctc ... ctttgaccagTCATTCAAAGAAGCACTC-TCTGAAGTCCGATTCTGCTCTAGAATGGAAGA
EST: gi|88669723|gb|CI723839.1|CI723839
EST:     AAGAAGACCATGCAAAAACTACGGAAAGGACTTCTGCTACAACTGTTGAG                         TCATTCAAAGAAGCACTCTCTGAA
genomic: AAGAAGACCATGCAAAAACTACGGAAAGGACTTCTGCTACAACTGTTGAGgtgttgcctc ... ctttgaccagTCATTCAAAGAAGCACTCTCTGAA
EST: gi|88687953|gb|CI731529.1|CI731529
EST:     AAGAAGACCATGCAAAAACTACGGAAAGGACTTCTGCTACAACTGTTGAG                         TCATTCAAAGAAGCACTCTCTGAAGTCCGATTC
genomic: AAGAAGACCATGCAAAAACTACGGAAAGGACTTCTGCTACAACTGTTGAGgtgttgcctc ... ctttgaccagTCATTCAAAGAAGCACTCTCTGAAGTCCGATTC
EST: gi|88905475|gb|CI712774.1|CI712774
EST:     AAGAAGACCATGCAAAAACTACGGAAAGGACTTCTGCTACAACTGTTGAG                         TCATTCAAAGAAGCACTCTC
genomic: AAGAAGACCATGCAAAAACTACGGAAAGGACTTCTGCTACAACTGTTGAGgtgttgcctc ... ctttgaccagTCATTCAAAGAAGCACTCTC
EST: gi|88593918|gb|CI713872.1|CI713872
EST:     AAGAAGACCATGCAAAAACTACGGAAAGGACTTCTGCTACAACTGTTGAG                         TCATTCAAAGAAGCAC
genomic: AAGAAGACCATGCAAAAACTACGGAAAGGACTTCTGCTACAACTGTTGAGgtgttgcctc ... ctttgaccagTCATTCAAAGAAGCAC
EST: gi|87017026|gb|CI286162.1|CI286162
EST:     AAGAAGACCATGCAAAAACTACGGAAAGGACTTCTGCTACAACTGTTGAG                         TCATTCAAAGAAGCACTCTCTGAAGTCCGATTCTGCTCTAGAATGGAAGAG
genomic: AAGAAGACCATGCAAAAACTACGGAAAGGACTTCTGCTACAACTGTTGAGgtgttgcctc ... ctttgaccagTCATTCAAAGAAGCACTCTCTGAAGTCCGATTCTGCTCTAGAATGGAAGAG

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), 58 (downstream exon)
Score: 26

GTTGTGGAAGAAACTAAATGAGAAGGAGACATCAAGAGTTCAACAAACTCAAGAAGACCATGCAAAAACTACGGAAAGGACTTCTGCTACAACTGTTGAGgtgttgcctc ... ctttgaccagTCATTCAAAGAAGCACTCTCTGAAGTCCGATTCTGCTCTAGAATGGAAGAGCTTTTACTGAAGAAAAAAACATCTACTGCCGGAGACTCCCTTGAGATTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttctgtttcacattggttttaagaagctaactgaattctctgctttgaccagTCATTCAAAGAAGCACTCTCTGAAGTCCGATTCTGCTCTAGAATGGAAGAGCTTTTACTGAAGAAAAAAACATCTACTGCCGGAGACTCCCTTGAGATTC
                           agctaac  putative branch site (score: 26)
                                      ttctctgcttt  putative PPT
                   ttttaagaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acgtggcccaatttggtttgacctgttctgtcttgtatttgaaatgttttctgtttcacattggttttaagaagctaactgaattctctgctttgaccagTCATTCAAAGAAGCACTCTCTGAAGTCCGATTCTGCTCTAGAATGGAAGAGCTTTTACTGAAGAAAAAAACATCTACTGCCGGAGACTCCCTTGAGATTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - tgacctg
- - - - - - - - - - - - - - tgtcttg