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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagattcattcttcttcattcggcctttagatttcagagggaacatcatttgctaaatttgcaacattagGTGTGGCTATGGAATTGGAGGATTCACTGTATCCATTGCTAAGGGAAGTCAGCATTGGTATAGACCCTTATGTAGTCTTCGAAGATGCAGAATGGGCTCT

Basic information

species Oryza sativa
transcript LOC_Os08g44810.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g44810.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G129513_T01 (Zea mays), 3'ss of exon 4
---------------------------------------------------------------------------------------------------gtagattcattcttctt-cattcggcctttagatttcagagggaacatcatttgct----aaatttgcaacat-tagGTGTGGCTATGGAATTGGAGGATTCACTGTATCCATTGCTAAGGGAAGTCAGCATTGGTATAGACCCTTATGTAGTCTTCGAAGATGCAGAATGGGCTCT
                                                                                                    |  ||  |||  | |  ||       | ||   |          | |||| ||||    |||  |||||  |  |||||| ||||||||| ||||||| || ||||||||| |||| ||||||||||||||||| ||||| ||||| || |||||  |||||| ||| ||||| ||
gtgaaacacttcttctttctacaccttactatctgagaagaagaaacaattcatagttgctagtacatacctacgatttcaagtgatgtgctctctgatatcaatggattactgtgacagcgaatatgtaatgtatcactttttcctcatgtgctctcaaaaactgcaatttgcagGTGTAGCTATGGAACTGGAGGACTCGCTGTATCCACTGCTGAGGGAAGTCAGCATTGGCATAGATCCTTACGTGGTCTTTCAAGATGTAGATTGGGCCCT

upper sequence: LOC_Os08g44810.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA20G33380.1 (Glycine max), 3'ss of exon 6
gtagattcattcttcttcattcggccttt-agatttcagagggaacatcatttgctaaatttgcaacattagGTGTGGCTATGGAATTGGAGGATTCACTGTATCCATTGCTAAGGGAAGTCAGCATTGGTATAGACCCTTATGTAGTCTTCGAAGATGCAGAATGGGCTCT
|||     ||   || | ||   |  ||  |   | ||||  |  | |   |   ||  |      |   |||    |  ||||||   |  || |   |  |  |||   |  |   | | |      |   ||                                     
gtattggtatcgatccttatgaagtgttccaagATGCAGAATGGGCTTTGCT-AATAGGTGCAAGCCTCGAGGACCTGGAATGGAACGAGCAGACTTGTTAGA--CATAAATGGGCAGATTTAT--GCAGCGCAG-------------------------------------

upper sequence: LOC_Os08g44810.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA10G34150.3 (Glycine max), 3'ss of exon 4
-------------------gtagattcattcttcttcattcggcctttagatttca-gagggaacatcatttg--ctaaat-ttgcaa-----cat-tagGTGTGGCTATGGAATTGGAGGATTCACTGTATCCATTGCTAAGGGAAGTCAGCATTGGTATAGACCCTTATGTAGTCTTCGAAGATGCAGAATGGGCTCT
                    ||  || | | ||    | |     | || ||  || |     |  |   |||  |||||| ||  ||     |||  |||||| || |||||||||||||| ||  ||| ||| ||| | ||||| || || |||||||| || ||||||| ||| ||| ||||||||||||||||| |
cttttaactaaaacaagatatacctttaatgttgagtaatgtaggtataaataacacgtactgatgtttgttgttctaaatgttataattgaacatgcagGTGTTGCAATGGAATTGGAGGACTCTTTGTTTCCTTTGTTGAGGGAGGTTAGTATTGGTATCGATCCTTATGAAGTGTTCCAAGATGCAGAATGGGCTTT

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|84117267|gb|CD151034.1|CD151034
EST:     AATAGCACTTAAGTTGTTGGGCTCTGAAAGATCAATACAAGCACTTGAAG                         GTGTGGCTATGGAATTGGAGGATTCACTGTATCCATTGCTAAGGGAAGTCA
genomic: AATAGCACTTAAGTTGTTGGGCTCTGAAAGATCAATACAAGCACTTGAAGgtagattcat ... gcaacattagGTGTGGCTATGGAATTGGAGGATTCACTGTATCCATTGCTAAGGGAAGTCA
EST: gi|29686259|gb|CB682534.1|CB682534
EST:     AATAGCACTTAAGTTGTTGGGCTCTGAAAGATCAATACAAGCACTTGAAG                         GTGTGGCTATGGAATTGGAGGATTCACTGTATCCATTGCTAAGGGAAGTCA
genomic: AATAGCACTTAAGTTGTTGGGCTCTGAAAGATCAATACAAGCACTTGAAGgtagattcat ... gcaacattagGTGTGGCTATGGAATTGGAGGATTCACTGTATCCATTGCTAAGGGAAGTCA
EST: gi|58606317|gb|CK034350.1|CK034350
EST:     AATAGCACTTAAGTTGTTGGGCTCTGAAAGATCAATACAAGCACTTGAAG                         GTGTGGCTATGGAATTGGAGGATTCACTGTATCCATTGCTAAGGGAAGTCA
genomic: AATAGCACTTAAGTTGTTGGGCTCTGAAAGATCAATACAAGCACTTGAAGgtagattcat ... gcaacattagGTGTGGCTATGGAATTGGAGGATTCACTGTATCCATTGCTAAGGGAAGTCA
EST: gi|30227408|gb|CB965300.1|CB965300
EST:     AATAGCACTTAAGTTGTTGGGCTCTGAAAGATCAATACAAGCACTTGAAG                         GTGTGGCTATGGAATTGGAGGATTCACTGTATCCATTGCTACGGGAAGTCA
genomic: AATAGCACTTAAGTTGTTGGGCTCTGAAAGATCAATACAAGCACTTGAAGgtagattcat ... gcaacattagGTGTGGCTATGGAATTGGAGGATTCACTGTATCCATTGCTAAGGGAAGTCA
EST: gi|30227998|gb|CB965890.1|CB965890
EST:     AATAGCACTTAAGTTGTTGGGCTCTGAAAGATCAATACAAGCACTTGAAG                         GTGTGGCTATGGAATTGGAGGATTCACTGTATCCATTGCTAAGGGAAGTCA
genomic: AATAGCACTTAAGTTGTTGGGCTCTGAAAGATCAATACAAGCACTTGAAGgtagattcat ... gcaacattagGTGTGGCTATGGAATTGGAGGATTCACTGTATCCATTGCTAAGGGAAGTCA
EST: gi|117251104|gb|CT844032.1|CT844032
EST:     AATAGCACTTAAGTTGTTGGGCTCTGAAAGATCAATACAAGCACTTGAAG                         GTGTGGCTATGGAATTGGAGGATTCACTGTATCCATTGCTAAGGGAAGTCA
genomic: AATAGCACTTAAGTTGTTGGGCTCTGAAAGATCAATACAAGCACTTGAAGgtagattcat ... gcaacattagGTGTGGCTATGGAATTGGAGGATTCACTGTATCCATTGCTAAGGGAAGTCA
EST: gi|29686257|gb|CB682532.1|CB682532
EST:     AATAGCACTTAAGTTGTTGGGCTCTGAAAGATCAATACAAGCACTTGAAG                         GTGTGGCTATGGAATTGGAGGATTCACTGTATCCATTGCTAAGGGAAGTCA
genomic: AATAGCACTTAAGTTGTTGGGCTCTGAAAGATCAATACAAGCACTTGAAGgtagattcat ... gcaacattagGTGTGGCTATGGAATTGGAGGATTCACTGTATCCATTGCTAAGGGAAGTCA
EST: gi|29677717|gb|CB673992.1|CB673992
EST:     AATAGCACTTAAGTTGTTGGGCTCTGAAAGATCAATACAAGCACTTGAAG                         GTGTGGCTATGGAATTGGAGGATTCACTGTATCCATTGCTAAGGGAAGTCA
genomic: AATAGCACTTAAGTTGTTGGGCTCTGAAAGATCAATACAAGCACTTGAAGgtagattcat ... gcaacattagGTGTGGCTATGGAATTGGAGGATTCACTGTATCCATTGCTAAGGGAAGTCA

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), 68 (downstream exon)
Score: 65

CTTGCCTCTGGTGAGGTTTTTGGACCGGACCAACCAATAGCACTTAAGTTGTTGGGCTCTGAAAGATCAATACAAGCACTTGAAGgtagattcat ... gcaacattagGTGTGGCTATGGAATTGGAGGATTCACTGTATCCATTGCTAAGGGAAGTCAGCATTGGTATAGACCCTTATGTAGTCTTCGAAGATGCAGAATGGGCTCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattcggcctttagatttcagagggaacatcatttgctaaatttgcaacattagGTGTGGCTATGGAATTGGAGGATTCACTGTATCCATTGCTAAGGGAAGTCAGCATTGGTATAGACCCTTATGTAGTCTTCGAAGATGCAGAATGGGCTCT
                                   tgctaaa  putative branch site (score: 65)
          tttagattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagattcattcttcttcattcggcctttagatttcagagggaacatcatttgctaaatttgcaacattagGTGTGGCTATGGAATTGGAGGATTCACTGTATCCATTGCTAAGGGAAGTCAGCATTGGTATAGACCCTTATGTAGTCTTCGAAGATGCAGAATGGGCTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG