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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCCACAGACCTCTACCAAGAGCAGATGAAAGGGCGTGTTGTTGATTGGGATGTGCCTGAACAAGCATCTGGCCAGCATGTAATGAAGGATGAGCCACAGgtagtgtttagtctagaatcatcctattattttcatttcctgaaattgggctatatgttctcatgctgtgcaaatttcag

Basic information

species Oryza sativa
transcript LOC_Os10g42439.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g42439.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G049288_T01 (Zea mays), 5'ss of exon 17
GGCCACAGACCTCTACCAAGAGCAGATGAAAGGGCGTGTTGTTGATTGGGATGTGCCTGAACAAGCATCTGGCCAGCATGTAATGAAGGATGAGCCACAGgtagtgtttagtctagaatcatcctattattttcatt--tcctgaaattgggct--atatgttctcatgctgtgcaaatttcag
|||  |||||||||| ||||||||||||||||| |||||||||||||||||||| ||||||||||| || || || ||||||||||||||||| ||||||||||| | || || ||||   |  | || | |  | |  | ||| || |  |||  | ||||    ||||||| ||||||||||
GGCATCAGACCTCTATCAAGAGCAGATGAAAGGACGTGTTGTTGATTGGGATGTACCTGAACAAGCTTCCGGACAACATGTAATGAAGGATGAACCACAGgtagtttctattccagaacttttttgttgtgtaaaataattctgtaactttgcttaagatgtcggtatgctgtccaaatttcag

upper sequence: LOC_Os10g42439.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G001895_T01 (Zea mays), 5'ss of exon 11
GGCCACAGACCTCTACCAAGAGCAGATGAAAGGGCGTGTTGTTGATTGGGATGTGCCTGAACAAGCATCTGGCCAGCATGTAATGAAGGATGAGCCACAGgtagtgtttagtctagaatcatcctattattt----tcatttcctgaaattgggctatatgttctcatgctgtgcaaatttcag
|||  |||||||||||||||||||||||||||| |||||||||||||||||||| ||||||||||||||||| || |||||||||||||| || ||||||||||  | || || ||||   |  | ||   |    | |||   | |  || |   | ||||    ||||||| ||||||||||
GGCATCAGACCTCTACCAAGAGCAGATGAAAGGACGTGTTGTTGATTGGGATGTACCTGAACAAGCATCTGGGCAACATGTAATGAAGGACGAACCACAGgtagcttctattccagaacttttttcttgcataatataattctgtaactttagttaagatgtcagtatgctgtccaaatttcag

upper sequence: LOC_Os10g42439.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GLYMA05G08040.1 (Glycine max), 5'ss of exon 17
GGCCACAGACCTCTACCAAGAGCAGATGAAAGGGCGTGTTGTTGATTGGGATGTGCCTGAACAAGCATCTGGCCAGCATGTAATGAAGGATGAGCCACAGgtagtgtttagtctagaatcatcc---------tattattttc-atttcctgaaattgggctatatgttctcatgctgtgcaaatttcag----------
|||   ||| || ||||  ||||||||||| ||||||||||||||||||||| ||||||| || |||||||||||||| | |||||  |||||||||||||||     |  | ||   |  ||          | ||| || | | ||  |      ||| |  |    | |   || | |    |||            
GGCATTAGAGCTATACCGTGAGCAGATGAAGGGGCGTGTTGTTGATTGGGATTTGCCTGAGCAGGCATCTGGCCAGCAGGAAATGAGAGATGAGCCACAGgtatcacctgatatatgtttttctataggcaaatgttagttgctaattgttagtgaggggattcaaacccacgacctctccccccttcccttctcccttc

upper sequence: LOC_Os10g42439.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GLYMA17G12950.1 (Glycine max), 5'ss of exon 18
GGCCACAGACCTCTACCAAGAGCAGATGAAAGGGCGTGTTGTTGATTGGGATGTGCCTGAACAAGCATCTGGCCAGCATGTAATGAAGGATGAGCCACAGgtagtgtttagtctagaatcatcctattattttcatttcctgaaattgggctatatgttctcatgctgtgcaaatttcag-----------------
|||  |||| || ||||  ||||||||||||||||||||||||||||||||||||||||| || |||||||| ||||| | |||||  ||||||||||||||| |    ||       | ||  | || | |  | ||    | |      ||||| |||||||         ||||||                  
GGCATCAGAGCTATACCGTGAGCAGATGAAAGGGCGTGTTGTTGATTGGGATGTGCCTGAGCAGGCATCTGGACAGCAGGAAATGAGAGATGAGCCACAGgtattcaccagatatatgtgatttttttttataaaattatgtatagaataatatattttctcata---aatggatttcaacttttgtgtggatgcag

upper sequence: LOC_Os10g42439.1 (Oryza sativa), 5'ss of exon 17
lower sequence: Vv11s0016g04420.t01 (Vitis vinifera), 5'ss of exon 17
GGCCACAGACCTCTACCAAGAGCAGATGAAAGGGCGTGTTGTTGATTGGGATGTGCCTGAACAAGCATCTGGCCAGCATGTAATGAAGGATGAGCCACAGgtagtgtttagtctagaatcatcctattattttcattt---cctgaaat------tgggctatatgttctcatgct-gtgcaaatttcag
|||  |||| || || |  || || |||||||| |||||||||||||||||||||||||| || |||||||||||||| | |||||  |||||||||||||||     |  ||||   |   | | |||||   || |   |||| | |      |||  |  |  || ||||| |  ||||        
GGCTTCAGATCTTTATCGTGAACAAATGAAAGGTCGTGTTGTTGATTGGGATGTGCCTGAGCAGGCATCTGGCCAGCAGGAAATGAGAGATGAGCCACAGgtatctcctgttctattctgtcctttttattcaaatatgtacctgtactgttgagtggatttcaaattttcatggtcatgcag-------

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|29679203|gb|CB675478.1|CB675478
EST:     ATGTGCCTGAACAAGCATCTGGCCAGCATGTAATGAAGGATGAGCCACAG                         GTTGGAGGTATTTATGTGAGACTCTTCCTAAAGGATCCCAAGTTTCCATTG
genomic: ATGTGCCTGAACAAGCATCTGGCCAGCATGTAATGAAGGATGAGCCACAGgtagtgttta ... caaatttcagGTTGGAGGTATTTATGTGAGACTCTTCCTAAAGGATCCCAAGTTTCCATTG
EST: gi|88361783|gb|CI680358.1|CI680358
EST:     ATGTGCCTGAACAAGCATCTGGCCAGCATGTAATGAAGGATGAGCCACAG                         GTTGGAGGTATTTATGTGAGACTCTTCCTAAAGGATCCCAAGTTTCCATTG
genomic: ATGTGCCTGAACAAGCATCTGGCCAGCATGTAATGAAGGATGAGCCACAGgtagtgttta ... caaatttcagGTTGGAGGTATTTATGTGAGACTCTTCCTAAAGGATCCCAAGTTTCCATTG
EST: gi|88590336|gb|CI709182.1|CI709182
EST:     ATGTGCCTGAACAAGCATCTGGCCAGCATGTAATGAAGGATGAGCCACAG                         GTTGGAGGTATTTATGTGAGACTCTTCCTAAAGGATCCCAAGTTTCCATTG
genomic: ATGTGCCTGAACAAGCATCTGGCCAGCATGTAATGAAGGATGAGCCACAGgtagtgttta ... caaatttcagGTTGGAGGTATTTATGTGAGACTCTTCCTAAAGGATCCCAAGTTTCCATTG
EST: gi|88444728|gb|CI694966.1|CI694966
EST:     ATGTGCCTGAACAAGCATCTGGCCAGCATGTAATGAAGGATGAGCCACAG                         GTTGGAGGTATTTATGTGAGACTCTTCCTAAAGGATCCCAAGTTTCCATTG
genomic: ATGTGCCTGAACAAGCATCTGGCCAGCATGTAATGAAGGATGAGCCACAGgtagtgttta ... caaatttcagGTTGGAGGTATTTATGTGAGACTCTTCCTAAAGGATCCCAAGTTTCCATTG
EST: gi|58671255|gb|CK059941.1|CK059941
EST:     ATGTGCCTGAACAAGCATCTGGCCAGCATGTAATGAAGGATGAGCCACAG                         GTTGGAGGTATTTATGTGAGACTCTTCCTAAAGGATCCCAAGTTTCCATTG
genomic: ATGTGCCTGAACAAGCATCTGGCCAGCATGTAATGAAGGATGAGCCACAGgtagtgttta ... caaatttcagGTTGGAGGTATTTATGTGAGACTCTTCCTAAAGGATCCCAAGTTTCCATTG
EST: gi|88581389|gb|CI698370.1|CI698370
EST:     ATGTGCCTGAACAAGCATCTGGCCAGCATGTAATGAAGGATGAGCCACAG                         GTTGGAGGTATTTATGTGAGACTCTTCCTAAAGGATCCCAAGTTTCCATTG
genomic: ATGTGCCTGAACAAGCATCTGGCCAGCATGTAATGAAGGATGAGCCACAGgtagtgttta ... caaatttcagGTTGGAGGTATTTATGTGAGACTCTTCCTAAAGGATCCCAAGTTTCCATTG
EST: gi|88588295|gb|CI706103.1|CI706103
EST:     ATGTGCCTGAACAAGCATCTGGCCAGCATGTAATGAAGGATGAGCCACAG                         GTTGGAGGTATTTATGTGAGACTCTTCCTAAAGGATCCCAAGTTTCCATTG
genomic: ATGTGCCTGAACAAGCATCTGGCCAGCATGTAATGAAGGATGAGCCACAGgtagtgttta ... caaatttcagGTTGGAGGTATTTATGTGAGACTCTTCCTAAAGGATCCCAAGTTTCCATTG
EST: gi|218488686|gb|FG961338.1|FG961338
EST:     ATGTGCCTGAACAAGCATCTGGCCAGCATGTAATGAAGGATGAGCCACAG                         GTTGGAGGTATTTATGTGAGACTCTTCCTAAAGGATCCCAAGTTTCCATTG
genomic: ATGTGCCTGAACAAGCATCTGGCCAGCATGTAATGAAGGATGAGCCACAGgtagtgttta ... caaatttcagGTTGGAGGTATTTATGTGAGACTCTTCCTAAAGGATCCCAAGTTTCCATTG
EST: gi|88580858|gb|CI697815.1|CI697815
EST:     ATGTGCCTGAACAAGCATCTGGCCAGCATGTAATGAAGGATGAGCCACAG                         GTTGGAGGTATTTATGTGAGACTCTTCCTAAAGGATCCCAAGTTTCCATTG
genomic: ATGTGCCTGAACAAGCATCTGGCCAGCATGTAATGAAGGATGAGCCACAGgtagtgttta ... caaatttcagGTTGGAGGTATTTATGTGAGACTCTTCCTAAAGGATCCCAAGTTTCCATTG
EST: gi|58664326|gb|CK053012.1|CK053012
EST:     ATGTGCCTGAACAAGCATCTGGCCAGCATGTAATGAAGGATGAGCCACAG                         GTTGGAGGTATTTATGTGAGACTCTTCCTAAAGGATCCCAAGTTTCCATTG
genomic: ATGTGCCTGAACAAGCATCTGGCCAGCATGTAATGAAGGATGAGCCACAGgtagtgttta ... caaatttcagGTTGGAGGTATTTATGTGAGACTCTTCCTAAAGGATCCCAAGTTTCCATTG
EST: gi|29638584|gb|CB643593.1|CB643593
EST:     ATGTGCCTGAACAAGCATCTGGCCAGCATGTAATGAAGGATGAGCCACAG                         GTTGGAGGTATTTATGTGAGACTCTTCCTAAAGGATCCCAAGTTTCCATTG
genomic: ATGTGCCTGAACAAGCATCTGGCCAGCATGTAATGAAGGATGAGCCACAGgtagtgttta ... caaatttcagGTTGGAGGTATTTATGTGAGACTCTTCCTAAAGGATCCCAAGTTTCCATTG

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: 53 (upstream exon), 56 (downstream exon)
Score: 10

GGCCACAGACCTCTACCAAGAGCAGATGAAAGGGCGTGTTGTTGATTGGGATGTGCCTGAACAAGCATCTGGCCAGCATGTAATGAAGGATGAGCCACAGgtagtgttta ... caaatttcagGTTGGAGGTATTTATGTGAGACTCTTCCTAAAGGATCCCAAGTTTCCATTGAGAAACCCTAAAAGGTTCCTAGAAGGGCTGCTAGATCAGTATGTCTCAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCCACAGACCTCTACCAAGAGCAGATGAAAGGGCGTGTTGTTGATTGGGATGTGCCTGAACAAGCATCTGGCCAGCATGTAATGAAGGATGAGCCACAGgtagtgtttagtctagaatcatcctattattttcatttcctgaaattgggctatatgttctcatgctgtgcaaatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG