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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGGGAATACAAGCTGAAGAACTACCTGTTGACCAATTCATTCCTCTTGGGAGGATGCTTTACAAGGCTCCATCTGATGGAAAATGGGGCGAACATGAACgtaaatatttgccctctgccctctacctgatacatttcagccttcatacttatcgtccagctatcacttgcctcttgtgtattttcaattgctgtcttttgaaatttttagaatataaccatctttcgccatttcag

Basic information

species Oryza sativa
transcript LOC_Os05g34180.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g34180.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G133082_T02 (Zea mays), 5'ss of exon 2
CTGGGAATACAAGCTGAAGAACTACCTGTTGACCAATTCATTCCTCTTGGGAGGATGCTTTACAAGGCTCCATCTGATGGAAAATGGGGCGAACATGAACgtaaatatttgc---cctctgccctctacctgatacatttc-agccttcatacttatcgt-ccagctatcacttgcctcttgtgtattttcaattgctgtcttttgaaatttttagaatataaccatctttcgccatttcag
|||||||||   ||||| ||| ||||||| ||||| |||||||| |||||||||||||||||||||||||| || |||||||||||||||||||| ||  ||| ||| |||    |||||  ||  ||| ||||   || | ||    ||||||  | ||    ||| |    ||| | ||       |    ||  || |  |||     |||| ||  |  ||     | |  |||||||
CTGGGAATAGTGGCTGACGAATTACCTGTCGACCAGTTCATTCCGCTTGGGAGGATGCTTTACAAGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGTgtacatacttgattgcctcttgccattacatgatgggttcccagttcccatactatttgtgtttgctgtactctgcatgtttcaagggtctgctt--tg-cagttgcgggctttaaaacctttcctatccttgttatttcag

upper sequence: LOC_Os05g34180.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G145029_T01 (Zea mays), 5'ss of exon 5
CTGGGAATACAAGCTGAAGAACTACCTGTTGACCAATTCATTCCTCTTGGGAGGATGCTTTACAAGGCTCCATCTGATGGAAAATGGGGCGAACATGAACgtaaatatttgccctctgccctctacctgatacatttcagccttcatacttatcgtccagctatcacttgcc---tcttgtgtattttcaattgctgtctt----ttgaaatttttagaatataaccatctttcgccatttcag
|||||||||   ||||| ||| ||||||||||||| ||||| |  ||||||||||||||||||| |||||| || |||||||||||||||||||| ||  ||| ||| |||     | || | |  |    ||||    |  |||  | || || | |   |     ||||       |   | |||  |    |||||||    ||| |   |||| ||  |  || | ||  |   ||||||
CTGGGAATAGTTGCTGACGAATTACCTGTTGACCAGTTCATCCTCCTTGGGAGGATGCTTTACATGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGTgtacatacttg---attacctttttgccatcacatcctgga-ttcccagttttcatactatttgtgtttgctgtactctacatgtttcaagggtctgtcttgcagttgcaggctttacaacctttcc-tattctgttgtttcag

upper sequence: LOC_Os05g34180.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA09G38550.1 (Glycine max), 5'ss of exon 5
CTGGGAATACAAGCTGAAGAACTACCTGTTGACCAATTCATTCCTCTTGGGAGGATGCTTTACAAGGCTCCATCTGATGGAAAATGGGGCGAACATGAACgtaaat--atttgccctctgccctctacc-tgatacatttcagccttcatacttatcgtccagctatcacttgcctcttgtgtattttcaattgctgtcttttgaaatttttagaatataaccatctttcgccatttcag
|| || ||    || |||||  |||| |||||  | ||||  ||  | ||  | || ||||||||||| || |||||||| |||||||| || |||||||||||    ||||      |  |   |        |   || |   ||  || | | |  | ||   | | |  |      |  |||    |||||   | |                                       
CTTGGTATTGTTGCCGAAGATGTACCAGTTGATAAGTTCACCCCCTTGGGTCGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACgtaagccaatttaattgatttcaagttttgcagcaagcttaattttttgta-taaccaactagggttaattcacactaatttaattaggcattgcaaacat---------------------------------------

upper sequence: LOC_Os05g34180.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA18G47770.1 (Glycine max), 5'ss of exon 5
CTGGGAATACAAGCTGAAGAACTACCTGTTGACCAATTCATTCCTCTTGGGAGGATGCTTTACAAGGCTCCATCTGATGGAAAATGGGGCGAACATGAACgtaaatatttgccctctgccctctacctgatacatttcagccttcatacttatcgtccagctatcacttgcctcttgtgtattttcaattgctgtcttttga----aatttttagaatataaccatctttcgccatttcag
 | || ||    ||||||||  |||| ||||| || ||||  ||  | ||  | || ||||||||||| || |||||||| |||||||| || ||||||||| |                  | |  | ||  |||||    || |           |||| |   |||   |  | |||||   ||| |   ||   || |    |||||   ||||  || |||   ||          
-TTGGTATTGTTGCTGAAGATGTACCAGTTGATCAGTTCACCCCATTGGGTCGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACGtgagc----------------caatttaattgatttctagtttta-----------cagcaa--gcttattttgt-tgtataaccaactagggttaattcacactaatttaaggaatgcaaacataaatc----------

upper sequence: LOC_Os05g34180.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT3G02780.1 (Arabidopsis thaliana), 5'ss of exon 5
CTGGGAATACAAGCTGAAGAACTACCTGTTGACCAATTCATTCCTCTTGGGAGGATGCTTTACAAGGCTCCATCTGATGGAAAATGGGGCGAACATGAACgtaaatatttgccctctgccctctacctgatacatttcagccttcatacttatcgtccagctatcacttgcctcttgtgtattttcaattgctgtcttttgaaatttttagaatataaccatctttcgccatttcag
|| || ||   |||||||||  |||| || ||  | |||| |||  | ||  | ||||| ||||||||||| |||||||| |||||||| || ||||||||||||||      |||    ||||   || |    | |    ||| |    |   |      | |    || |||| ||| ||  |     ||  |||||| |                                  
CTTGGTATTGTAGCTGAAGATGTACCAGTCGATGAGTTCACTCCCTTGGGACGTATGCTGTACAAGGCTCCTTCTGATGGCAAATGGGGAGAGCATGAACgtaaataccatttctcaagactct---tggt----tcccattttcttgaacagaataataaaaccttaagcttcttctgtgttggc-----cttccttttgcag---------------------------------

upper sequence: LOC_Os05g34180.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv04s0023g00600.t01 (Vitis vinifera), 5'ss of exon 5
CTGGGAATACAAGCTGAAGAACTACCTGTTGACCAATTCATTCCTCTTGGGAGGATGCTTTACAAGGCTCCATCTGATGGAAAATGGGGCGAACATGAACgtaaatatttgccctctgccctctacctgatacatttcagccttcatacttatcgtccagctatcacttgcctcttgtgtattttcaattgctgtcttttgaaatttttagaatataaccatctttcgccatttcag
|| || || |  ||||||||   ||||||||| || |||| ||| || ||  | |||||||||||||| ||||| ||||| || ||||| || |||||||||||  || ||  || ||   | |  |    | || ||| |     ||  |   |    | | | |||      |   ||  | | ||  ||| |         |                                
CTCGGCATTCCTGCTGAAGATGCACCTGTTGATCAGTTCACTCCACTGGGCCGCATGCTTTACAAGGCACCATCAGATGGCAAGTGGGGAGAGCATGAACgtaataatctgaactttgatttatttc----aaatctcaactgatttatatggtgctttgttttaactgtttcataaagttgtctgaa--gctttgagccagggtc-------------------------------

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|88516291|gb|CI443945.1|CI443945
EST:     GAGGATGCTTTACAAGGCTCCATCTGATGGAAAATGGGCCGAACATGAAC                         TGGACTACCTCCTATTCATGGTTCGTGATGTGGAGCTCAGCCCGAATCCTG
genomic: GAGGATGCTTTACAAGGCTCCATCTGATGGAAAATGGGGCGAACATGAACgtaaatattt ... gccatttcagTGGACTACCTCCTATTCATGGTTCGTGATGTGGAGCTCAGCCCGAATCCTG
EST: gi|3760979|gb|C98233.1|C98233
EST:     AGGATGCTTTACCAAGGCTCCATCTGATGGAAAATGGGGCGAACATGAAC                         TGGACTACCTCCTATTCATGGGTCCGTGATGTGGAGCTCAGCCCGAATCCT
genomic: AGGATGCTTTA-CAAGGCTCCATCTGATGGAAAATGGGGCGAACATGAACgtaaatattt ... gccatttcagTGGACTACCTCCTATTCAT-GGTTCGTGATGTGGAGCTCAGCCCGAATCCT
EST: gi|86524308|gb|CI164514.1|CI164514
EST:     GAGGATGCTTTACAAGGCTCCATCTGATGGAAAATGGGGCGAACATGAAC                         TGGACTACCTCCTATTCATGGTTCGTGATGTGGAGCTCAGCCCGAATCCTG
genomic: GAGGATGCTTTACAAGGCTCCATCTGATGGAAAATGGGGCGAACATGAACgtaaatattt ... gccatttcagTGGACTACCTCCTATTCATGGTTCGTGATGTGGAGCTCAGCCCGAATCCTG
EST: gi|87012425|gb|CI280329.1|CI280329
EST:     GAGGATGCTTTACAAGGCTCCATCTGATGGAAAATGGGGCGAACATGAAC                         TGGACTACCTCCTATTCATGGTTCGTGATGTGGAGCTCAGCCCGAATCCTG
genomic: GAGGATGCTTTACAAGGCTCCATCTGATGGAAAATGGGGCGAACATGAACgtaaatattt ... gccatttcagTGGACTACCTCCTATTCATGGTTCGTGATGTGGAGCTCAGCCCGAATCCTG
EST: gi|86596293|gb|CI268593.1|CI268593
EST:     GAGGATGCTTTACAAGGCTCCATCTGATGGAAAATGGGGCGAACATGAAC                         TGGACTACCTCCTATTCATGGTTCGTGATGTGGAGCTCAGCCCGAATCCTG
genomic: GAGGATGCTTTACAAGGCTCCATCTGATGGAAAATGGGGCGAACATGAACgtaaatattt ... gccatttcagTGGACTACCTCCTATTCATGGTTCGTGATGTGGAGCTCAGCCCGAATCCTG
EST: gi|86596305|gb|CI268605.1|CI268605
EST:     GAGGATGCTTTACAAGGCTCCATCTGATGGAAAATGGGGCGAACATGAAC                         TGGACTACCTCCTATTCATGGTTCGTGATGTGGAGCTCAGCCCGAATCCTG
genomic: GAGGATGCTTTACAAGGCTCCATCTGATGGAAAATGGGGCGAACATGAACgtaaatattt ... gccatttcagTGGACTACCTCCTATTCATGGTTCGTGATGTGGAGCTCAGCCCGAATCCTG
EST: gi|86544184|gb|CI184390.1|CI184390
EST:     GAGGATGCTTTACAAGGCTCCATCTGATGGAAAATGGGGCGAACATGAAC                         TGGGCTACCTCCTATTCATGGTTCGTGATGTGGAGCTCAGCCCGAATCCTG
genomic: GAGGATGCTTTACAAGGCTCCATCTGATGGAAAATGGGGCGAACATGAACgtaaatattt ... gccatttcagTGGACTACCTCCTATTCATGGTTCGTGATGTGGAGCTCAGCCCGAATCCTG
EST: gi|86506440|gb|CI149073.1|CI149073
EST:     GAGGATGCTTTACAAGGCTCCATCTGATGGAAAATGGGGCGAACATGAAC                         TGGACTACCTCCTATTCATGGTTCGTGATGTGGAGCTCAGCCCGAATCCTG
genomic: GAGGATGCTTTACAAGGCTCCATCTGATGGAAAATGGGGCGAACATGAACgtaaatattt ... gccatttcagTGGACTACCTCCTATTCATGGTTCGTGATGTGGAGCTCAGCCCGAATCCTG
EST: gi|88847873|gb|CI006059.1|CI006059
EST:     GAGGATGCTTTACAAGGCTCCATCTGATGGAAAATGGGGCGAACATGAAC                         TGGACTACCTCCTATTCATGGTTCGTGATGTGGAGCTCAGCCCGAATCCTG
genomic: GAGGATGCTTTACAAGGCTCCATCTGATGGAAAATGGGGCGAACATGAACgtaaatattt ... gccatttcagTGGACTACCTCCTATTCATGGTTCGTGATGTGGAGCTCAGCCCGAATCCTG
EST: gi|86855536|gb|CI267065.1|CI267065
EST:     GAGGATGCTTTACAAGGCTCCATCTGATGGAAAATGGGGCGAACATGAAC                         TGGACTACCTCCTATTCATGGTTCGTGATGTGGAGCTCAGCCCGAATCCTG
genomic: GAGGATGCTTTACAAGGCTCCATCTGATGGAAAATGGGGCGAACATGAACgtaaatattt ... gccatttcagTGGACTACCTCCTATTCATGGTTCGTGATGTGGAGCTCAGCCCGAATCCTG
EST: gi|88210823|gb|CI209099.1|CI209099
EST:     GAGGATGCTTTACAAGGCTCCATCTGATGGAAAATGGGGCGAACATGAAC                         TGGACTACCTCCTATTCATGGTTCGTGATGTGGAGCTCAGCCCGAATCCTG
genomic: GAGGATGCTTTACAAGGCTCCATCTGATGGAAAATGGGGCGAACATGAACgtaaatattt ... gccatttcagTGGACTACCTCCTATTCATGGTTCGTGATGTGGAGCTCAGCCCGAATCCTG
EST: gi|88409434|gb|CI561920.1|CI561920
EST:     ATCTGATGGAAAATGGGGCGAACATGAAC                         TGGACTACCTCCTATTCATGGTTCGTGATGTGGAGCTCAGCCCGAATCCTG
genomic: ATCTGATGGAAAATGGGGCGAACATGAACgtaaatattt ... gccatttcagTGGACTACCTCCTATTCATGGTTCGTGATGTGGAGCTCAGCCCGAATCCTG

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: 73 (upstream exon), 64 (downstream exon)
Score: 35

CTGGGAATACAAGCTGAAGAACTACCTGTTGACCAATTCATTCCTCTTGGGAGGATGCTTTACAAGGCTCCATCTGATGGAAAATGGGGCGAACATGAACgtaaatattt ... gccatttcagTGGACTACCTCCTATTCATGGTTCGTGATGTGGAGCTCAGCCCGAATCCTGAAGAAGTGGCCGACGTCAAGTACGTGAATCGTGATGAGCTGAAGGAGTT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGGGAATACAAGCTGAAGAACTACCTGTTGACCAATTCATTCCTCTTGGGAGGATGCTTTACAAGGCTCCATCTGATGGAAAATGGGGCGAACATGAACgtaaatatttgccctctgccctctacctgatacatttcagccttcatacttatcgtccagctatcacttgcctcttgtgtattttcaattgctgtcttttgaaatttttagaatataaccatctttcgccatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA