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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCAGATCGGCGCCATGTCCAAGGCCAGGGTCTACACCGACGTCAACGTGCTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtgagtgcctcccactcctacctcgctacctcgctcttgcttccaccctgtgttgtcgcctctgcatctgcgtgggtcagtttagattcagtgtcggatg...

Basic information

species Oryza sativa
transcript LOC_Os07g02350.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g02350.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM5G845755_T01 (Zea mays), 5'ss of exon 1
CCCAGATCGGCGCCATGTCCAAGGCCAGGGTCTACACCGACGTCAACGTGCTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtgagtg-cctcccactcctacctcgctacctcgctcttgct--tccaccctgtgttgtcgcctctgcatctgcgtgggtcagtttagattcagtgtcggatg
    |  ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||| |||||||||| ||||  |||   | |   |||| || || | | || ||     | | |  | |  ||||  | || || ||    |||| ||| |   || | ||   ||
GATCGGCCGGCGCCATGTCCAAGGCCAGGGTCTACACCGACGTCAACGTGCTGCGCCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTTCAATGGGGgtcagtgatctcttcccctcccctcccttccgctccctcgccagctcgcgcgctctcctcgca-cggcctcggccattgtcaattttg--ccattatcatttg

upper sequence: LOC_Os07g02350.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G143602_T03 (Zea mays), 5'ss of exon 1
CCCAGATCGGCGCCATGTCCAAGGCCAGGGTCTACACCGACGTCAACGTGCTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtgagtgcctcccactcctacctcgctacctcgctctt-gcttccaccctgtgttgtcgcctctgcatctgcg-tgggtcagtttagattcagtgtcggatg
    | ||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||| |||||||| |||||||| |||||||||||||||| |  | | |   |    ||  | ||  ||  ||  |  |   |  |   |    ||  | || || |    ||||         ||| | |   
GATCGGTCGGCGCCATGTCCAAGGCCAGGGTCTACGCCGACGTCAACGTGCTGCGCCCCAAGGAGTACTGGGATTACGAGGCGCTCACCGTTCAATGGGGgtgagtgc-tatctcgcgcgctctcctctcgcgtcctccgcccctcctgcgcataaccctacctcaagcttcggtttcgcagtgctacgagcgtgcctgta-

upper sequence: LOC_Os07g02350.1 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 2
CCCAGATCGGCGCCATGTCCAAGGCCAGGGTCTACACCGACGTCAACGTGCTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtgagtgcctcccactcctacctcgctacctcgctcttgcttccaccctgtgttgtcgcctctgcatctgcgtgggtcagtttagattcagtgtcggatg---
  | |   || |  |||||||||||| |||| ||||| || || || || |  || || || || || |||||||||||||||||||||||||||||||||| ||| ||             || || |||   |  | | |  |  |     |    |      |||||   ||  | ||   || |||  | |        
GACGGCCAGGTGTTATGTCCAAGGCCCGGGTTTACACAGATGTGAATGTCCAACGTCCGAAAGATTATTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtaagttccatggctattcgattcactccctttatgcttccttaattccaatgttctacagagatatctg---ggcacggtgaggaatcatcgactagaaacc

upper sequence: LOC_Os07g02350.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ28543 (Selaginella moellendorffii), 5'ss of exon 1
CCCAGATCGGCGCCATGTCCAAGGCCAGGGTCTACACCGACGTCAACGTGCTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtgagtgcctcccactcctacctcgct--acctcgctct-tgcttccaccctgtgttgtcgcctctgcatctgcgtgggtcagtttagattcagtgtcggatg
       ||||||||||||||||||| || | ||| |||| || |||||||||||||| ||||||||||||||||||||| | ||| | ||  | ||||||||||    |        |   | | |  | || | ||| | ||||     || || |  |                                          
GTGGCCCCGGCGCCATGTCCAAGGCCCGGATATACGCCGATGTGAACGTGCTGCGCCCAAAGGAGTACTGGGACTACGAGTCTCTCTCGGTGGAGTGGGGgtgaggcttttgtttcgtttttttgttggatctagatctcttcttcttgtttgggtggcag------------------------------------------

upper sequence: LOC_Os07g02350.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ20478 (Selaginella moellendorffii), 5'ss of exon 1
CCCAGATCGGCGCCATGTCCAAGGCCAGGGTCTACACCGACGTCAACGTGCTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtgagtgcctcccactcctacctcgct--acctcgctct-tgcttccaccctgtgttgtcgcctctgcatctgcgtgggtcagtttagattcagtgtcggatg
       ||||||||||||||||||| || | ||| |||| || |||||||||||||| ||||||||||||||||||||| | ||| | ||  | ||||||||||    |        |   | | |  | || | ||| | ||||  |  || || |  |                                          
GTGGCCCCGGCGCCATGTCCAAGGCCCGGATATACGCCGATGTGAACGTGCTGCGCCCAAAGGAGTACTGGGACTACGAGTCTCTCTCGGTGGAGTGGGGgtgaggcttttgtttcgtttttttgttggatctagatctcttcttcttctttgggtggcag------------------------------------------

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|29661177|gb|CB657452.1|CB657452
EST:     CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGG                         TGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtgagtgcct ... ctttgagcagTGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
EST: gi|58591038|gb|CF989346.1|CF989346
EST:     CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGG                         TGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtgagtgcct ... ctttgagcagTGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
EST: gi|117220732|gb|CT845509.1|CT845509
EST:     CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGG                         TGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtgagtgcct ... ctttgagcagTGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
EST: gi|58658866|gb|CK047546.1|CK047546
EST:     CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGG                         TGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtgagtgcct ... ctttgagcagTGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
EST: gi|88362961|gb|CI614317.1|CI614317
EST:     TGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATTGGGG                         TGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACA
genomic: TGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAAT-GGGGgtgagtgcct ... ctttgagcagTGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACA
EST: gi|58659986|gb|CK048666.1|CK048666
EST:     CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGG                         TGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtgagtgcct ... ctttgagcagTGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
EST: gi|66917302|gb|CX104150.1|CX104150
EST:     CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGG                         TGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtgagtgcct ... ctttgagcagTGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
EST: gi|2317607|gb|C22661.1|C22661
EST:     CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGG                         TGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtgagtgcct ... ctttgagcagTGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
EST: gi|58593999|gb|CF992307.1|CF992307
EST:     CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGG                         TGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtgagtgcct ... ctttgagcagTGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
EST: gi|29663346|gb|CB659621.1|CB659621
EST:     CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGG                         TGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtgagtgcct ... ctttgagcagTGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
EST: gi|2317323|gb|C22377.1|C22377
EST:     CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGG                         TGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtgagtgcct ... ctttgagcagTGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
EST: gi|87008795|gb|CI302950.1|CI302950
EST:     CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGG                         TGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtgagtgcct ... ctttgagcagTGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
EST: gi|29657465|gb|CB653740.1|CB653740
EST:     CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGG                         TGAGCAGGATGATTATGAAGTTGTCCCGAAAGTTGGGAGAGGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtgagtgcct ... ctttgagcagTGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
EST: gi|88725222|gb|CI748481.1|CI748481
EST:     CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGAG                         TGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtgagtgcct ... ctttgagcagTGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
EST: gi|88760570|gb|CI770126.1|CI770126
EST:     CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGG                         TGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtgagtgcct ... ctttgagcagTGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
EST: gi|58600654|gb|CK011182.1|CK011182
EST:     CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGG                         TGAGCAGGATGATTATGAAGTTGTCACGAAAGTTGGGAGAGGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtgagtgcct ... ctttgagcagTGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
EST: gi|88447529|gb|CI584644.1|CI584644
EST:     CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGG                         TGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtgagtgcct ... ctttgagcagTGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
EST: gi|29662230|gb|CB658505.1|CB658505
EST:     CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGG                         TGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtgagtgcct ... ctttgagcagTGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
EST: gi|58653242|gb|CK041922.1|CK041922
EST:     TGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAGGTGGGG                         TGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACA
genomic: TGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCA-ATGGGGgtgagtgcct ... ctttgagcagTGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACA
EST: gi|11442779|gb|BF430681.1|BF430681
EST:     CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGG                         TGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtgagtgcct ... ctttgagcagTGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
EST: gi|58681564|gb|CK070251.1|CK070251
EST:     CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGG                         TGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtgagtgcct ... ctttgagcagTGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
EST: gi|88357707|gb|CI624958.1|CI624958
EST:     CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGG                         TGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtgagtgcct ... ctttgagcagTGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
EST: gi|5607464|gb|AU076249.1|AU076249
EST:     CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGG                         TGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtgagtgcct ... ctttgagcagTGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
EST: gi|88445038|gb|CI589516.1|CI589516
EST:     CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGG                         TGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtgagtgcct ... ctttgagcagTGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG
EST: gi|218485894|gb|FG960234.1|FG960234
EST:     CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAGTGGGG                         TGAGCAGGATGATTATGAAGTTGTCAGGAAAGTGGGGAGAGGAAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtgagtgcct ... ctttgagcagTGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAG

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: 74 (upstream exon), 69 (downstream exon)
Score: 53

CCCAGATCGGCGCCATGTCCAAGGCCAGGGTCTACACCGACGTCAACGTGCTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtgagtgcct ... ctttgagcagTGAGCAGGATGATTATGAAGTTGTCAGGAAAGTTGGGAGAGGAAAATACAGCGAGGTCTTTGAGGGTATTAATGTCAACAACAATGAAAAATGCATTATC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCAGATCGGCGCCATGTCCAAGGCCAGGGTCTACACCGACGTCAACGTGCTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtgagtgcctcccactcctacctcgctacctcgctcttgcttccaccctgtgttgtcgcctctgcatctgcgtgggtcagtttagattcagtgtcggatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcctccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcgctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaccct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcgtggg