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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCAGTAGGCAAAGAAATGCTCATGCCCAAAGATCCCAATGCTAATATTATAATGgtgagcttaaattgcatggtgaattgatccatctcaaaaaatctacaccacaacaaattttaaccttgtgcggttacttgcag

Basic information

species Oryza sativa
transcript LOC_Os06g01850.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g01850.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G168143_T02 (Zea mays), 5'ss of exon 3
--------GTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCAGTAGGCAAAGAAATGCTCATGCCCAAAGATCCCAATGCTAATATTATAATGgtgagctt-aaattgcatggtgaattgatccatctcaaaaaatctacacc-acaacaaattttaaccttg--tgcggtta--cttgcag-----------
        ||||  |  |||| |||  | | ||| ||||||| |||||||| |||||||||||||| ||||||||||| || || ||||  ||||||||||| ||||| | |  ||    |  | |     | |||   |  |  ||||  || |||       |  ||   | | || |  |||||             
TAATGCAGGTGATCTTCAGCCAGGTGATAACGTCCAGATAACAGGACCAGTCGGCAAAGAAATGCTGATGCCCAAAGACCCAAACGCTACCATTATAATGgtaagcttcagagagccgactccagtccagtacctccttacgtacacactgacgacagccagagattttacttacagtcatgcttgccaattgcttgcag

upper sequence: LOC_Os06g01850.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G168143_T01 (Zea mays), 5'ss of exon 4
GTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCAGTAGGCAAAGAAATGCTCATGCCCAAAGATCCCAATGCTAATATTATAATGgtgagctt-aaattgcatggtgaattgatccatctcaaaaaatctacacc-acaacaaattttaaccttg--tgcggtta--cttgcag-----------
||||  |  |||| |||  | | ||| ||||||| |||||||| |||||||||||||| ||||||||||| || || ||||  ||||||||||| ||||| | |  ||    |  | |     | |||   |  |  ||||  || |||       |  ||   | | || |  |||||             
GTGATCTTCAGCCAGGTGATAACGTCCAGATAACAGGACCAGTCGGCAAAGAAATGCTGATGCCCAAAGACCCAAACGCTACCATTATAATGgtaagcttcagagagccgactccagtccagtacctccttacgtacacactgacgacagccagagattttacttacagtcatgcttgccaattgcttgcag

upper sequence: LOC_Os06g01850.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv18s0001g14450.t01 (Vitis vinifera), 5'ss of exon 5
GTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCAGTAGGCAAAGAAATGCTCATGCCCAAAGATCCCAATGCTAATATTATAATGgtgagcttaaatt--gcatggtgaattgatccatctcaaaa-aatctac-accacaacaaattttaaccttgtgcggtta-cttgcag
||||||||||||||||  |||||||||| || || ||||| || || ||||||||||| ||||| |||||||| ||||| | | | ||||||||||| |    ||  | ||    ||        | | |    ||||  |     |    |      |      ||  | | |||||||
GTGACTTGAAGCCTGGGGCTGATGTCAAAATCACAGGACCTGTTGGGAAAGAAATGCTTATGCCAAAAGATCCAAATGCCACTGTCATAATGgtgagttctgcttcagtatcaccaaccatcttctgttatgtcaatcagctgtttctttgagaaagtattgaaagcaatcatcttgcag

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|29657697|gb|CB653972.1|CB653972
EST:     TAGGCAAAGAAATGCTCATGCCCAAAGATCCCAATGCTAATATTATAATG                         CTTGCGACCGGTACTGGTATTGCCCCGTTCCGCTCATTCTTGTGGAAAATG
genomic: TAGGCAAAGAAATGCTCATGCCCAAAGATCCCAATGCTAATATTATAATGgtgagcttaa ... ttacttgcagCTTGCGACCGGTACTGGTATTGCCCCGTTCCGCTCATTCTTGTGGAAAATG
EST: gi|86521026|gb|CI161232.1|CI161232
EST:     TAGGCAAAG-AATGCTCATGCCCGAAGATCCCAATGCTAATATTATAATG                         CTTGCGACCGGTACTGGTATTGCCCCGTTCCGCTTATTCTTGTGGAAAATG
genomic: TAGGCAAAGAAATGCTCATGCCCAAAGATCCCAATGCTAATATTATAATGgtgagcttaa ... ttacttgcagCTTGCGACCGGTACTGGTATTGCCCCGTTCCGCTCATTCTTGTGGAAAATG
EST: gi|29659028|gb|CB655303.1|CB655303
EST:     TAGGCAAAGAAATGCTCATGCCCAAAGATCCCAATGCTAATATTATAATG                         CTTGCGACCGGTACTGGTATTGCCCCGTTCCGCTCATTCTTGTGGAAAATG
genomic: TAGGCAAAGAAATGCTCATGCCCAAAGATCCCAATGCTAATATTATAATGgtgagcttaa ... ttacttgcagCTTGCGACCGGTACTGGTATTGCCCCGTTCCGCTCATTCTTGTGGAAAATG
EST: gi|38475687|gb|CF959820.1|CF959820
EST:     GCTAATATTAT-ATG                         CTTGCGACCGGTACTGGTATTGCCCCGTTCCGCTCATTCTTGTGGAAAATG
genomic: GCTAATATTATAATGgtgagcttaa ... ttacttgcagCTTGCGACCGGTACTGGTATTGCCCCGTTCCGCTCATTCTTGTGGAAAATG
EST: gi|58695210|gb|CK083897.1|CK083897
EST:     TAGGCAAAGAAATGCTCATGCCCAAAGATCCCAATGCTAATATTATAATG                         CTTGCGACCGGTACTGGTATTGCCCCGTTCCGCTCATTCTTGTGGAAAATG
genomic: TAGGCAAAGAAATGCTCATGCCCAAAGATCCCAATGCTAATATTATAATGgtgagcttaa ... ttacttgcagCTTGCGACCGGTACTGGTATTGCCCCGTTCCGCTCATTCTTGTGGAAAATG
EST: gi|29683077|gb|CB679352.1|CB679352
EST:     TAGGCAAAGAAATGCTCATGCCCAAAGATCCCAATGCTAATATTATAATG                         CTTGCGACCGGTACTGGTATTGCCCCGTTCCGCTCATTCTTGTGGAAAATG
genomic: TAGGCAAAGAAATGCTCATGCCCAAAGATCCCAATGCTAATATTATAATGgtgagcttaa ... ttacttgcagCTTGCGACCGGTACTGGTATTGCCCCGTTCCGCTCATTCTTGTGGAAAATG
EST: gi|87025972|gb|CI257130.1|CI257130
EST:     GGCAAAGAAATGCTCATGCCCAAAGATCCCAATGCTAATATTATAATG                         CTTGCGACCGGTACTGGTATTGCCCCGTTCCGCTCATTCTTGTGGAAAATG
genomic: GGCAAAGAAATGCTCATGCCCAAAGATCCCAATGCTAATATTATAATGgtgagcttaa ... ttacttgcagCTTGCGACCGGTACTGGTATTGCCCCGTTCCGCTCATTCTTGTGGAAAATG
EST: gi|29683657|gb|CB679932.1|CB679932
EST:     TAGGCAAAGAAATGCTCATGCCCAAAGATCCCAATGCTAATATTATAATG                         CTTGCGACCGGTACTGGTATTGCCCCGTTCCGCTCATTCTTGTGGAAAATG
genomic: TAGGCAAAGAAATGCTCATGCCCAAAGATCCCAATGCTAATATTATAATGgtgagcttaa ... ttacttgcagCTTGCGACCGGTACTGGTATTGCCCCGTTCCGCTCATTCTTGTGGAAAATG
EST: gi|33798466|gb|CF325091.1|CF325091
EST:     TAGGCAAAGAAATGCTCATGCCCAAAGATCCCAATGCTAATATTATAATG                         CTTGCGACCGGTACTGGTATTGCCCCGTTCCGCTCATTCTTGTGGAAAATG
genomic: TAGGCAAAGAAATGCTCATGCCCAAAGATCCCAATGCTAATATTATAATGgtgagcttaa ... ttacttgcagCTTGCGACCGGTACTGGTATTGCCCCGTTCCGCTCATTCTTGTGGAAAATG
EST: gi|29685686|gb|CB681961.1|CB681961
EST:     TAGGCAAAGAAATGCTCATGCCCAAAGATCCCAATGCTAATATTATAATG                         CTTGCGACCGGTACTGGTATTGCCCCGTTCCGCTCATTCTTGTGGAAAATG
genomic: TAGGCAAAGAAATGCTCATGCCCAAAGATCCCAATGCTAATATTATAATGgtgagcttaa ... ttacttgcagCTTGCGACCGGTACTGGTATTGCCCCGTTCCGCTCATTCTTGTGGAAAATG
EST: gi|29685685|gb|CB681960.1|CB681960
EST:     TAGGCAAAGAAATGCTCATGCCCAAAGATCCCAATGCTAATATTATAATG                         CTTGCGACCGGTACTGGTATTGCCCCGTTCCGCTCATTCTTGTGGAAAATG
genomic: TAGGCAAAGAAATGCTCATGCCCAAAGATCCCAATGCTAATATTATAATGgtgagcttaa ... ttacttgcagCTTGCGACCGGTACTGGTATTGCCCCGTTCCGCTCATTCTTGTGGAAAATG
EST: gi|87026011|gb|CI257169.1|CI257169
EST:     AGGCAAAGAAATGCTCATGCCCAGAGATCCCAATGCTAATATTATAATG                         CTTGCGACCGGTACTGGTATTGCCCCGTTCCGCTCATTCTTGTGGAAAATG
genomic: AGGCAAAGAAATGCTCATGCCCAAAGATCCCAATGCTAATATTATAATGgtgagcttaa ... ttacttgcagCTTGCGACCGGTACTGGTATTGCCCCGTTCCGCTCATTCTTGTGGAAAATG

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), 74 (downstream exon)
Score: 155

GTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCAGTAGGCAAAGAAATGCTCATGCCCAAAGATCCCAATGCTAATATTATAATGgtgagcttaa ... ttacttgcagCTTGCGACCGGTACTGGTATTGCCCCGTTCCGCTCATTCTTGTGGAAAATGTTTTTTGAGAAGTATGATGACTACAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCAGTAGGCAAAGAAATGCTCATGCCCAAAGATCCCAATGCTAATATTATAATGgtgagcttaaattgcatggtgaattgatccatctcaaaaaatctacaccacaacaaattttaaccttgtgcggttacttgcag

- - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - AAGAAA