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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGAGAAGATTCTCACGGCGTACAGAAAAGCTTCAAAGCAATGGTGCGCTACTACGAACAAGCTAGCTCAAGgtatggccattgtactgatccttaagcgaagcaccacacaatccatcactcattttaccatctcgccttgacttgcttctgttcttaccaattttacag

Basic information

species Oryza sativa
transcript LOC_Os10g28640.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g28640.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G313649_T05 (Zea mays), 5'ss of exon 8
ATGGAGAAGATTCTCACGGCGTACAGAAAAGCTTCAAAGCAATGGTGCGCTACTACGAACAAGCTAGCTCAAGgtatggcc--attgtactgatccttaagcgaagcaccacacaatccatcactcattttaccatctcgcct--tgacttgct-tctgttcttaccaattttacag
|||||||| || ||  | ||||||||||| ||||| |||||||||||| | ||   ||||||||| ||||||||||||||    |  | ||| ||| |  | | ||| | |    || | |  ||   |          |  |  ||||||  | |||  ||||  |||    ||||
ATGGAGAAAATCCTGGCTGCGTACAGAAAGGCTTCGAAGCAATGGTGCTCCACCCAGAACAAGCTGGCTCAAGgtatggcgtggtcttgctggtccctgtg-gcagcgc-atggtattcgttgctagctgcgatgatgtgagtagtgactttttgtctactctttgcaaa---acag

upper sequence: LOC_Os10g28640.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G324727_T01 (Zea mays), 5'ss of exon 10
ATGGAGAAGATTCTCACGGCGTACAGAAAAGCTTCAAAGCAATGGTGCGCTACTACGAACAAGCTAGCTCAAGgtatggccattgtactgatc-cttaagcgaagcaccacacaatccatcactcattttaccatctcgcct--tgacttgct-tctgttcttaccaattttacag
|||||||| || ||  |||| |||||||| ||||| |||||||||||| ||||   ||||||||| |||||||||||||| || ||  ||    |  | | | |    ||     | | |  ||   |  ||      |  |  ||||||  | |||  ||||  |||    ||||
ATGGAGAAAATCCTTGCGGCATACAGAAAGGCTTCGAAGCAATGGTGCTCTACCCGGAACAAGCTGGCTCAAGgtatggc-atggtcttgtcggcccatgtggaagcgcatggccttcgttgctagctgcactgatctgagtagtgactttttgtctactctttgcaaa---acag
















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|88973874|gb|CI718282.1|CI718282
EST:     CAGAAAAGCTTCAAAGCAATGGTGCGCTACTACGAACAAGCTAGCTCAAG                         TCAGGCAACGTGGCAGAAAGCGAACAATGATTGGATGAAAGTTAAGCTGGA
genomic: CAGAAAAGCTTCAAAGCAATGGTGCGCTACTACGAACAAGCTAGCTCAAGgtatggccat ... aattttacagTCAGGCAACGTGGCAGAAAGCGAACAATGATTGGATGAAAGTTAAGCTGGA
EST: gi|88675818|gb|CI729390.1|CI729390
EST:     CAGAAAAGCTTCAAAGCAATGGTGCGCTACTACGAACAAGCTAGCTCAAG                         TCAGGCAACGTGGCAGAAAGCGAACAATGATTGGATGAAAGTTAAGCTGGA
genomic: CAGAAAAGCTTCAAAGCAATGGTGCGCTACTACGAACAAGCTAGCTCAAGgtatggccat ... aattttacagTCAGGCAACGTGGCAGAAAGCGAACAATGATTGGATGAAAGTTAAGCTGGA
EST: gi|88262561|gb|CI366335.1|CI366335
EST:     CAGAAAAGCTTCAAAGCAATGGTGCGCTACTACGAACAAGCTAGCTCAAG                         TCAGGCAACGTGGCAGAAAGCGAACAATGATTGGATGAAAGTTAAGCTGGA
genomic: CAGAAAAGCTTCAAAGCAATGGTGCGCTACTACGAACAAGCTAGCTCAAGgtatggccat ... aattttacagTCAGGCAACGTGGCAGAAAGCGAACAATGATTGGATGAAAGTTAAGCTGGA
EST: gi|33663122|gb|CF294089.1|CF294089
EST:     CAGAAAAGCTTCAAAGCAATGGTGCGCTACTACGAACAAGCTAGCTCAAG                         TCAGGCAACGTGGCAGAAAGCGAACAATGATTGAATGAAAGTTAAGCTGGA
genomic: CAGAAAAGCTTCAAAGCAATGGTGCGCTACTACGAACAAGCTAGCTCAAGgtatggccat ... aattttacagTCAGGCAACGTGGCAGAAAGCGAACAATGATTGGATGAAAGTTAAGCTGGA
EST: gi|88905485|gb|CI712784.1|CI712784
EST:     CAGAAAAGCTTCAAAGCAATGGTGCGCTACTACGAACAAGCTAGCTCAAG                         TCAGGCAANGTGGCAGAAAGCGAACAATGATTGGATGAAAGTTACGCTGGA
genomic: CAGAAAAGCTTCAAAGCAATGGTGCGCTACTACGAACAAGCTAGCTCAAGgtatggccat ... aattttacagTCAGGCAACGTGGCAGAAAGCGAACAATGATTGGATGAAAGTTAAGCTGGA
EST: gi|86530471|gb|CI170677.1|CI170677
EST:     CAGAAAAGCTTCAAAGCAATGGTGCGCTACTACGAACAAGCTAGCTCAAG                         TCAGGCAACGTGGCAGAAAGCGAACAATGATTGGATGAAAGTTAAGCTGGA
genomic: CAGAAAAGCTTCAAAGCAATGGTGCGCTACTACGAACAAGCTAGCTCAAGgtatggccat ... aattttacagTCAGGCAACGTGGCAGAAAGCGAACAATGATTGGATGAAAGTTAAGCTGGA
EST: gi|88980055|gb|CI026345.1|CI026345
EST:     CAGAAAAGCTTCAAAGCAATGGTGCGCTACTACGAACAAGCTAGCTCAAG                         TCAGGCAACGTGGCAGAAAGCGAACAATGATTGGATGAAAGTTAAGCTGGA
genomic: CAGAAAAGCTTCAAAGCAATGGTGCGCTACTACGAACAAGCTAGCTCAAGgtatggccat ... aattttacagTCAGGCAACGTGGCAGAAAGCGAACAATGATTGGATGAAAGTTAAGCTGGA
EST: gi|88272277|gb|CI386731.1|CI386731
EST:     CAGAAAAGCTTCAAAGCAATGGTGCGCTACTACGAACAAGCTAGCTCAAG                         TCAGGCAACGTGGCAGAAAGCGAACAATGATTGGATGAAAGTTAAGCTGGA
genomic: CAGAAAAGCTTCAAAGCAATGGTGCGCTACTACGAACAAGCTAGCTCAAGgtatggccat ... aattttacagTCAGGCAACGTGGCAGAAAGCGAACAATGATTGGATGAAAGTTAAGCTGGA
EST: gi|88675599|gb|CI729712.1|CI729712
EST:     CAGAAAAGCTTCAAAGCAATGGTGCGCTACTACGAACAAGCTAGCTCCAG                         TCAGGCAACGTGGCAGAAAGCGAACAATGATTGGATGAAAGTTAAGCTGGA
genomic: CAGAAAAGCTTCAAAGCAATGGTGCGCTACTACGAACAAGCTAGCTCAAGgtatggccat ... aattttacagTCAGGCAACGTGGCAGAAAGCGAACAATGATTGGATGAAAGTTAAGCTGGA
EST: gi|88833965|gb|CI077446.1|CI077446
EST:     CAGAAAAGCTTCAAAGCAATGGTGCGCTACTACGAACAAGCTAGCTCAAG                         TCAGGCAACGTGGCAGAAAGCGAACAA--ATTGGATGAAAGTTAAGCTGGA
genomic: CAGAAAAGCTTCAAAGCAATGGTGCGCTACTACGAACAAGCTAGCTCAAGgtatggccat ... aattttacagTCAGGCAACGTGGCAGAAAGCGAACAATGATTGGATGAAAGTTAAGCTGGA

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: 62 (upstream exon), 72 (downstream exon)
Score: 14

ATGGAGAAGATTCTCACGGCGTACAGAAAAGCTTCAAAGCAATGGTGCGCTACTACGAACAAGCTAGCTCAAGgtatggccat ... aattttacagTCAGGCAACGTGGCAGAAAGCGAACAATGATTGGATGAAAGTTAAGCTGGAACTTGCTGGACAATACAGTTGCTCGACCAGATGATTCAACACTTTACAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGAGAAGATTCTCACGGCGTACAGAAAAGCTTCAAAGCAATGGTGCGCTACTACGAACAAGCTAGCTCAAGgtatggccattgtactgatccttaagcgaagcaccacacaatccatcactcattttaccatctcgccttgacttgcttctgttcttaccaattttacag

- - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA