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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTCACGCCTTACGACCCCTGAAGGAGACTGCCCATATGTTAGCGCACAAAGAGGACTGGCCCCCACTGTATGATGTCAACGTGCTGAACAACAATAAGgttcgttcttcttgctgagaaaaagccatgaactcctcaccatcatcctctgttaaggaaggctagtttcaggagaatctagagctgaacccatttgcct...

Basic information

species Oryza sativa
transcript LOC_Os06g06820.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g06820.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G075488_T02 (Zea mays), 5'ss of exon 9
GATTCACGCCTTACGACCCCTGAAGGAGACTGCCCATATGTTAGCGCACAAAGAGGACTGGCCCCCACTGTATGATGTCAACGTGCTGAACAACAATAAGgttcgttcttcttgctgagaaaaagccatgaactcctcaccatcatcctctgttaaggaaggctagtttcaggagaatctagagctgaacccatttgcct----
 || |  ||  |||||  ||| |||||| |||||  | |||||||  | || || |||||||| || || |||||||||| |||| |||||||||||||||| |||| ||| |     |      |||| |  | |  ||  | |      |||  ||||    | ||||   ||    |     |   || |      |    
CATCCCTGCTCTACGAGACCTAAAGGAGGCTGCCTGTTTGTTAGCTGAGAAGGAAGACTGGCCTCCGCTCTATGATGTCAGCGTGTTGAACAACAATAAGgtgcgttgttcata--agggtcgtaccataa--ttcatactgtaagggctagtttgggaaccacattttcctaagggatttttatttttccaaggaaaattagt
















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|86595030|gb|CI260269.1|CI260269
EST:     AAGAGGACTGGCCCCCACTGTATGATGTCAACGTGCTGAACAACAATAAG                         GTCCCGGTGGCTGCCGCCGTCTACTACGAGGACATGTACGTCAACTTCAAC
genomic: AAGAGGACTGGCCCCCACTGTATGATGTCAACGTGCTGAACAACAATAAGgttcgttctt ... aattctgcagGTCCCGGTGGCTGCCGCCGTCTACTACGAGGACATGTACGTCAACTTCAAC
EST: gi|87018040|gb|CI275854.1|CI275854
EST:     AAGAGGACTGGCCCCCACTGTATGATGTCAACGTGCTGAACAACAATAAG                         GTCCCGGTGGCTGCCGCCGTCTACTACGAGGACATGTACGTCAACTTCAAC
genomic: AAGAGGACTGGCCCCCACTGTATGATGTCAACGTGCTGAACAACAATAAGgttcgttctt ... aattctgcagGTCCCGGTGGCTGCCGCCGTCTACTACGAGGACATGTACGTCAACTTCAAC
EST: gi|86497289|gb|CI139922.1|CI139922
EST:     AAGAGGACTGGCCCCCACTGTATGATGTCAACGTGCTGAACAACCATAAG                         GTCCCGGTGGCTGCCGCCGTCTACTACGAGGACATGTACGTCAACTTCAAC
genomic: AAGAGGACTGGCCCCCACTGTATGATGTCAACGTGCTGAACAACAATAAGgttcgttctt ... aattctgcagGTCCCGGTGGCTGCCGCCGTCTACTACGAGGACATGTACGTCAACTTCAAC
EST: gi|88353743|gb|CI634534.1|CI634534
EST:     AAGAGGACTGGCCCCCACTGTATGATGTCAACGTGCTGAACAACAATAAG                         GTCCCGGTGGCTGCCGCCGTCTACTACGAGGACATGTACGTCAACTTCAAC
genomic: AAGAGGACTGGCCCCCACTGTATGATGTCAACGTGCTGAACAACAATAAGgttcgttctt ... aattctgcagGTCCCGGTGGCTGCCGCCGTCTACTACGAGGACATGTACGTCAACTTCAAC
EST: gi|86858904|gb|CI275118.1|CI275118
EST:     AAGAGGACTGGCCCCCACTGTATGATGTCAACGTGCTGAACAACAATAAG                         GTCCCGGTGGCTGCCGCCGTCTACTACGAGGACATGTACGTCAACTTCAAC
genomic: AAGAGGACTGGCCCCCACTGTATGATGTCAACGTGCTGAACAACAATAAGgttcgttctt ... aattctgcagGTCCCGGTGGCTGCCGCCGTCTACTACGAGGACATGTACGTCAACTTCAAC
EST: gi|87029615|gb|CI257410.1|CI257410
EST:     AAGAGGACTG-CCCCCACTGTATGATGTCAACGTGCTGAACAACAATAAG                         GTCCCGGTGGCTGCCGCCGTCTACTACGAGGACATGTACGTCAACTTCAAC
genomic: AAGAGGACTGGCCCCCACTGTATGATGTCAACGTGCTGAACAACAATAAGgttcgttctt ... aattctgcagGTCCCGGTGGCTGCCGCCGTCTACTACGAGGACATGTACGTCAACTTCAAC
EST: gi|112786319|gb|EE590521.1|EE590521
EST:     AAGAGGACTGGCCCCCACTGTATGATGTCAACGTGCTGAACAACAATAAG                         GTCCCGGTGGCTGCCGCCGTCTACTACGAGGACATGTACGTCAACTTCAAC
genomic: AAGAGGACTGGCCCCCACTGTATGATGTCAACGTGCTGAACAACAATAAGgttcgttctt ... aattctgcagGTCCCGGTGGCTGCCGCCGTCTACTACGAGGACATGTACGTCAACTTCAAC
EST: gi|88344031|gb|CI638766.1|CI638766
EST:     AAGAGGACTGGCCCCCACTGTATGATGTCAACGTGCTGAACAACAATAAG                         GTCCCGGTGGCTGCCGCCGTCTACTACGAGGACATGTACGTCAACTTCAAC
genomic: AAGAGGACTGGCCCCCACTGTATGATGTCAACGTGCTGAACAACAATAAGgttcgttctt ... aattctgcagGTCCCGGTGGCTGCCGCCGTCTACTACGAGGACATGTACGTCAACTTCAAC
EST: gi|88306063|gb|CI635067.1|CI635067
EST:     AAGAGGACTGGCCCCCACTGTATGATGTCAACGTGCTGAACAACAATAAG                         GTCCCGGTGGCTGCCGCCGTCTACTACGAGGACATGTACGTCAACTTCAAC
genomic: AAGAGGACTGGCCCCCACTGTATGATGTCAACGTGCTGAACAACAATAAGgttcgttctt ... aattctgcagGTCCCGGTGGCTGCCGCCGTCTACTACGAGGACATGTACGTCAACTTCAAC
EST: gi|88569436|gb|CI660611.1|CI660611
EST:     AAGAGGACTGGCCCCCACTGTATGATGTCAACGTGCTGAACAACAATAAG                         GTCCCGGTGGCTGCCGCCGTCTACTACGAGGACATGTACGTCAACTTCAAC
genomic: AAGAGGACTGGCCCCCACTGTATGATGTCAACGTGCTGAACAACAATAAGgttcgttctt ... aattctgcagGTCCCGGTGGCTGCCGCCGTCTACTACGAGGACATGTACGTCAACTTCAAC
EST: gi|88573704|gb|CI665473.1|CI665473
EST:     AAGAGGACTGGCCCCCACTGTATGATGTCAACGTGCTGAACAACAATAAG                         GTCCCGGTGGCTGCCGCCGTCTACTACGAGGACATGTACGTCAACTTCAAC
genomic: AAGAGGACTGGCCCCCACTGTATGATGTCAACGTGCTGAACAACAATAAGgttcgttctt ... aattctgcagGTCCCGGTGGCTGCCGCCGTCTACTACGAGGACATGTACGTCAACTTCAAC
EST: gi|86863602|gb|CI345279.1|CI345279
EST:     CAACGTGCTGAACAACAATAAG                         GTCCCGGTGGCTGCCGCCGTCTACTACGAGGACATGTACGTCAACTTCAAC
genomic: CAACGTGCTGAACAACAATAAGgttcgttctt ... aattctgcagGTCCCGGTGGCTGCCGCCGTCTACTACGAGGACATGTACGTCAACTTCAAC

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: 75 (upstream exon), 74 (downstream exon)
Score: 21

GATTCACGCCTTACGACCCCTGAAGGAGACTGCCCATATGTTAGCGCACAAAGAGGACTGGCCCCCACTGTATGATGTCAACGTGCTGAACAACAATAAGgttcgttctt ... aattctgcagGTCCCGGTGGCTGCCGCCGTCTACTACGAGGACATGTACGTCAACTTCAACATCGCCAAGGAGACGGCCTCCCAGATCGCGGGCATCCGGCTCTGGATTA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTCACGCCTTACGACCCCTGAAGGAGACTGCCCATATGTTAGCGCACAAAGAGGACTGGCCCCCACTGTATGATGTCAACGTGCTGAACAACAATAAGgttcgttcttcttgctgagaaaaagccatgaactcctcaccatcatcctctgttaaggaaggctagtttcaggagaatctagagctgaacccatttgcct

- - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcacc