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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCTCAAGTCCCAGCTGCAGGAATTGATTCCTGAACAACAGgtttgttactttctagcacgtctaataattcacacaaagttggaaagtatatggcatccagttctttatctaccctttttgctttactgctttagcctgt...

Basic information

species Oryza sativa
transcript LOC_Os02g10070.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G064023_T04 (Zea mays), 5'ss of exon 4
GATCTCAAGTCCCAGCTGCAGGAATTGATTCCTGAACAACAGgtttgttactttctagcacgtctaataattcacacaaagttggaaagtatatggcatccagttctttatctaccctttttgctttactgctttagcctgt--------
||||| ||||||||| |||||||||||||||| ||||| |||||||| ||||   |||  | |||      | ||  ||  ||| |||||  | || |||   | | |||||| |  || ||  |   |     ||||   |        
GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAGCAGgtttgctactcg-tagaccttctg-----tgacg-aaccttgtaaagtcgagggtatctgatgccttatctgctgttctt-ttggccaatgctagcaaatagtgtcaa

upper sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G063851_T02 (Zea mays), 5'ss of exon 4
GATCTCAAGTCCCAGCTGCAGGAATTGATTCCTGAACAACAGgtttgttactttctagcacgtctaataattcacacaaagttggaaagtatatggcatccagttctt-tatctaccctttttgctttactgctttagcctgt-
||||| ||||||||| |||||||||||||||| |||||||||||||| | |    |||    |||  ||| ||    ||||| | |||||   |||     |  |  |   | || | | | | ||||    |  ||||   | 
GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAGgtttgctgcgcg-tagactatctg-taaatcttgtaaagtcgaaaagttcttggggggtatctgatgcctttatcttctgttcttttagccaatagcagcta

upper sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G063909_T02 (Zea mays), 5'ss of exon 3
GATCTCAAGTCCCAGCTGCAGGAATTGATTCCTGAACAACAGgtttgttacttt-ctagcacgtctaataat---tcacacaaagttggaaagtatatggcatccagttctttatctacccttt--ttgctttactgctttagcctgt
||||| ||||||||||||| |||| ||||||| ||||| |||||| | |||    ||  |  | ||  |  |   | |  ||  | | | ||  || |  || |||  || | |   | |  ||  |||  | | || |||       
GATCTTAAGTCCCAGCTGCGGGAACTGATTCCGGAACAGCAGgttcgctacacagctgccttgcctgctgttcttttagccagtgctagcaaacatct--caaccatgtcgtgaggaagcacttgcttgtctgaatgttttcat----

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|58693317|gb|CK082004.1|CK082004
EST:     GATCTCAAGTCCCAGCTGCAGGAATTGATTCCTGAACAACAG                         GACCGCTTAAAGAAACTTAAATCGGAGCATGGAAAGGTCCAACTTGGAAAT
genomic: GATCTCAAGTCCCAGCTGCAGGAATTGATTCCTGAACAACAGgtttgttact ... tctgttacagGACCGCTTAAAGAAACTTAAATCGGAGCATGGAAAGGTCCAACTTGGAAAT
EST: gi|58695278|gb|CK083965.1|CK083965
EST:     GATCTCAAGTCCCAGCTGCAGGAATTGATTCCTGAACAACAG                         GACCGCTTAAAGAAACTTAAATCGGAGCATGGAAAGGTCCAACTTGGAAAT
genomic: GATCTCAAGTCCCAGCTGCAGGAATTGATTCCTGAACAACAGgtttgttact ... tctgttacagGACCGCTTAAAGAAACTTAAATCGGAGCATGGAAAGGTCCAACTTGGAAAT
EST: gi|29614058|gb|CB619071.1|CB619071
EST:     GATCTCAAGTCCCAGCTGCAGGAATTGATTCCTGAACAACAG                         GACCGCTTAAAGAAACTTAAATCGGAGCATGGAAAGGTCCAACTTGGAAAT
genomic: GATCTCAAGTCCCAGCTGCAGGAATTGATTCCTGAACAACAGgtttgttact ... tctgttacagGACCGCTTAAAGAAACTTAAATCGGAGCATGGAAAGGTCCAACTTGGAAAT
EST: gi|29667252|gb|CB663527.1|CB663527
EST:     GATCTCAAGTCCCAGCTGCAGGAATTGATTCCTGAACAACAG                         GACCGCTTAAAGAAACTTAAATCGGAGCATGGAAAGGTCCAACTTGGAAAT
genomic: GATCTCAAGTCCCAGCTGCAGGAATTGATTCCTGAACAACAGgtttgttact ... tctgttacagGACCGCTTAAAGAAACTTAAATCGGAGCATGGAAAGGTCCAACTTGGAAAT
EST: gi|88573691|gb|CI665460.1|CI665460
EST:     GATCTCAAGTCCCAGCTGCAGGAATTGATTCCTGAACAACAG                         GACCGCTTAAAGAAACTTAAATCGGAGCATGGAAAGGTCCAACTTGGAAAT
genomic: GATCTCAAGTCCCAGCTGCAGGAATTGATTCCTGAACAACAGgtttgttact ... tctgttacagGACCGCTTAAAGAAACTTAAATCGGAGCATGGAAAGGTCCAACTTGGAAAT
EST: gi|58658570|gb|CK047250.1|CK047250
EST:     GATCTCAAGTCCCAGCTGCAGGAATTGATTCCTGAACAACAG                         GACCGCTTAAAGAAACTTAAATCGGAGCATGGAAAGGTCCAACTTGGAAAT
genomic: GATCTCAAGTCCCAGCTGCAGGAATTGATTCCTGAACAACAGgtttgttact ... tctgttacagGACCGCTTAAAGAAACTTAAATCGGAGCATGGAAAGGTCCAACTTGGAAAT
EST: gi|58599089|gb|CK009617.1|CK009617
EST:     GCAGGAATTGATTCCTGAACAACAG                         GACCGCTTAAAGAAACTTAAATCGGAGCATGG-GGGGTCCAACTTGGAAAT
genomic: GCAGGAATTGATTCCTGAACAACAGgtttgttact ... tctgttacagGACCGCTTAAAGAAACTTAAATCGGAGCATGGAAAGGTCCAACTTGGAAAT
EST: gi|58611144|gb|CK038856.1|CK038856
EST:     GATCTCAAGTCCCAGCTGCAGGAATTGATTCCTGAACAACAG                         GACCGCTTAAAGAAACTTAAATCGGAGCATGGAAAGGTCCAACTTGGAAAT
genomic: GATCTCAAGTCCCAGCTGCAGGAATTGATTCCTGAACAACAGgtttgttact ... tctgttacagGACCGCTTAAAGAAACTTAAATCGGAGCATGGAAAGGTCCAACTTGGAAAT
EST: gi|29614020|gb|CB619033.1|CB619033
EST:     GATCTCAAGTCCCAGCTGCAGGAATTGATTCCTGAACAACAG                         GACCGCTTAAAGAAACTTAAATCGGAGCATGGAAAGGTCCAACTTGGAAAT
genomic: GATCTCAAGTCCCAGCTGCAGGAATTGATTCCTGAACAACAGgtttgttact ... tctgttacagGACCGCTTAAAGAAACTTAAATCGGAGCATGGAAAGGTCCAACTTGGAAAT
EST: gi|88400849|gb|CI616854.1|CI616854
EST:     GATCTCAAGTCCCAGCTGCAGGAATTGATTCCTGAACAACAG                         GACCGCTTAAAGAAACTTAAATCGGAGCATGGAAAGGTCCAACTTGGAAAT
genomic: GATCTCAAGTCCCAGCTGCAGGAATTGATTCCTGAACAACAGgtttgttact ... tctgttacagGACCGCTTAAAGAAACTTAAATCGGAGCATGGAAAGGTCCAACTTGGAAAT
EST: gi|58690828|gb|CK079515.1|CK079515
EST:     GATCTCAAGTCCCAGCTGCAGGAATTGATTCCTGAACAACAG                         GACCGCTTAAAGAAACTTAAATCGGAGCATGGAAAGGTCCAACTTGGAAAT
genomic: GATCTCAAGTCCCAGCTGCAGGAATTGATTCCTGAACAACAGgtttgttact ... tctgttacagGACCGCTTAAAGAAACTTAAATCGGAGCATGGAAAGGTCCAACTTGGAAAT
EST: gi|58678175|gb|CK066862.1|CK066862
EST:     GATCTCAAGTCCCAGCTGCAGGAATTGATTCCTGAACAACAG                         GACCGCTTAAAGAAACTTAAATCGGAGCATGGAAAGGTCCAACTTGGAAAT
genomic: GATCTCAAGTCCCAGCTGCAGGAATTGATTCCTGAACAACAGgtttgttact ... tctgttacagGACCGCTTAAAGAAACTTAAATCGGAGCATGGAAAGGTCCAACTTGGAAAT

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: 51 (upstream exon), 66 (downstream exon)
Score: 78

GATCTCAAGTCCCAGCTGCAGGAATTGATTCCTGAACAACAGgtttgttact ... tctgttacagGACCGCTTAAAGAAACTTAAATCGGAGCATGGAAAGGTCCAACTTGGAAATATAACAGTCGATATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATCTCAAGTCCCAGCTGCAGGAATTGATTCCTGAACAACAGgtttgttactttctagcacgtctaataattcacacaaagttggaaagtatatggcatccagttctttatctaccctttttgctttactgctttagcctgt

- - - - - - CAGCTG
- - - - - -  AGCTGC
- - - - - - -  CTGCAG