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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGGGCAAACTTATGCACATTGAAGTTCAAAAGAGAGGAGGAAAAGAGCACGAGGACTTGCTAAATGCTGATGATGACAACCACTTCCAGGAAAAGATGgtctgtttcttatttagttgcaaacatatccttgaaactctaaacaacatttcctttaaaatcatttttaatgcag

Basic information

species Oryza sativa
transcript LOC_Os02g44510.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g44510.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM5G846198_T01 (Zea mays), 5'ss of exon 1
GAGGGGCAAACTTATGCACATTGAAGTTCAAAAGAGAGGAGGAAAAGAGCACGAGGACTTGCTAAATGCTGATGATGACAACCACTTCCAGGAAAAGATGgtctgtttcttatttagttgcaaacatatccttgaaactctaaacaacatttcctttaaaatcattttt--aatgcag
||| |||||||| ||||| |||||||| |||||||    ||| || ||||| |||||||||||||||||||  |||||| |||||||||||||||||| |||||||||||| ||||||| |    ||| | |||||| |||| ||| || ||  ||||   |  |||||  |||||||
GAGAGGCAAACTAATGCATATTGAAGTGCAAAAGAAGAAAGGCAAGGAGCATGAGGACTTGCTAAATGCTGCCGATGACTACCACTTCCAGGAAAAGACGgtctgtttcttgtttagttactgggatacctttgaaattctacacatcacttattttacctttttttttgaaatgcag
















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|88591648|gb|CI709696.1|CI709696
EST:     ACGAGGACTTGCTAAATGCTGATGATGACAACCACTTCCAGGAAAAGATG                         GATAACAAAGGCTGGAATAACAACCTTTTGAAGTGGGCTTCTAGTTTCATT
genomic: ACGAGGACTTGCTAAATGCTGATGATGACAACCACTTCCAGGAAAAGATGgtctgtttct ... tttaatgcagGATAACAAAGGCTGGAATAACAACCTTTTGAAGTGGGCTTCTAGTTTCATT
EST: gi|88337938|gb|CI676916.1|CI676916
EST:     ACGAGGACTTGCTAAATGCTGATGATGACAACCACTTCCAGGAAAAGATG                         GATAACAAAGGCTGGAATAACAACCTTTTGAAGTGGGCTTCTAGTTTCATT
genomic: ACGAGGACTTGCTAAATGCTGATGATGACAACCACTTCCAGGAAAAGATGgtctgtttct ... tttaatgcagGATAACAAAGGCTGGAATAACAACCTTTTGAAGTGGGCTTCTAGTTTCATT
EST: gi|88422253|gb|CI689057.1|CI689057
EST:     ACGAGGACTTGCTAAATGCTGATGATGACAACCACTTCCAGGAAAAGATG                         GATAACAAAGGCTGGAATAACAACCTTTTGAAGTGGGCTTCTAGTTTCATT
genomic: ACGAGGACTTGCTAAATGCTGATGATGACAACCACTTCCAGGAAAAGATGgtctgtttct ... tttaatgcagGATAACAAAGGCTGGAATAACAACCTTTTGAAGTGGGCTTCTAGTTTCATT
EST: gi|58654435|gb|CK043115.1|CK043115
EST:     ACGAGGACTTGCTAAATGCTGATGATGACAACCACTTCCAGGAAAAGATG                         GATAACAAAGGCTGGAATAACAACCTTTTGAAGTGGGCTTCTAGTTTCATT
genomic: ACGAGGACTTGCTAAATGCTGATGATGACAACCACTTCCAGGAAAAGATGgtctgtttct ... tttaatgcagGATAACAAAGGCTGGAATAACAACCTTTTGAAGTGGGCTTCTAGTTTCATT
EST: gi|88590027|gb|CI708851.1|CI708851
EST:     ACGAGGACTTGCTAAATGCTGATGATGACAACCACTTCCAGGAAAAGATG                         GATAACAAAGGCTGGAATAACAACCCTTTTGAAGTGGGCTTCTAGTTTCAT
genomic: ACGAGGACTTGCTAAATGCTGATGATGACAACCACTTCCAGGAAAAGATGgtctgtttct ... tttaatgcagGATAACAAAGGCTGGAATAACAACC-TTTTGAAGTGGGCTTCTAGTTTCAT
EST: gi|88592646|gb|CI710765.1|CI710765
EST:     ACGAGGACTTGCTAAATGCTGATGATGACAACCACTTCCAGGAAAAGATG                         GATAACAAAGGCTGGAATAACAACCTTTTGAAGTGGGCTTCTAGTTTCATT
genomic: ACGAGGACTTGCTAAATGCTGATGATGACAACCACTTCCAGGAAAAGATGgtctgtttct ... tttaatgcagGATAACAAAGGCTGGAATAACAACCTTTTGAAGTGGGCTTCTAGTTTCATT
EST: gi|29624544|gb|CB629555.1|CB629555
EST:     ACGAGGACTTGCTAAATGCTGATGATGACAACCACTTCCAGGAAAAGATG                         GATAACAAAGGCTGGAATAACAACCTTTTGAAGTGGGCTTCTAGTTTCATT
genomic: ACGAGGACTTGCTAAATGCTGATGATGACAACCACTTCCAGGAAAAGATGgtctgtttct ... tttaatgcagGATAACAAAGGCTGGAATAACAACCTTTTGAAGTGGGCTTCTAGTTTCATT
EST: gi|58695325|gb|CK084012.1|CK084012
EST:     ACGAGGACTTGCTAAATGCTGATGATGACAACCACTTCCAGGAAAAGATG                         GATAACAAAGGCTGGAATAACAACCTTTTGAAGTG
genomic: ACGAGGACTTGCTAAATGCTGATGATGACAACCACTTCCAGGAAAAGATGgtctgtttct ... tttaatgcagGATAACAAAGGCTGGAATAACAACCTTTTGAAGTG
EST: gi|33794022|gb|CF322901.1|CF322901
EST:     ACGAGGACTTGCTAAATGCTGATGATGACAACCACTTCCAGGAAAAGATG                         GATAACAAAGGCTGGAATAACAACCTTTTGAAGTGGGCTTCTAGTTTCATT
genomic: ACGAGGACTTGCTAAATGCTGATGATGACAACCACTTCCAGGAAAAGATGgtctgtttct ... tttaatgcagGATAACAAAGGCTGGAATAACAACCTTTTGAAGTGGGCTTCTAGTTTCATT
EST: gi|88414347|gb|CI691507.1|CI691507
EST:     ACGAGGACTTGCTAAATGCTGATGATGACAACCACTTCCAGGAAAAGATG                         GATAACAAAGGCTGGAATAACAACCTTTTGAAGTGGGCTTCTAGTTTCATT
genomic: ACGAGGACTTGCTAAATGCTGATGATGACAACCACTTCCAGGAAAAGATGgtctgtttct ... tttaatgcagGATAACAAAGGCTGGAATAACAACCTTTTGAAGTGGGCTTCTAGTTTCATT
EST: gi|58689586|gb|CK078273.1|CK078273
EST:     ACGAGGACTTGCTAAATGCTGATGATGACAACCACTTCCAGGAAAAGATG                         GATAACAAAGGCTGGAATAACAACCTTTTGAAGTGGGCTTCTAGTTTCATT
genomic: ACGAGGACTTGCTAAATGCTGATGATGACAACCACTTCCAGGAAAAGATGgtctgtttct ... tttaatgcagGATAACAAAGGCTGGAATAACAACCTTTTGAAGTGGGCTTCTAGTTTCATT

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: 66 (upstream exon), 70 (downstream exon)
Score: 34

GAGGGGCAAACTTATGCACATTGAAGTTCAAAAGAGAGGAGGAAAAGAGCACGAGGACTTGCTAAATGCTGATGATGACAACCACTTCCAGGAAAAGATGgtctgtttct ... tttaatgcagGATAACAAAGGCTGGAATAACAACCTTTTGAAGTGGGCTTCTAGTTTCATTAGTGGCGACTCATCATCAAAAAAGAAGGATGAGAAAATCTCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGGGCAAACTTATGCACATTGAAGTTCAAAAGAGAGGAGGAAAAGAGCACGAGGACTTGCTAAATGCTGATGATGACAACCACTTCCAGGAAAAGATGgtctgtttcttatttagttgcaaacatatccttgaaactctaaacaacatttcctttaaaatcatttttaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG