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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgttatgttatcctgattcagatcattcccttcctgggattgaacggaaagttctggtagtttgcttacagttcttttggttatgttttgatctatcagGGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTGTGAGTTCTCCCATGATTGGAATGATCAACCAAACAAT

Basic information

species Oryza sativa
transcript LOC_Os06g21390.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g21390.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G395842_T02 (Zea mays), 3'ss of exon 1
------ttgttatgttatcct--gattcagatca----ttcccttcctgggattgaacggaaagttctggtagtttgcttacagttcttttggttatgttttgatctatcagGGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTGTGAGTTCTCCCATGATTGGAATGATCAACCAAACAAT
      ||| ||   |||  |  ||   ||        |   ||  ||  |||  |||  | | || |||| ||||||| || | |  ||| ||            |||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||| || |||| ||||||| |||| |||
gtttacttgataaagtatttttagaactagtctggaattattctgtctcagatgaaaccaacaattttggttgtttgctcactgcttcttttgt------------tatcagAGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAAT
















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|88402321|gb|CI596182.1|CI596182
EST:     AGGTGCGGGGGCCGTTCCGATCGAGTCGGTCCTGCCATGTCGACCAAGAG                         GGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAG--TACTG
genomic: AGGTGCGGGGGCCGTTCCGATCGAGTCGGTCCTGCCATGTCGACCAAGAGgtaatctcga ... gatctatcagGGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
EST: gi|58606524|gb|CK034557.1|CK034557
EST:     AGGTGCGGGGGCCGTTCCGATCGAGTCGGTCCTGCCATGTCGACCAAGAG                         GGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
genomic: AGGTGCGGGGGCCGTTCCGATCGAGTCGGTCCTGCCATGTCGACCAAGAGgtaatctcga ... gatctatcagGGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
EST: gi|88344776|gb|CI624427.1|CI624427
EST:     AGGTGCGGGGGCCGTTCCGATCGAGTCGGTCCTGCCATGTCGACCAAGAG                         GGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
genomic: AGGTGCGGGGGCCGTTCCGATCGAGTCGGTCCTGCCATGTCGACCAAGAGgtaatctcga ... gatctatcagGGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
EST: gi|88389034|gb|CI595268.1|CI595268
EST:     AGGTGCGGGGGCCGTTCCGATCGAGTCGGTCCTGCCATGTCGACCAAGAG                         GGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
genomic: AGGTGCGGGGGCCGTTCCGATCGAGTCGGTCCTGCCATGTCGACCAAGAGgtaatctcga ... gatctatcagGGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
EST: gi|88370752|gb|CI592518.1|CI592518
EST:     AGGTGCGGGGGCCGTTCCGATCGAGTCGGTCCTGCCATGTCGACCAAGAG                         GGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
genomic: AGGTGCGGGGGCCGTTCCGATCGAGTCGGTCCTGCCATGTCGACCAAGAGgtaatctcga ... gatctatcagGGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
EST: gi|88411921|gb|CI571413.1|CI571413
EST:     AGGTGCGGGGGCCGTTCCGATCGAGTCGGTCCTGCCATGTCGACCAAGAG                         GGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
genomic: AGGTGCGGGGGCCGTTCCGATCGAGTCGGTCCTGCCATGTCGACCAAGAGgtaatctcga ... gatctatcagGGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
EST: gi|88357849|gb|CI625100.1|CI625100
EST:     AGGTGCGGGGGCCGTTCCGATCGAGTCGGTCCTGCCATGTCGAACAAGAG                         GGTTCTTTGCAAGTTCTTCATGCATGGAGCTT
genomic: AGGTGCGGGGGCCGTTCCGATCGAGTCGGTCCTGCCATGTCGACCAAGAGgtaatctcga ... gatctatcagGGTTCTTTGCAAGTTCTTCATGCATGGAGCTT
EST: gi|88456027|gb|CI567743.1|CI567743
EST:     AGGTGCGGGGGCCGTTCCGATCGAGTCGGTCCTGCCATGTCGACCAAGAG                         GGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
genomic: AGGTGCGGGGGCCGTTCCGATCGAGTCGGTCCTGCCATGTCGACCAAGAGgtaatctcga ... gatctatcagGGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
EST: gi|29659493|gb|CB655768.1|CB655768
EST:     AGGTGCGGGGGCCGTTCCGATCGAGTCGGTCCTGCCATGTCGACCAAGAG                         GGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
genomic: AGGTGCGGGGGCCGTTCCGATCGAGTCGGTCCTGCCATGTCGACCAAGAGgtaatctcga ... gatctatcagGGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
EST: gi|88353474|gb|CI631659.1|CI631659
EST:     AGGTGCGGGGGCCGTTCCGATCGAGTCGGTCCTGCCATGTCGACCAAGAG                         GGTTCTTTGCAAGTTCTTCATGCA
genomic: AGGTGCGGGGGCCGTTCCGATCGAGTCGGTCCTGCCATGTCGACCAAGAGgtaatctcga ... gatctatcagGGTTCTTTGCAAGTTCTTCATGCA

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: 40 (upstream exon), 73 (downstream exon)
Score: 8

TCTCGTGCTCCGGCGCTGCTCGTCGTCTCCTTGGCCGAATCCAATCCGGGAGGTGCGGGGGCCGTTCCGATCGAGTCGGTCCTGCCATGTCGACCAAGAGgtaatctcga ... gatctatcagGGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTGTGAGTTCTCCCATGATTGGAATGATCAACCAAACAAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggaaagttctggtagtttgcttacagttcttttggttatgttttgatctatcagGGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTGTGAGTTCTCCCATGATTGGAATGATCAACCAAACAAT
                                    ttatgtttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgttatgttatcctgattcagatcattcccttcctgggattgaacggaaagttctggtagtttgcttacagttcttttggttatgttttgatctatcagGGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTGTGAGTTCTCCCATGATTGGAATGATCAACCAAACAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
-tgttatg
- -ttatgtt
- - - - - - - tgattca
- - - - - - - - - - - - cattccc
- - - - - - - - - - - - - - - -ttcctgg
- - - - - - - - - - - - - - - - - - - - - -aacggaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttac