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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcacttgcatacattctgtttgtgttttttcttcccactgcttccttttactcaaaacactgtcgaaatttttgtttttaacagGCTGAGTCTCATAGGAGGGCTGCTGCAGCCACAGCTGCTGGGAAATTCAAAGATGAGATTGTTCCGGTGCCTACAAAG

Basic information

species Oryza sativa
transcript LOC_Os02g57260.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g57260.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G848768_T02 (Zea mays), 3'ss of exon 7
gtgagtcacttgcatacattctgtttgtgttttttcttcccactgcttccttttactcaaaacactgtcgaaatttttgtttttaacagGCTGAGTCTCATAGGAGGGCTGCTGCAGCCACAGCTGCTGGGAAATTCAAAGATGAGATTGTTCCGGTGCCTACAAAG
||||||  ||    ||      |  ||| |   ||  |    |||     ||    | || | |    | |||  ||| |||||  |||||||||||||||||||| |||||||||||||| ||  |||| |||||||| |||||||| || || ||||| ||||||
gtgagttcctcat-taagcatcgactgtatgaattaattat-ctggggttttccggttaatataacaactaaagcttt-tttttgtcagGCTGAGTCTCATAGGAGAGCTGCTGCAGCCACGGCCTCTGGAAAATTCAAGGATGAGATCGTCCCCGTGCCAACAAAG

upper sequence: LOC_Os02g57260.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA10G24590.3 (Glycine max), 3'ss of exon 7
---------------gtgagtca-cttgcatacattctgtttgtgttttttcttcccactgcttccttttactcaaaacactgtcgaaatttttgtttttaacagGCTGAGTCTCATAGGAGGGCTGCTGCAGCCACAGCTGCTGGGAAATTCAAAGATGAGATTGTTCCGGTGCCTACAAAG
               | |||| | || |      |  |  |  || || |   |   | || |  |   |  | |  | ||  ||  ||    |  | || | ||| ||||||||| ||| | ||||||||||| || |||||||| ||||| |||||||| ||||| || ||  | || |||
aactcgtaagagttagcgagttaactcgagagtttgataatcatggttctatcttata-tgttaacaactcttaaccaaaccttcttaa----taatgttgatagGTTGAGTCTCACAGGCGAGCTGCTGCAGCTACTGCTGCTGGTAAATTTAAAGATGAAATTGTCCCAGTTACCACCAAG
















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|29661674|gb|CB657949.1|CB657949
EST:     ATGTTGCGCACCGATATGGTGTAACAAGACAAGAGCAGGATCAGGCTGCT                         GCTGAGTCTCATAGGAGGGCTGCTGCAGCCACAGCTGCTGGGAAATTCAAA
genomic: ATGTTGCGCACCGATATGGTGTAACAAGACAAGAGCAGGATCAGGCTGCTgtgagtcact ... tttttaacagGCTGAGTCTCATAGGAGGGCTGCTGCAGCCACAGCTGCTGGGAAATTCAAA
EST: gi|33793905|gb|CF322841.1|CF322841
EST:     ATGTTGCGCACCGATATGGTGTAACAAGACAAGAGCAGGATCAGGCTGCT                         GCTGAGTCT-ATAGGAGGGCTGCTGCAGCCACAGCTGCTGGGAAATTCAAA
genomic: ATGTTGCGCACCGATATGGTGTAACAAGACAAGAGCAGGATCAGGCTGCTgtgagtcact ... tttttaacagGCTGAGTCTCATAGGAGGGCTGCTGCAGCCACAGCTGCTGGGAAATTCAAA
EST: gi|29664436|gb|CB660711.1|CB660711
EST:     ATGTTGCGCACCGATATGGTGTAACAAGACAAGAGCAGGATCAGGCTGCT                         GCTGAGTCTCATAGGAGGGCTGCTGCAGCCACAGCTGCTGGGAAATTCAAA
genomic: ATGTTGCGCACCGATATGGTGTAACAAGACAAGAGCAGGATCAGGCTGCTgtgagtcact ... tttttaacagGCTGAGTCTCATAGGAGGGCTGCTGCAGCCACAGCTGCTGGGAAATTCAAA
EST: gi|218485684|gb|FG959002.1|FG959002
EST:     ATGTTGCGCACCGATATGGTGTAACAAGACAAGAGCAGGATCAGGCTGCT                         GCTGAGTCTCATAGGAGGGCTGCTGCAGCCAAAGCTGCTGGGAAATTCAAA
genomic: ATGTTGCGCACCGATATGGTGTAACAAGACAAGAGCAGGATCAGGCTGCTgtgagtcact ... tttttaacagGCTGAGTCTCATAGGAGGGCTGCTGCAGCCACAGCTGCTGGGAAATTCAAA
EST: gi|29663747|gb|CB660022.1|CB660022
EST:     ATGTTGCGCACCGATATGGTGTAACAAGACAAGAGCAGGATCAGGCTGCT                         GCTGAGTCTCATAGGAGGGCTGCTGCAGCCACAGCTGCTGGGAAATTCAAA
genomic: ATGTTGCGCACCGATATGGTGTAACAAGACAAGAGCAGGATCAGGCTGCTgtgagtcact ... tttttaacagGCTGAGTCTCATAGGAGGGCTGCTGCAGCCACAGCTGCTGGGAAATTCAAA
EST: gi|29687731|gb|CB684006.1|CB684006
EST:     ATGTTGCGCACCGATATGGTGTAACAAGACAAGAGCAGGATCAGGCTGCT                         GCTGAGTCTCATAGGAGGGCTGCTGCAGCCACAGCTGCTGGGAAATTCAAA
genomic: ATGTTGCGCACCGATATGGTGTAACAAGACAAGAGCAGGATCAGGCTGCTgtgagtcact ... tttttaacagGCTGAGTCTCATAGGAGGGCTGCTGCAGCCACAGCTGCTGGGAAATTCAAA
EST: gi|218500667|gb|FG957553.1|FG957553
EST:     ATGTTGCGCACCGATATGGTGTAACAAGACAAGAGCAGGATCAGGCTGCT                         GCTGAGTCTCATAGGAGGGCTGCTGCAGCCACAGCTGCTGGGAAATTCAAA
genomic: ATGTTGCGCACCGATATGGTGTAACAAGACAAGAGCAGGATCAGGCTGCTgtgagtcact ... tttttaacagGCTGAGTCTCATAGGAGGGCTGCTGCAGCCACAGCTGCTGGGAAATTCAAA
EST: gi|38471798|gb|CF955929.1|CF955929
EST:     ATGTTGCGCACCGATATGGTGTAACAAGACAAGAGCAGGATCAGGCTGCT                         GCTGAGTCTCATAGGAGGGCTGCTGCAGCCACAGCTGCTGGGAAATTCAAA
genomic: ATGTTGCGCACCGATATGGTGTAACAAGACAAGAGCAGGATCAGGCTGCTgtgagtcact ... tttttaacagGCTGAGTCTCATAGGAGGGCTGCTGCAGCCACAGCTGCTGGGAAATTCAAA
EST: gi|38565849|gb|CK085302.1|CK085302
EST:     ATGTTGCGCACCGATATGGTGTAACAAGACAAGAGCAGGATCAGGCTGCT                         GCTGAGTCTCATAGGAGGGCTGCTGCAGCCACAGCTGCTGGGAAATTCAAA
genomic: ATGTTGCGCACCGATATGGTGTAACAAGACAAGAGCAGGATCAGGCTGCTgtgagtcact ... tttttaacagGCTGAGTCTCATAGGAGGGCTGCTGCAGCCACAGCTGCTGGGAAATTCAAA
EST: gi|29667870|gb|CB664145.1|CB664145
EST:     ATGTTGCGCACCGATATGGTGTAACAAGACAAGAGCAGGATCAGGCTGCT                         GCTGAGTCTCATAGGAGGGCTGCTGCAGCCACAGCTGCTGGGAAATTCAAA
genomic: ATGTTGCGCACCGATATGGTGTAACAAGACAAGAGCAGGATCAGGCTGCTgtgagtcact ... tttttaacagGCTGAGTCTCATAGGAGGGCTGCTGCAGCCACAGCTGCTGGGAAATTCAAA
EST: gi|33681865|gb|CF310104.1|CF310104
EST:     ATGTTGCGCACCGATATGGTGTAACAAGACAAGAGCAGGATCAGGCTGCT                         GCTGAGTCTCATAGGAGGGCTGCTGCAGCCACAGCTGCTGGGAAATTCAAA
genomic: ATGTTGCGCACCGATATGGTGTAACAAGACAAGAGCAGGATCAGGCTGCTgtgagtcact ... tttttaacagGCTGAGTCTCATAGGAGGGCTGCTGCAGCCACAGCTGCTGGGAAATTCAAA
EST: gi|25800239|gb|CA756200.1|CA756200
EST:     GCAGGATCAGGCTGCT                         GCTGAGTCTCATAGGAGGGCTGCTGCAGCCACAGCTGCTGGGAAATTCAAA
genomic: GCAGGATCAGGCTGCTgtgagtcact ... tttttaacagGCTGAGTCTCATAGGAGGGCTGCTGCAGCCACAGCTGCTGGGAAATTCAAA
EST: gi|58606960|gb|CK034993.1|CK034993
EST:     ATGTTGCGCACCGATATGGTGTAACAAGACAAGAGCAGTATCAGGCTGCT                         GCTGAGTCTCATAGGAGGGCTGCTGCAGCCACAGCTGCTGGGAAATTCAAA
genomic: ATGTTGCGCACCGATATGGTGTAACAAGACAAGAGCAGGATCAGGCTGCTgtgagtcact ... tttttaacagGCTGAGTCTCATAGGAGGGCTGCTGCAGCCACAGCTGCTGGGAAATTCAAA

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: 73 (upstream exon), 65 (downstream exon)
Score: 19

AGTCCAGAAAGCACAGGATTGTCTTTTGCCCATGGGGATAACGTCCGAAAATGTTGCGCACCGATATGGTGTAACAAGACAAGAGCAGGATCAGGCTGCTgtgagtcact ... tttttaacagGCTGAGTCTCATAGGAGGGCTGCTGCAGCCACAGCTGCTGGGAAATTCAAAGATGAGATTGTTCCGGTGCCTACAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttcccactgcttccttttactcaaaacactgtcgaaatttttgtttttaacagGCTGAGTCTCATAGGAGGGCTGCTGCAGCCACAGCTGCTGGGAAATTCAAAGATGAGATTGTTCCGGTGCCTACAAAG
                                       tttttgttttt  CT-rich tract
                                    aaatttttgtttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtcacttgcatacattctgtttgtgttttttcttcccactgcttccttttactcaaaacactgtcgaaatttttgtttttaacagGCTGAGTCTCATAGGAGGGCTGCTGCAGCCACAGCTGCTGGGAAATTCAAAGATGAGATTGTTCCGGTGCCTACAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG