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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaacaacgtgcgattcaggcatttttttacgaggtcagagttagcagttgcagaaacttatgtttatttgatgtggtttgcgcattctcagGTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGATGGGAGACCTGGATGTGTTATGAACACATGTGCTCACAGAGCTTGCCCTC

Basic information

species Oryza sativa
transcript LOC_Os10g41780.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g41780.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G171390_T05 (Zea mays), 3'ss of exon 4
gtaaaaacaacgtgcgattcaggcatttttttacgaggtcagagttagcagttgcagaaacttatgtttatttgatgtggtttgcgcattctcagGTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGATGGGAGACCTGGATGTGTTATGAACACATGTGCTCACAGAGCTTGCCCTC
     |||   |  | |||||| | | | | |  | |  |    ||    | |  |  | ||  ||   |  |       ||      |  |||||||||||| || || || |||||||||||||| || |||||||| || || || || || || ||||||  ||||||||| || ||||| || ||||| |
---gtaactcagcac-attcag-cgtgtgtgtgtgtgtgcgtgcttgctcgcttaattacctgctgacaacctacgcgcattcaattctcatcagGTGCCAATCGACTGCTTCGAGGAGCAGTGGGTGATCTTCCGAGGCAAAGACGGAAGGCCCGGGTGTGTTCAGAACACATGCGCCCACAGGGCATGCCCGC

upper sequence: LOC_Os10g41780.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G038487_T01 (Zea mays), 3'ss of exon 4
gtaaa---aacaacgtgcgattcag-gcatttttttacgaggtcagagttagcagttgcagaaacttatgtttatttgat--gtggtttgcgcattctcagGTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGATGGGAGACCTGGATGTGTTATGAACACATGTGCTCACAGAGCTTGCCCTC
|||||   | ||  |   |  |||| ||  ||    |    | ||||| | | |||||| ||| | | ||| |  ||  |   ||   || ||||||||||||||| |||| ||| || |||||||||||||| || ||||| ||||| || || || ||||| ||||||  |||||||||||||||||| |||||||| |
gtaaactaaccactgaatgcctcagagccattgcacagacagacagagctgggagttgctgaagcctgtgtgtgcttacttgatgagctgtgcattctcagGTGCCGATAGCTTGCTTCGAGGAGCAGTGGGTGATATTCCGTGGAAAAGACGGAAGGCCTGGGTGTGTTCAGAACACATGTGCTCACAGGGCTTGCCCGC

upper sequence: LOC_Os10g41780.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA04G42840.1 (Glycine max), 3'ss of exon 4
gtaaaaacaacgtgcgattcaggcatttttttacgaggtcagag-ttagcagttgcagaaact-----tatgtttatttgatgtggtt-----tgcgcattctcagGTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGATGGGAGACCTGGATGTGTTATGAACACATGTGCTCACAGAGCTTGCCCTC
     ||   | || | |  | | | || | |   || | ||||  || | ||     || ||     ||  ||   || |    |||     |   | || |||| | |||||||| ||||||||||| |  ||||| || |||||||| || |||||||  ||||| ||||||  |||||| ||||| |||||||| || ||||
-----aatttcttggggtg-acggagttctgtgtcagataagagactacctgtactccaatctggatgtaaattctcttaagcatgttaatccttttctttttcagATCCCAATAGAATGTTTTGAGGAACCATGGGTCATCTTCCGAGGGAAAGATGGGAAGCCTGGGTGTGTTCAGAACACCTGTGCACACAGAGCATGTCCTC

upper sequence: LOC_Os10g41780.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA06G11920.1 (Glycine max), 3'ss of exon 4
----gtaaaaaca-acgtgcg---attcaggcatttttttacgaggtcagagttagcagttgcagaaacttatgtttatttgatgtggtttgcgcattctcagGTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGATGGGAGACCTGGATGTGTTATGAACACATGTGCTCACAGAGCTTGCCCTC
     ||| | |     || |   | | | |  ||| |  | |       | |     | || | |  || ||    || | |     |||   | || |||| | |||||||| ||||||||||| |  ||||| ||||| ||||| || |||||||  ||||||||||||   || || || || |||||||| |||||||
ccagataagagcccgtctgtggaaagttatggttttatacaagttactccaatctctggatgtaaattctcataagcatgttaatcctttt---ctttttcagATCCCAATAGAATGTTTTGAGGAACCATGGGTCATTTTTCGAGGGAAAGATGGGAAGCCTGGATGTGTTCAAAATACCTGCGCACACAGAGCATGCCCTC

upper sequence: LOC_Os10g41780.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA14G23860.1 (Glycine max), 3'ss of exon 4
--gtaaaaacaacgtgcgat-tcaggcatttttttacgaggtcagagttagcagttgcag--aaacttatgtttatttgatgtggtttgcgcattctcagGTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGATGGGAGACCTGGATGTGTTATGAACACATGTGCTCACAGAGCTTGCCCTC
   ||         || | | |||   ||  |   |    | || | | |  || |  |   ||| |    |  || || |     ||      |||||| | |||||||| ||||||||||| |  ||||| || |||||||| || |||||||  |||||||||||   |||||| ||||| ||| |||| || ||||
atttaggggggtaatggggtgtcatatatgataaaagatagacatactcataagctaaatgcaaattctcataaatgtgttactccttttcttatctcagATCCCAATAGAATGTTTTGAGGAACCATGGGTTATCTTCCGAGGGAAAGATGGGAAGCCTGGATGTGTGCAGAACACCTGTGCACACCGAGCCTGTCCTC

upper sequence: LOC_Os10g41780.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA13G03430.1 (Glycine max), 3'ss of exon 4
---gtaaaaacaacgtgcgat-tcaggcatttttttacgaggtcagagttagcagttgcag--aaacttatgtttatttgatgtggtttgcgcattctcagGTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGATGGGAGACCTGGATGTGTTATGAACACATGTGCTCACAGAGCTTGCCCTC
    |||        || | | |||   ||  ||  |    | || | | |  || |  |   ||| |    |  || || |     ||    || ||||| | |||||||| ||||||||||| |  ||||| || || ||||| || |||||||  |||||||||||   |||||| ||||| || ||||| |||||||
tatttaagggggtaatggggtgtcatatatgattaaagatagacatactcataagctaaatgcaaattctcataaatgtgttactccttttctat-ctcagATCCCAATAGAATGTTTTGAGGAACCATGGGTTATCTTTCGAGGGAAAGATGGGAAGCCTGGATGTGTGCAGAACACCTGTGCACATAGAGCCTGCCCTC

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|29616566|gb|CB621578.1|CB621578
EST:     ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATG                         GTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
genomic: ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATGgtaaaaacaa ... gcattctcagGTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
EST: gi|29673392|gb|CB669667.1|CB669667
EST:     ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATG                         GTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
genomic: ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATGgtaaaaacaa ... gcattctcagGTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
EST: gi|29618942|gb|CB623954.1|CB623954
EST:     ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATG                         GTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
genomic: ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATGgtaaaaacaa ... gcattctcagGTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
EST: gi|58591367|gb|CF989675.1|CF989675
EST:     ACTTCTGGTACCCAGTTGGTGGCTCCAGTGACCTAAAAGACGATACAATG                         GTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
genomic: ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATGgtaaaaacaa ... gcattctcagGTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
EST: gi|29615262|gb|CB620274.1|CB620274
EST:     ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATG                         GTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
genomic: ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATGgtaaaaacaa ... gcattctcagGTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
EST: gi|58673738|gb|CK062424.1|CK062424
EST:     ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATG                         GTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
genomic: ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATGgtaaaaacaa ... gcattctcagGTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
EST: gi|29671985|gb|CB668260.1|CB668260
EST:     ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATG                         GTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAA-GGAT
genomic: ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATGgtaaaaacaa ... gcattctcagGTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
EST: gi|29617556|gb|CB622568.1|CB622568
EST:     ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATG                         GTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
genomic: ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATGgtaaaaacaa ... gcattctcagGTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
EST: gi|29614576|gb|CB619589.1|CB619589
EST:     ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTANAAGACGATACAATG                         GTGCCAATAGATTGTTTTGAG
genomic: ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATGgtaaaaacaa ... gcattctcagGTGCCAATAGATTGTTTTGAG
EST: gi|66926053|gb|CX112901.1|CX112901
EST:     ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATG                         GTGCCAATAGATTTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGA
genomic: ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATGgtaaaaacaa ... gcattctcagGTGCCAATAGATT-GTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGA
EST: gi|29613349|gb|CB618362.1|CB618362
EST:     ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATG                         GTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
genomic: ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATGgtaaaaacaa ... gcattctcagGTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
EST: gi|700022|gb|D46313.1|D46313
EST:     ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATG                         GTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
genomic: ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATGgtaaaaacaa ... gcattctcagGTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
EST: gi|29670404|gb|CB666679.1|CB666679
EST:     ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTANAAGACGATACAATG                         GTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTT
genomic: ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATGgtaaaaacaa ... gcattctcagGTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTT
EST: gi|58611249|gb|CK038961.1|CK038961
EST:     ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATG                         GTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
genomic: ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATGgtaaaaacaa ... gcattctcagGTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagttagcagttgcagaaacttatgtttatttgatgtggtttgcgcattctcagGTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGATGGGAGACCTGGATGTGTTATGAACACATGTGCTCACAGAGCTTGCCCTC
                             atttgat  putative branch site (score: 5)
                                              cattctc  putative PPT
                 aaacttatgtttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaacaacgtgcgattcaggcatttttttacgaggtcagagttagcagttgcagaaacttatgtttatttgatgtggtttgcgcattctcagGTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGATGGGAGACCTGGATGTGTTATGAACACATGTGCTCACAGAGCTTGCCCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT