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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctatatgacattttctgatgaataatcaagatatatatgtaacactgtttttatgcttgaaatgatatcattatctgacccaatatgtgaactttgcagGTATGCAATGACCGGTCAGCTGACACAGAAAAGTGATGTGTATAGCTTCGGAGTTGTTCTCTTGGAACTTCTGACAGGAAGAAAACCAGTAGATCATACA

Basic information

species Oryza sativa
transcript LOC_Os01g67340.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g67340.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G346132_T01 (Zea mays), 3'ss of exon 5
tctatatgacattttctgatgaataatcaagatatatatgtaacactgtt--tttatgcttgaaatgatatcattatctgacc------caatatgtgaact----ttgcagGTATGCAATGACCGGTCAGCTGACACAGAAAAGTGATGTGTATAGCTTCGGAGTTGTTCTCTTGGAACTTCTGACAGGAAGAAAACCAGTAGATCATACA
             |       | ||||      ||     |     | |   ||  || ||| | | ||    || | ||| |      |||||  ||   |     ||||||||||||||||||||||| || || |||||||||||||| |||||||||||||| ||||| ||||| ||| ||||||| ||||| |||||||| ||||||
------------ctagcagcaactaatttgataatgcgcattgttttttagattagtgattggagtaatgctgttgtttgaacaatccacaatacttggtttgcttctgcagGTATGCAATGACCGGTCAACTAACCCAGAAAAGTGATGTATATAGCTTCGGAGTAGTTCTTTTGGAGCTTTTGACAGGTAGAAAGCCAGTAGACCATACA

upper sequence: LOC_Os01g67340.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA20G38980.1 (Glycine max), 3'ss of exon 6
tctatatgacattttctgatgaataatcaa----gatatatatgtaacactgtttttatgcttgaaatgatatcattatctgacccaatatgtgaactttgcagGTATGCAATGACCGGTCAGCTGACACAGAAAAGTGATGTGTATAGCTTCGGAGTTGTTCTCTTGGAACTTCTGACAGGAAGAAAACCAGTAGATCATACA
| || || |  || | |      | |||      ||    | ||  |   | ||||  |   |  | |  || | |  ||||       |    |||||| ||| ||||||||||| || ||| |||| || ||||||||||| ||||| || || ||||||||  | || ||||| |||||||||||||| || || ||||| 
tttaaattaatttgtttctcatctcatctcttttgactcctttgagattttattttgttttattgattcttagcttcttctgtgttgcca----aactttacagATATGCAATGACTGGGCAGTTGACTCAAAAAAGTGATGTCTATAGTTTTGGTGTTGTTCTTCTTGAGCTTCTTACAGGAAGAAAACCTGTTGACCATACC

upper sequence: LOC_Os01g67340.3 (Oryza sativa), 3'ss of exon 5
lower sequence: AT2G43230.1 (Arabidopsis thaliana), 3'ss of exon 4
tctatatgacattttctgatgaataatcaagatatatatgtaacactgtttttatgcttgaaatgatatcattatctgacccaatatg---tgaactttgcagGTATGCAATGACCGGTCAGCTGACACAGAAAAGTGATGTGTATAGCTTCGGAGTTGTTCTCTTGGAACTTCTGACAGGAAGAAAACCAGTAGATCATACA
                   | ||||  |   | | ||   || | | |  |||   |||||     | | | || ||||   ||| |    |    ||||||| ||||| ||||| || ||| |||||||||| |||||||| || || || |||||||| || ||||||||||| || || |||||||| || |||||||| 
------------------gtaaatatgcttca-acattgatagctcggaatttt--cttgat----tcttagtaactgaaagaatgtaactttgggtttgcagATATGCGATGACAGGACAGTTGACACAGAAGAGTGATGTTTACAGTTTTGGAGTTGTGCTTTTGGAACTTCTTACCGGGAGAAAACCGGTTGATCATACT

upper sequence: LOC_Os01g67340.3 (Oryza sativa), 3'ss of exon 5
lower sequence: AT3G59350.1 (Arabidopsis thaliana), 3'ss of exon 3
tctatatgacattttctgatgaataatcaagatatatatgtaacactgtttttatgcttgaaatgatatcattatctgacccaatatgtgaact-ttgcagGTATGCAATGACCGGTCAGCTGACACAGAAAAGTGATGTGTATAGCTTCGGAGTTGTTCTCTTGGAACTTCTGACAGGAAGAAAACCAGTAGATCATACA
                | ||||||  |   || |||   ||    |      ||| |||||      |    | | | ||   | || |   || |||||||||||| ||||| ||||| ||||||||||| |||||||| ||||| || || || || || ||||| ||  |||| || || ||||| || |||||||| 
---------------gtaatgaatgcttctgaaataatagttgatcacacagtattcttgaggaaggaaagat-tgtaactgtacattttcgctgttgcagGTATGCGATGACTGGTCAACTGACACAGAAGAGTGATGTTTATAGTTTTGGTGTGGTGCTTTTGGAGCTCTTGACTGGTAGGAAACCCGTCGATCATACG

upper sequence: LOC_Os01g67340.3 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv05s0124g00360.t01 (Vitis vinifera), 3'ss of exon 5
---tctatatgacattttctgatgaataatcaagatatatatgtaacactgtttttatgcttgaaatgatatcattatctgacccaatatgtgaactttgcagGTATGCAATGACCGGTCAGCTGACACAGAAAAGTGATGTGTATAGCTTCGGAGTTGTTCTCTTGGAACTTCTGACAGGAAGAAAACCAGTAGATCATACA
     |||  |    || ||    | |    | ||  ||| | ||  |   ||  ||       | |||| |||   |  |      ||       | |  |||||||||||||| || ||  |||| ||||| |||||||||||||| || ||||||||||| || || ||||| || || |||||||| || |||||||| 
aaaattattagttgcttgctttcaattgtctaggaagtat-tatagtaa-attactaaatcctgactgat-tcacatttggtgtgtgtaaaacccttctttagGTATGCAATGACTGGACAATTGACTCAGAAGAGTGATGTGTATAGTTTTGGAGTTGTTCTGTTAGAGCTTCTAACTGGGAGAAAACCTGTTGATCATACC

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|29644034|gb|CB649041.1|CB649041
EST:     CGTCTGCATTGTACTCGTGTACTGGGAACCTTTGGTTATCATGCTCCAGA                         GTATGCAATGACCGGTCAGCTGACACAGAAAAGTGATGTGTATAGCTTCGG
genomic: CGTCTGCATTCTACTCGTGTACTGGGAACCTTTGGTTATCATGCTCCAGAgtaaaaattc ... aactttgcagGTATGCAATGACCGGTCAGCTGACACAGAAAAGTGATGTGTATAGCTTCGG
EST: gi|88830237|gb|CI076493.1|CI076493
EST:     TGTCTGCATTCTACTCGTGTACTGGGAACCTTTGGTTATCATGCTCCAGA                         GTATGCAATGACCGGTCAGCTGACACAGAAAAGTGATGTGTATAGCTTCGG
genomic: CGTCTGCATTCTACTCGTGTACTGGGAACCTTTGGTTATCATGCTCCAGAgtaaaaattc ... aactttgcagGTATGCAATGACCGGTCAGCTGACACAGAAAAGTGATGTGTATAGCTTCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtttttatgcttgaaatgatatcattatctgacccaatatgtgaactttgcagGTATGCAATGACCGGTCAGCTGACACAGAAAAGTGATGTGTATAGCTTCGGAGTTGTTCTCTTGGAACTTCTGACAGGAAGAAAACCAGTAGATCATACA
                            atctgac  putative branch site (score: 3)
               aaatgatatcattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctatatgacattttctgatgaataatcaagatatatatgtaacactgtttttatgcttgaaatgatatcattatctgacccaatatgtgaactttgcagGTATGCAATGACCGGTCAGCTGACACAGAAAAGTGATGTGTATAGCTTCGGAGTTGTTCTCTTGGAACTTCTGACAGGAAGAAAACCAGTAGATCATACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - -ctgatga
- - - - - - - - - - - - - - - - - -atatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - -atgcttg