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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagaataggcatgagcacatcttcctgcaaagatgttactcatgaaaacaatcattgtgaagttctgatgacatatacattctgaaataccacttcacagGTCATAGTGCTGTATTACAAGGATGTACTGTTGAGGACGAAGCATTTGTTGGTATGGGGGCGACCCTGTTAGATGGTGTTGTCGTGGAAAAGCATGGGAT

Basic information

species Oryza sativa
transcript LOC_Os01g18070.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g18070.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G140885_T02 (Zea mays), 3'ss of exon 2
aagaataggcatgagcacatcttcct--gcaaagatgttactcatgaaaacaatcatt---gtgaagttctgatgacatatacattctgaaataccacttcacagGTCATAGTGCTGTATTACAAGGATGTACTGTTGAGGACGAAGCATTTGTTGGTATGGGGGCGACCCTGTTAGATGGTGTTGTCGTGGAAAAGCATGGGAT
     | ||||| |        |     ||  ||      | | | |||||| |   |   |  ||      |  | |  ||  || |  ||  |   ||  ||||||| |||||||| ||||||||||| || |||||||| ||||| |||||||| |||||||| ||||| ||||||||||| || || | ||||||||||||
-----ttggcataactttgctctgtatggccgagccagagcacttcaaaacagttgatccaggaaaaaatacacaaaacttaacttttccaactctgtttggcagGTCACAGTGCTGTGTTACAAGGATGCACGGTTGAGGATGAAGCTTTTGTTGGCATGGGGGCAACCCTATTAGATGGTGTCGTTGTTGGAAAGCATGGGAT

upper sequence: LOC_Os01g18070.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G046924_T02 (Zea mays), 3'ss of exon 3
aagaataggcatgagcacatcttcctg-caaagatgttactcatgaaaacaat-cattgtg----aagttctgatgacatatacattctgaaataccacttcacagGTCATAGTGCTGTATTACAAGGATGTACTGTTGAGGACGAAGCATTTGTTGGTATGGGGGCGACCCTGTTAGATGGTGTTGTCGTGGAAAAGCATGGGAT
     | ||||| |     |||   || |  || |    | | | |||||| | ||  | |    ||  | |  | |  |  |||||   || | |   ||  |||||||||||||||| ||||||||||| || |||||||| || || |||||||| || ||||| ||||| |||||||||||||| || |||||||| || ||
-----ttggcataatttgctctgtatggccgagctagagcactttaaaacagttcaccgaggaaaaaaatgtactaaagttaacatttccaact-ctgtttggcagGTCATAGTGCTGTGTTACAAGGATGCACGGTTGAGGATGAGGCTTTTGTTGGCATTGGGGCAACCCTATTAGATGGTGTTGTTGTTGAAAAGCACGGAAT

upper sequence: LOC_Os01g18070.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA11G07540.1 (Glycine max), 3'ss of exon 3
aagaataggcatgagcacatcttcctgcaaagatgttactcatgaaaacaatcattgtgaagttctgatgacatatacattctgaaataccacttcacagGTCATAGTGCTGTATTACAAGGATGTACTGTTGAGGACGAAGCATTTGTTGGTATGGGGGCGACCCTGTTAGATGGTGTTGTCGTGGAAAAGCATGGGAT
  || |     |||    ||  || |        || |||  | |  |   |  | ||| |  |||      || ||   | || |        |   ||||||||||||||| ||||||||||||||||||||||| || |||||| |||| ||||| || ||| || | ||||||||    || || || ||||  ||
gtgagtgaaagtga-tgaattatcatttttgtgagtgact--taagcatttttttagtgcaactct------atctaaggtttggacactgtgattttagGTCATAGTGCTGTGTTACAAGGATGTACTGTTGAGGATGAGGCATTTATTGGCATGGGTGCAACCTTGCTTGATGGTGTATATGTTGAGAAACATGCCAT

upper sequence: LOC_Os01g18070.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA01G37780.1 (Glycine max), 3'ss of exon 3
aagaataggcatgagcacatcttcctgcaaagatgttactcatgaaaacaatcattgtgaagttctgatgacatatacattctgaaataccacttcacagGTCATAGTGCTGTATTACAAGGATGTACTGTTGAGGACGAAGCATTTGTTGGTATGGGGGCGACCCTGTTAGATGGTGTTGTCGTGGAAAAGCATGGGAT
  || |     |||  |  | ||  ||  |    || |||   | |     | | ||||||      ||       |  || ||| |      ||  |||||||||||||||| |||||||||||||| |||||||| || |||||| |||| ||||| || ||| || | ||||||||    || || || ||||  ||
gtgagtgaaagtgatgaattattattgtga----gtgacttcagcattgttttagtgtgaaaactctat----ctaaggttttgacactgtgattt-cagGTCATAGTGCTGTGTTACAAGGATGTACAGTTGAGGATGAGGCATTTATTGGCATGGGTGCAACCTTGCTTGATGGTGTATATGTTGAGAAACATGCCAT

upper sequence: LOC_Os01g18070.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA04G03310.2 (Glycine max), 3'ss of exon 2
aagaataggcatgagcacatcttcctgcaaagat-gttactcatgaaaacaatcattgtgaagttctgatgacatatacattctgaaataccacttcacagGTCATAGTGCTGTATTACAAGGATGTACTGTTGAGGACGAAGCATTTGTTGGTATGGGGGCGACCCTGTTAGATGGTGTTGTCGTGGAAAAGCATGGGAT
           |||| | | |||  ||  | |||    | || ||         | | | ||      ||    | || ||| |    |   |||   |||| || ||||||||  | || || ||||||||||||||||| || |||||||||||||| || |  ||  | || ||||| || || || ||  |||  ||
----------gtgagta-acctttttgtcatgattaagaatcgtgctgtgttctactcttaatgggaaattttgt-taaatttt----ttttactgagcagGCCACAGTGCTGTTATCCATGGTTGTACTGTTGAGGACGAGGCTTTTGTTGGTATGGGTGCAATACTACTTGACGGTGTAGTAGTTGAGAAAAATGCCAT

upper sequence: LOC_Os01g18070.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA04G03300.1 (Glycine max), 3'ss of exon 3
aagaataggcatgagcacatcttcctgcaaagatgttactcatgaaaacaatcattgtgaagttctgatgacatatacattctgaaatac-cacttcacagGTCATAGTGCTGTATTACAAGGATGTACTGTTGAGGACGAAGCATTTGTTGGTATGGGGGCGACCCTGTTA---GATGGTGTTGTCGTGGAAAAGCATGGGAT
              | | |  ||  ||  | |||       | ||| |      |  |  | || | |||  | ||  ||  |  | |   ||||   |||||||||||||||| ||||| || ||||| ||||||||||| || |||||||||||||| || |  ||  ||   ||||||||  | || || ||  |||    
--------------gta-acatttttgtcatgat------taagaatagtgctgtgttctacttttaatgggaaatttatgttatagttttcactgagcagGTCATAGTGCTGTTTTACATGGTTGTACCGTTGAGGACGAGGCTTTTGTTGGTATGGGTGCAATACTACTACTTGATGGTGTAATTGTTGAGAAAAATGC---

upper sequence: LOC_Os01g18070.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G19580.2 (Arabidopsis thaliana), 3'ss of exon 3
------aagaataggcatgagcacatcttcctgcaaagatgttactcatgaaaacaatcattgtgaagttctgatgacatatacattctgaaataccacttcacagGTCATAGTGCTGTATTACAAGGATGTACTGTTGAGGACGAAGCATTTGTTGGTATGGGGGCGACCCTGTTAGATGGTGTTGTCGTGGAAAAGCATGGGAT
        ||||   | |   |||   ||  |   || |||||    ||| | ||| ||     ||||   |  ||  |||||   |   |   |     | ||||||||||||||||| ||||| ||||||||||||||||| ||  | ||| |||| ||||| ||||| ||  | ||||| || || || ||||||||||||||
gttagtgggaatct-cttactcactgtttattttgaaaatgtttaatatgcataca-tctccaagaagcatt--tgggatatagtcttaaattaaatgtgtaacagGTCATAGTGCTGTTTTACATGGATGTACTGTTGAGGATGAGACCTTTATTGGGATGGGTGCGACACTTCTTGATGGGGTCGTTGTTGAAAAGCATGGGAT

upper sequence: LOC_Os01g18070.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv04s0023g02060.t01 (Vitis vinifera), 3'ss of exon 2
aagaataggcatgagcacatcttcctgcaaagatgttactcatgaaaacaatcattgtgaagttctgatgacata---tacattctgaaatacca-cttcacagGTCATAGTGCTGTATTACAAGGATGTACTGTTGAGGACGAAGCATTTGTTGGTATGGGGGCGACCCTGTTAGATGGTGTTGTCGTGGAAAAGCATGGGAT
  || ||  ||||  |||   |  |    | ||| |  |         | ||  || | |  |||    | | ||   ||   |||  |||   | ||  ||||||||  ||||||| ||||| ||||||||||||||| | || |||||| |||||||||| || |||||  | ||||| | | | || || || ||||  ||
gtgagtaa-catgc-caccaatgtcaaatatgatatggcctggtcctgccatggttttta--ttcaagcgtcctactttatgatctccaatttaaactggacagGTCACGGTGCTGTCTTACATGGATGTACTGTTGAGAATGAGGCATTTATTGGTATGGGTGCTACCCTCCTTGATGGGGCTTTTGTTGAGAAACATGCAAT

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|87016255|gb|CI271666.1|CI271666
EST:     GGATAACGTCACAGTAG                         GTCATAGTGCTGTATTACAAGGATGTACTGTTGAGGACGAAGCATTTGTTG
genomic: GGATAACGTCACAGTAGgtaaatatga ... cacttcacagGTCATAGTGCTGTATTACAAGGATGTACTGTTGAGGACGAAGCATTTGTTG
EST: gi|29667595|gb|CB663870.1|CB663870
EST:     TCTTAGTGGAAAAGTCTTTCCAACCATCATTGGGGATAACGTCACAGTAG                         GTCATAGTGCTGTATTACAAGGATGTACTGTTGAGGACGAAGCATTTGTTG
genomic: TCTTAGTGGAAAAGTCTTTCCAACCATCATTGGGGATAACGTCACAGTAGgtaaatatga ... cacttcacagGTCATAGTGCTGTATTACAAGGATGTACTGTTGAGGACGAAGCATTTGTTG
EST: gi|3766564|gb|AU030674.1|AU030674
EST:     TCTTAGTGGAAAAGTCTTTCCAACCATCATTGGGGATAACGTCACAGTAG                         GTCATAGTGCTGTATTACAAGGATGTACTGTTGAGGACGAAGCATTTGTTG
genomic: TCTTAGTGGAAAAGTCTTTCCAACCATCATTGGGGATAACGTCACAGTAGgtaaatatga ... cacttcacagGTCATAGTGCTGTATTACAAGGATGTACTGTTGAGGACGAAGCATTTGTTG
EST: gi|1854199|gb|AA231827.1|AA231827
EST:     CTTAGTGGAAAAAGTCTTTCCAACCATCATTGGGGATAACGTCACAGTAG                         GTCATAGTGCTGTATTACAAGGATGTACTGTTGAGGACGAAGCATTTGTTG
genomic: CTTAGTGG-AAAAGTCTTTCCAACCATCATTGGGGATAACGTCACAGTAGgtaaatatga ... cacttcacagGTCATAGTGCTGTATTACAAGGATGTACTGTTGAGGACGAAGCATTTGTTG
EST: gi|163929273|gb|EG712702.1|EG712702
EST:     TCTTAGTGGAAAAGTCTTTCCAACCATCATTGGGGATAACGTCACAGTAG                         GTCATAGTGCTGTATTACAAGGATGTACTGTTGAGGACGAAGCATTTGTTG
genomic: TCTTAGTGGAAAAGTCTTTCCAACCATCATTGGGGATAACGTCACAGTAGgtaaatatga ... cacttcacagGTCATAGTGCTGTATTACAAGGATGTACTGTTGAGGACGAAGCATTTGTTG
EST: gi|163927400|gb|EG713864.1|EG713864
EST:     TCTTAGTGGAAAAGTCTTTCCAACCATCATTGGGGATAACGTCACAGTAG                         GTCATAGTGCAGTATTACAAGGATGTACTGTTGAGGACGAAGCATTTGTTG
genomic: TCTTAGTGGAAAAGTCTTTCCAACCATCATTGGGGATAACGTCACAGTAGgtaaatatga ... cacttcacagGTCATAGTGCTGTATTACAAGGATGTACTGTTGAGGACGAAGCATTTGTTG
EST: gi|88844391|gb|CI005764.1|CI005764
EST:     ACCATCATTGGGGATAACGTCACAGTAG                         GTCATAGTGCTGTATTACAAGGATGTACTGTTGAGGACGAAGCATTTGTTG
genomic: ACCATCATTGGGGATAACGTCACAGTAGgtaaatatga ... cacttcacagGTCATAGTGCTGTATTACAAGGATGTACTGTTGAGGACGAAGCATTTGTTG

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: 75 (upstream exon), 75 (downstream exon)
Score: 104

TCTGGGACCAATATACAAGACAATTCTCTTGTCCATGTGGCAAAATCTAATCTTAGTGGAAAAGTCTTTCCAACCATCATTGGGGATAACGTCACAGTAGgtaaatatga ... cacttcacagGTCATAGTGCTGTATTACAAGGATGTACTGTTGAGGACGAAGCATTTGTTGGTATGGGGGCGACCCTGTTAGATGGTGTTGTCGTGGAAAAGCATGGGAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaacaatcattgtgaagttctgatgacatatacattctgaaataccacttcacagGTCATAGTGCTGTATTACAAGGATGTACTGTTGAGGACGAAGCATTTGTTGGTATGGGGGCGACCCTGTTAGATGGTGTTGTCGTGGAAAAGCATGGGAT
                 ttctgat  putative branch site (score: 104)
                                            ccacttc  putative PPT
                           atatacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagaataggcatgagcacatcttcctgcaaagatgttactcatgaaaacaatcattgtgaagttctgatgacatatacattctgaaataccacttcacagGTCATAGTGCTGTATTACAAGGATGTACTGTTGAGGACGAAGCATTTGTTGGTATGGGGGCGACCCTGTTAGATGGTGTTGTCGTGGAAAAGCATGGGAT

- - - -ggcatga
- - - - - - - gcacatc
- - - - - - - - - - - tcctgca
- - - - - - - - - - - - - - - - -tgttact
- - - - - - - - - - - - - - - - - - - - catgaaa
- - - - - - - - - - - - - - - - - - - - - - - -acaatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cattctg