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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaattgatagtactatttggttatgctttggactatttgttttcgaacatttctataaagtattcacttgttttgaaatgaatgaacaaattcactcctttgcaaatgtgtgaacatgataacctcaatttttttctttactgtagGCAAGAATTAGTCTTCTTGGATAATGAGATCGTGTTCAATGAGGCCGTCATTGAGGAGAGGGATCAGGGAATACAAGAAATTCAGCACCAAATTACTGAA

Basic information

species Oryza sativa
transcript LOC_Os01g15110.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g15110.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G120115_T01 (Zea mays), 3'ss of exon 4
gtgaattgatagtactatttggttatgctttggactatttgttttcgaacatttctataaagtattcacttgttttgaaatgaatgaacaaattcactcctttgcaaatgtgtgaacatgataacctcaatttttttctttactgtagGCAAGAATTAGTCTTCTTGGATAATGAGATCGTGTTCAATGAGGCCGTCATTGAGGAGAGGGATCAGGGAATACAAGAAATTCAGCACCAAATTACTGAA
                                     ||||||| |         ||||||  ||  |    ||||       |      | ||   |  |||   ||| |   ||  || |||  ||||  ||||  |||||  |||||| || || ||||||||||| ||||| || ||||||||||||||| ||||||||||||||||||||||||||||||| ||||| |||||||| ||||||
------------------------------------ctttgtttgca--------tataaaa-atcgagacattttccctcctacaggtcattt---ttttttctgaatatcccaaggtgctaatttcaaacttttaatttaccatagGCAGGAGTTGGTCTTCTTGGACAATGAAATAGTGTTCAATGAGGCCATCATTGAGGAGAGGGATCAGGGAATACAAGAGATTCAACACCAAATCACTGAA

upper sequence: LOC_Os01g15110.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G017329_T01 (Zea mays), 3'ss of exon 4
gtgaattgatagtactatttggttatgctttggactatttgttttcgaacatttctataaagtattcacttgttttgaaatgaatgaacaaattcactcctttgcaaatgtgtgaacatgataacctcaatttttttctttactgtagGCAAGAATTAGTCTTCTTGGATAATGAGATCGTGTTCAATGAGGCCGTCATTGAGGAGAGGGATCAGGGAATACAAGAAATTCAGCACCAAATTACTGAA
                                     || |||| | |        || |   |||  |     |||   |  |||       ||| |  | ||  |||   | ||  || |||  ||||  ||||  |||||  |||||| || || ||||||||||||||||| |||||||||||||||||| ||||||||||||||||||||||||||||||| |||||||||||||| ||||||
------------------------------------cttcgtttgcaatgtcaagaatgagacattttccctccttg---tacatg-------tcatttttctg--aatacctcaaggtgctaatttcaaacttttgatttacaatagGCAGGAGTTGGTCTTCTTGGATAATGAAATCGTGTTCAATGAGGCCATCATTGAGGAGAGGGATCAGGGAATACAAGAGATTCAGCACCAAATCACTGAA

upper sequence: LOC_Os01g15110.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G015509_T01 (Zea mays), 3'ss of exon 3
gtgaattgatagtactatttggttatgctttggactatttgttttcgaacatttctataaagtattcacttgttttgaaatgaatgaacaaattcactcctttgcaaatgtgtgaacatgataacctcaatttttttctttactgtagGCAAGAATTAGTCTTCTTGGATAATGAGATCGTGTTCAATGAGGCCGTCATTGAGGAGAGGGATCAGGGAATACAAGAAATTCAGCACCAAATTACTGAA-------------------------
                                      |  |||||   ||| ||   ||| |    || |  ||| |  ||        |      |  | || |    ||| |   || |||| |    | |  || || ||  |  ||     |||||||||||||||||| ||       |||        |  |||||||||||||||||||||||||||| |||||||||||||||||||||                         
--------------------------------------tcattttc---catgtca--aaaatcagaaccttcttttacctg------ttatcctttttgtctgtattcctgtaag-gtgctaactt----tgtactccttgcttcaacca-----tagTCTTCTTGGATAATGCGA-------CAAC-------TTGTTGAGGAGAGGGATCAGGGAATACAAGAGATTCAGCACCAAATTACTGAAGTAAACGAAATTTTCAAAGATCTTG

upper sequence: LOC_Os01g15110.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA16G13410.1 (Glycine max), 3'ss of exon 4
gtgaattgatagtactatttggttatgctttggactatttgttttcgaacatttctataaa-gtattcacttgttttgaaatgaatgaacaaattcactcctttgcaaatgtgtgaacatgataacctcaatttttttctttactgtagGCAAGAATTAGTCTTCTTGGATAATGAGATCGTGTTCAATGAGGCCGTCATTGAGGAGAGGGATCAGGGAATACAAGAAATTCAGCACCAAATTACTGAA
                                               |  |  |  | ||  | ||||| || | ||   |  |||   ||||||| |  | |||||  | | | | ||   || |       || ||| |  ||| ||||| ||  |  | ||||| ||||||||||| |  |||||||||||  |||||||||| ||||| || || || |||||||| ||||| ||||||  ||||
----------------------------------------------aagtagatgaacaactgaattcatttatgttatta-aaattttcaaattctccacattgcat-tatttcagcaccttagctattgcattattcat-gctgcagGCAGGAGGTTTTATTCTTAGATAATGAGATTGCCTTCAATGAGGCTATCATTGAGGAAAGGGAGCAAGGCATTCAAGAAATACAGCAGCAAATTGGTGAA

upper sequence: LOC_Os01g15110.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT4G17730.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgaattgatagtactatttggttatgctttggactatttgttttcgaacatttctataaagtattcacttgttttgaaatgaatgaacaaattcactcctttgcaaatgtgtgaacatgataacctcaatttttttctttactgtagGCAAGAATTAGTCTTCTTGGATAATGAGATCGTGTTCAATGAGGCCGTCATTGAGGAGAGGGATCAGGGAATACAAGAAATTCAGCACCAAATTACTGAA
                                                                ||   || |   || |    ||  ||  ||   ||  |||   ||| || | | |  | |      | || || |||  || || |||||| | ||  | ||||| |||||||| | |||||||||||| || |||||||| || || || || ||||||||||||||||| ||||||   || 
---------------------------------------------------------------gttagtttatacagacaatggtgtccatctttgttcggttg---atgagttatc-tattgattggtttgttgttttttgttgcagACAAGAACTTGTACTGTTGGACAATGAGATTGCGTTCAATGAGGCTGTTATTGAGGAAAGAGAGCAAGGGATACAAGAAATTCAGCAGCAAATTGGCGAG

upper sequence: LOC_Os01g15110.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv02s0012g01850.t01 (Vitis vinifera), 3'ss of exon 4
gtgaattgatagtactatttggttatgctttggactatttgttttcgaacatttctataaagtattcacttgttttgaaatgaatgaacaaattcactcctttgcaaatgtgtgaacatgataacctcaatttttttctttactgtagGCAAGAATTAGTCTTCTTGGATAATGAGATCGTGTTCAATGAGGCCGTCATTGAGGAGAGGGATCAGGGAATACAAGAAATTCAGCACCAAATTACTGAA
                                           |  | ||||  |  || | |||   | | | | |  || || ||| |  |||     ||   | |||      |     |||    |  |  || | | ||| || || ||  |  | || ||||| |||||||| || |||||||||||  ||||||| || ||||| ||||||||||||||||| ||||||||||||   || 
---------------------------------------aaactgggcacatgccc-tacattatat-catttctaggcattaa-gaataggttc-----ttctaatatgctctctcccctaaactattagatgatt-tgtgctgcagACAGGAGGTCTTGTTGTTGGACAATGAGATTGTCTTCAATGAGGCTATCATTGAAGAAAGGGAGCAGGGAATACAAGAAATCCAGCACCAAATTGGCGAG

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|300216044|gb|HO088670.1|HO088670
EST:     GGTGCTGAT-AGTTGGCTGAGCAACGCACGGCGCTTCTAGAATCAAGAAG                         GCAAGAATTAGTCTTCTTGGATAATGAGATCGTGTTCAATGAGGCCGTCAT
genomic: GGTGCTGATAAGTTGGCTGAGCAACGCACGGCGCTTCTAGAATCAAGAAGgtgaattgat ... tttactgtagGCAAGAATTAGTCTTCTTGGATAATGAGATCGTGTTCAATGAGGCCGTCAT
EST: gi|29666448|gb|CB662723.1|CB662723
EST:     GGTGCTGATAAGTTGGCTGAGCAACGCACGGCGCTTCTAGAATCAAGAAG                         GCAAGAATTAGTCTTCTTGGATAATGAGATCGTGTTCAATGAGGCCGTCAT
genomic: GGTGCTGATAAGTTGGCTGAGCAACGCACGGCGCTTCTAGAATCAAGAAGgtgaattgat ... tttactgtagGCAAGAATTAGTCTTCTTGGATAATGAGATCGTGTTCAATGAGGCCGTCAT
EST: gi|27578001|gb|CB000696.1|CB000696
EST:     GGTGCTGATAAGTTGGCTGAGCAACGCACGGCGCTTCTAGAATCAAGAAG                         GCAAGAATTAGTCTTCTTGGATAATGAGATCGTGTTCAATGAGGCCGTCAT
genomic: GGTGCTGATAAGTTGGCTGAGCAACGCACGGCGCTTCTAGAATCAAGAAGgtgaattgat ... tttactgtagGCAAGAATTAGTCTTCTTGGATAATGAGATCGTGTTCAATGAGGCCGTCAT
EST: gi|29662791|gb|CB659066.1|CB659066
EST:     GGTGCTGATAAGTTGGCTGAGCAACGCACGGCGCTTCTAGAATCAAGAAG                         GCAAGAATTAGTCTTCTTGGATAATGAGATCGTGTTCAATGAGGCCGTCAT
genomic: GGTGCTGATAAGTTGGCTGAGCAACGCACGGCGCTTCTAGAATCAAGAAGgtgaattgat ... tttactgtagGCAAGAATTAGTCTTCTTGGATAATGAGATCGTGTTCAATGAGGCCGTCAT
EST: gi|29662790|gb|CB659065.1|CB659065
EST:     GGTGCTGATAAGTTGGCTGAGCAACGCACGGCGCTTCTAGAATCAAGAAG                         GCAAGAATTAGTCTTCTTGGATAATGAGATCGTGTTCAATGAGGCCGTCAT
genomic: GGTGCTGATAAGTTGGCTGAGCAACGCACGGCGCTTCTAGAATCAAGAAGgtgaattgat ... tttactgtagGCAAGAATTAGTCTTCTTGGATAATGAGATCGTGTTCAATGAGGCCGTCAT
EST: gi|218500481|gb|FG960261.1|FG960261
EST:     GGTGCTGATAAGTTGGCTGAGCAACGCACGGCGCTTCTAGAATCAAGAAG                         GCAAGAATTAGTCTTCTTGGATAATGAGATCGTGTTCAATGAGGCCGTCAT
genomic: GGTGCTGATAAGTTGGCTGAGCAACGCACGGCGCTTCTAGAATCAAGAAGgtgaattgat ... tttactgtagGCAAGAATTAGTCTTCTTGGATAATGAGATCGTGTTCAATGAGGCCGTCAT

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: 72 (upstream exon), 75 (downstream exon)
Score: 119

CTATAACTCGAGCGAGGTGAACAATGGTGCTGATAAGTTGGCTGAGCAACGCACGGCGCTTCTAGAATCAAGAAGgtgaattgat ... tttactgtagGCAAGAATTAGTCTTCTTGGATAATGAGATCGTGTTCAATGAGGCCGTCATTGAGGAGAGGGATCAGGGAATACAAGAAATTCAGCACCAAATTACTGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcactcctttgcaaatgtgtgaacatgataacctcaatttttttctttactgtagGCAAGAATTAGTCTTCTTGGATAATGAGATCGTGTTCAATGAGGCCGTCATTGAGGAGAGGGATCAGGGAATACAAGAAATTCAGCACCAAATTACTGAA
                         tgataac  putative branch site (score: 119)
                               cctcaatttttttctt  CT-rich tract
                                 tcaatttttttcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaattgatagtactatttggttatgctttggactatttgttttcgaacatttctataaagtattcacttgttttgaaatgaatgaacaaattcactcctttgcaaatgtgtgaacatgataacctcaatttttttctttactgtagGCAAGAATTAGTCTTCTTGGATAATGAGATCGTGTTCAATGAGGCCGTCATTGAGGAGAGGGATCAGGGAATACAAGAAATTCAGCACCAAATTACTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA