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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgttttgtttcttcataatcatcagacttggaacatttcatataatgcatttaaggcacttagctaaacattgttcatttcaggcaaaacctttgtaaattaattttctttacatttttcatgaaatcagGCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCCAAGAGAAAGCCGAGTGGTGGCATCGAGTCACTCCGTGCCATCCCATGGA

Basic information

species Oryza sativa
transcript LOC_Os08g27840.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g27840.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA12G35840.1 (Glycine max), 3'ss of exon 8
gtgagtgttttgtttcttcataatcatcagacttggaacatttcatataatgcatttaaggc---acttagctaaacattgttcatttcaggcaaa--acctttgtaaattaattttcttta-catttttcatgaaatcagGCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCCAAGAGAAAGCCGAGTGGTGGCATCGAGTCACTCCGTGCCATCCCATGGA
                                          || | ||| |     |||     | ||    |   | |  |||||| ||  |||  || |||  |   | |   ||  |  ||  |||  |  |   |||| ||||||||| |||||||||||||||||||||| |||||  | ||| | |||||||  || ||||| ||||| ||  |||| ||||| || || ||||
-----------------------------------------gtcctttaaaggtcccaagatctaattttatcatcaacttctcatttaagtaaaatgacatttaaatgatgacaatcactgtcaactttgtttcatgtagGCTACACCAGAGTTGGAGTATGGAAGGATGAATATTGGAAGTCGACCAGCAAAGAGAAGACCTAGTGGAGGCATTGAAACACTGCGTGCAATACCTTGGA

upper sequence: LOC_Os08g27840.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA13G34560.1 (Glycine max), 3'ss of exon 9
gtgagtgttttgtttcttcataatcatcagacttggaacatttcatataatgcatttaaggcacttagctaaacattgttcatttcaggcaaaacctttgtaaattaattttctttacatttttcatgaaatcagGCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCCAAGAGAAAGCCGAGTGGTGGCATCGAGTCACTCCGTGCCATCCCATGGA
                            || | |  ||     |  |  ||  | || |  ||   |  |     ||  | | || |     ||    ||  ||| | | |    |   ||  |||||     |||| ||||| ||| ||||||||||||||||||| || |||||  | ||| | ||||||||||| ||||| ||||| ||  |||| ||||| || || ||||
----------------------------agtccttaaaaggccccca-gatataattgaatcatcaacttctctgttagtaaattgatatttaaatgatgacaatcactgtcaactttgtt--tcatg----tagGCTACACCGGAGTTGGAGTATGGAAGGATGAACATTGGAAGTCGACCAGCAAAGAGAAAGCCTAGTGGAGGCATTGAAACACTGCGTGCAATACCTTGGA

upper sequence: LOC_Os08g27840.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT3G14940.1 (Arabidopsis thaliana), 3'ss of exon 9
gtgagtgttttgtttcttcataatcatcagacttggaacatttcatataatgcatttaaggcacttagctaaa-cattgttcatttcaggcaaaacctttgtaaatta-attttctttacatttttcatgaaat---cagGCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCCAAGAGAAAGCCGAGTGGTGGCATCGAGTCACTCCGTGCCATCCCATGGA
                                                          | | | | |   | | || |    ||||||  ||||   |||||   ||  |  | | | | |   ||  |    |   ||||| || || ||| ||||||||||| | |||||||| ||||| || || || ||| |||| || || ||||| ||||| || |||||||| ||||||||||
--------------------------------------------------------gtaagtattcattcatatcaatccaaatttcac-caaagtttttgtgtgttttaagtacctaaaaccgttggtttggtttgcagGCTACTCCGGAGCTGGAGTATGGACGTATGAATATTGGAAGTAGACCTTCAAAGCGAAAACCAAGCGGTGGGATCGAATCTCTCCGTGCAATCCCATGGA

upper sequence: LOC_Os08g27840.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT2G42600.1 (Arabidopsis thaliana), 3'ss of exon 9
gtgagtgttttgtttcttcataatcatcagacttggaacatttcatataatgcatttaaggcacttagctaaacattgttcatttcaggcaaaacctttgtaaattaattttctttacatttttcatgaaatcagGCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCCAAGAGAAAGCCGAGTGGTGGCATCGAGTCACTCCGTGCCATCCCATGGA
                                  | ||  | | |   |   || |||   | ||    ||||||   |  | || |   | |   | |       | ||    ||    |||  || |    |||||||||||||| | ||||||||||||||||| ||||||||| | ||||| ||  | || || || || || |||||||| || ||||| ||||| ||||
----------------------------------gtaagttcttaaccagctcaattactcctctc--ttaaacaaattgtagttaaaaaagagagtcta------agttcaggtttgggtttgtatta---tagGCAACACCAGAGCTCGAGTATGGAAGGATGAACATAGGAAGCCGACCATCAAAACGTAAACCAAGCGGAGGAATCGAGTCGCTGCGTGCAATCCCGTGGA

upper sequence: LOC_Os08g27840.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv12s0028g02180.t01 (Vitis vinifera), 3'ss of exon 8
gtgagtgttttgtttcttcataatcatcagacttggaacatttcatataatgcatttaaggcacttagctaaacattgttcatttcaggcaaaacctttgtaaattaattttctttacatttttcatgaaatcagGCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCCAAGAGAAAGCCGAGTGGTGGCATCGAGTCACTCCGTGCCATCCCATGGA
                          ||| | || |    || ||| ||   ||  |||  | || |||    ||||  ||| |        ||   | || |  |  | || | |  |||  |  | ||  |||||||| |||||| ||||||||||  ||||||| || |||||  | ||||| ||  ||||||| ||||| ||||| ||||||||||| || ||||| ||||
--------------------------tcataatttg---cttgcattta---caaataattc-ctgagccctgcatttctcactgtgaaggcaataatggtga--tggtattatctctattccttttaaatgcagGCAACTCCAGAGTTGGAGTATGGCCGGATGAACATTGGAAGTCGTCCATCAAAACGAAAGCCAAGTGGGGGCATTGAGTCACTCCGCGCAATCCCCTGGA

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|58695193|gb|CK083880.1|CK083880
EST:     ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTT                         GCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCC
genomic: ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTTgtgagtgttt ... atgaaatcagGCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCC
EST: gi|14571360|gb|BI118728.1|BI118728
EST:     ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTT                         GCAACACCAGAGATGGAGTATGGAAGGATGAACATAGGAAGCAGGCCATCC
genomic: ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTTgtgagtgttt ... atgaaatcagGCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCC
EST: gi|25778121|gb|CA752873.1|CA752873
EST:     ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTT                         GCAACACCAGAGATGGAGTATGGAAGGATGAACATAGGAAGCAGGCCATCC
genomic: ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTTgtgagtgttt ... atgaaatcagGCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCC
EST: gi|5667216|gb|AU077502.1|AU077502
EST:     ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTT                         GCAACACCAGAGATGGAGTATGGAAGGATGAATATANGAAGCAGGCCATCC
genomic: ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTTgtgagtgttt ... atgaaatcagGCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCC
EST: gi|25778152|gb|CA752904.1|CA752904
EST:     ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTT                         GCAACACCAGAGATGGAGTATGGAAGGATGAACATAGGAAGCAGGCCATCC
genomic: ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTTgtgagtgttt ... atgaaatcagGCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCC
EST: gi|42591805|gb|CK738291.1|CK738291
EST:     ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTT                         GCAACACCAGAGATGGAGTATGGAAGGATGAACATAGGAAGCAGGCCATCC
genomic: ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTTgtgagtgttt ... atgaaatcagGCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCC
EST: gi|33799325|gb|CF325521.1|CF325521
EST:     ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTT                         GCAACACCAGAGATGGAGTATGGAAGGATGAATAT
genomic: ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTTgtgagtgttt ... atgaaatcagGCAACACCAGAGATGGAGTATGGAAGGATGAATAT
EST: gi|29672056|gb|CB668331.1|CB668331
EST:     ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTT                         GCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCC
genomic: ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTTgtgagtgttt ... atgaaatcagGCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCC
EST: gi|27547042|gb|CA765088.2|CA765088
EST:     ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTT                         GCAACACCAGAGATGGAGTATGGAAGGATGAACATAGGAAGCAGGCCATCC
genomic: ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTTgtgagtgttt ... atgaaatcagGCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCC
EST: gi|58667732|gb|CK056418.1|CK056418
EST:     ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTT                         GCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCC
genomic: ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTTgtgagtgttt ... atgaaatcagGCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCC
EST: gi|29660927|gb|CB657202.1|CB657202
EST:     ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTT                         GCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCC
genomic: ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTTgtgagtgttt ... atgaaatcagGCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCC

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: 65

AGAATGGCGTGCTCTGCTTGATGAGATGGCTGTGGTGGCTACAAAGGAATACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTTgtgagtgttt ... atgaaatcagGCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCCAAGAGAAAGCCGAGTGGTGGCATCGAGTCACTCCGTGCCATCCCATGGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttcaggcaaaacctttgtaaattaattttctttacatttttcatgaaatcagGCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCCAAGAGAAAGCCGAGTGGTGGCATCGAGTCACTCCGTGCCATCCCATGGA
                      aattaat  putative branch site (score: 65)
                                       tttttcat  putative PPT
                tttgtaaattaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgttttgtttcttcataatcatcagacttggaacatttcatataatgcatttaaggcacttagctaaacattgttcatttcaggcaaaacctttgtaaattaattttctttacatttttcatgaaatcagGCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCCAAGAGAAAGCCGAGTGGTGGCATCGAGTCACTCCGTGCCATCCCATGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA