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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagttcctggaccagtttatatctgtatgctttgatattataattttgtagcttcagtaaacatcttttaaggattacacagctagtgtcatgaaacatttaatgatggcccacacttgctttcgtatttcagCGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTTTAAGAAAAGACACGGCCCTTCCTTCTCCTGAATGGTCTTCGGATCATAT

Basic information

species Oryza sativa
transcript LOC_Os10g27230.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g27230.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G118467_T01 (Zea mays), 3'ss of exon 10
gtcagttcctgga--ccagtttatat---ctgtatgctttgatattataattttgtagcttcagtaaacatcttttaaggattacacagctagtgtcatgaaacatttaatgatggcccacacttgctttcgtatttcagCGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTTTAAGAAAAGACACGGCCCTTCCTTCTCCTGAATGGTCTTCGGATCATAT
||  || | ||||  |      |      | |||  |||| ||  |||   |||| |||||| ||| |    ||||      |  |     | |||  | |  | ||| ||||||||  |   ||| | ||   |||||||||| |||||| ||||||| || || ||||||||||||||||| ||||| |||||||||||||| || || || || ||||||||||| || ||||| ||
gttggtgcatggagactcacccacgcacacagtagactttaattctatg--tttgcagcttctgtatattcattttc----ctctaataagattgtgcttattcttttgatgatggcg-atgtttgttctc---tttcagCGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCTTAAGAAAAGACACAGCTCTCCCATCCCCTGAATGGTCATCAGATCACAT

upper sequence: LOC_Os10g27230.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G043509_T01 (Zea mays), 3'ss of exon 10
gtcagttcctggaccagtttatatctgtatgctttgatattataattttgtagcttcagtaaacatcttttaaggattacacagctagtgtcatgaaacatttaatgatggcccacacttgctttcgtatttcagCGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTTTAAGAAAAGACACGGCCCTTCCTTCTCCTGAATGGTCTTCGGATCATAT
                 | | | | || | ||||   |||    |||||      || | ||  |  ||  | | | ||       | |||  | |  | ||| || ||| || |   ||| | ||    ||||||||| || ||| ||||||| || || |||||||||||||||||||||||||||||||||||||| || ||||| ||||||| |||||| || ||||| ||
-----------------tctgtgtttgca-gcttctgtatctccatttt------tctggaataagattaaaggcacta-------attgtgcttattcttttgataatgacc-atgtttgttctc---cttcagCGGACTCCTTGACAGTGGATTCATTATTGGAACTTTTGGATGAGGAAAGTTTAAGAAAAGACACAGCTCTTCCATCTCCTGGATGGTCATCAGATCACAT

upper sequence: LOC_Os10g27230.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA09G15980.2 (Glycine max), 3'ss of exon 10
gtcagttcctggaccagtttatatctgtatgctttgatattataattttgtagcttcagtaaacatcttttaaggattacacagctagtgtcatgaaacatttaatgatggcccacacttgctttcgtatttcagCGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTTTAAGAAAAGACACGGCCCTTCCTTCTCCTGAATGGTCTTCGGATCATAT
                                  |||   |    || | |   ||   |||||||  | |  | ||       || || |||  |    ||| |||| |    | |  ||  ||    |||||||||||||||||   |||||||| || |||||  |  |||||||||| ||||| || || ||||| || |||||||| ||||||||||| || ||||| ||
---------------------------------gtgagcatggtgttatatcattttgataaacataatatctgtat-------cttgt-tcacaa----ttttatgaag----agatatgacttgtggtttcagCGGATTCATTGGTTGTGGAGTCATTATTGGAGTTGCTGGATGAGGAGAGTTTGAGGAAGGACACAGCACTTCCTTCACCTGAATGGTCCTCAGATCACAT

upper sequence: LOC_Os10g27230.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA02G26620.2 (Glycine max), 3'ss of exon 10
gtcagttcctggaccagtttatatctgtatgctttgatattataattttgtagcttcagtaaacatcttttaaggattacacagctagtgtcatgaaacatttaatgatggcccacacttgctttcgtatttcagCGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTTTAAGAAAAGACACGGCCCTTCCTTCTCCTGAATGGTCTTCGGATCATAT
                       |  | ||| | | |||| ||  |||  ||   | | ||    | | ||   | | |||       | | ||||||                | |  ||  ||    |||||||||||||||||   |||||||| || |||||  |  |||||||||| ||||| || || ||||| || |||||||| ||||||||||| || ||||| ||
----------------------gtgagcatggtgttatatcat--tttgataaacttaatatctgtatctt---ggtcacat------ttttatgaaa----------------agatatgacttgtggtttcagCGGATTCATTGGTTGTGGAGTCATTATTGGAGTTACTGGATGAGGAGAGTTTGAGGAAGGACACAGCACTTCCTTCACCTGAATGGTCCTCAGATCACAT

upper sequence: LOC_Os10g27230.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA03G36550.1 (Glycine max), 3'ss of exon 10
gtcagttcctggaccagtttatatctgtatgctttgatattataattttgtagcttcagtaaacatcttttaaggattacacagctagtgtcatgaaacatttaatgatggcccacacttgctttcgtattt-cagCGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTTTAAGAAAAGACACGGCCCTTCCTTCTCCTGAATGGTCTTCGGATCATAT
                                             | |  || |||        || |  | |   | | | |  ||   || |||  || ||  | |||        |  |||| || ||| ||||||||||||||   |||||||| |||||||| || ||||||||||||||||| || |||||||| || |||||||||||||||||||| || ||||||||
--------------------------------------------gtgtgatatcttgcaatgttatgtcattaatttgataaatttaacatcctgat-caattgtttatga--agtgataccttttgtgttttcagCGGATTCATTGGTTGTGGAGTCATTGTTGGAGCTATTGGATGAGGAAAGTTTGAGGAAAGACACAGCACTTCCTTCTCCTGAATGGTCCTCTGATCATAT

upper sequence: LOC_Os10g27230.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA19G39210.3 (Glycine max), 3'ss of exon 10
gtcagttcctggaccagtttatatctgtatgctttgatattataattttgtagcttcagtaaacatcttttaaggattacacagctagtgtcatgaaacatttaatgatggcccacacttgctttcgtatttcagCGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTTTAAGAAAAGACACGGCCCTTCCTTCTCCTGAATGGTCTTCGGATCATAT
                                     | | ||| | ||| |   | |    |    ||| ||  |||       ||   || |||  || ||  | |||        |  |||  || |||||||||||||||||   |||||||| ||| ||||  | ||||||||||||||||| || |||||||| || |||||||||||||||||||| || ||||||||
------------------------------------gtgtgata-tcttgcaatgttatgtcattaatttgaataatt-------taacatcctgat-cacttgtttatga--agtgatatcttgtgt-tttcagCGGATTCATTGGTTGTGGAGTCATTGCTGGAGTTATTGGATGAGGAAAGTTTGAGGAAAGACACAGCACTTCCTTCTCCTGAATGGTCCTCTGATCATAT

upper sequence: LOC_Os10g27230.3 (Oryza sativa), 3'ss of exon 11
lower sequence: AT3G58580.1 (Arabidopsis thaliana), 3'ss of exon 10
gtcagttcctggaccagtttatatctgtatgctttgatattataattttgtagcttcagtaaacatcttttaaggattacacagctagtgtcatgaaacatttaatgatggcccacacttgctttcgtatttcagCGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTTTAAGAAAAGACACGGCCCTTCCTTCTCCTGAATGGTCTTCGGATCATAT
                                     | | |  ||||| || || || |   | | |||| |  | ||||     | |  || |  | | |||||            |||  || |  ||||||||||| ||||    ||||| ||  | |||||| |  ||||||| ||  | |||||||||||||| || |||||||| || |||||||||||  |||| ||
------------------------------------gtttcaccatttt-taactccattgtccttgttttca--actacatcagaaataacaagtta-acttaattggaagatttttttgtgtttgggtttcagCGGATACATTAATGGTGGAATCTCTATTGGAATTACTGGATGAAGATGGATTAAGAAAAGACACAGCTCTTCCTTCCCCAGAATGGTCTTCTAATCACAT

upper sequence: LOC_Os10g27230.3 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv08s0007g07020.t01 (Vitis vinifera), 3'ss of exon 10
gtcagttcctggaccagtttatatctgtatgctttgatattataattttgtagcttcagtaaacatcttttaaggattacacagctagtgtcatgaaacatttaatgatggcccacacttgctttcgtatttcagCGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTTTAAGAAAAGACACGGCCCTTCCTTCTCCTGAATGGTCTTCGGATCATAT
|| |  |  |       | |   | || ||  |||  |  |||| |||  |  |    ||         ||   | ||   | | || ||   |  |  |||   | ||     | | |||        || |||| || || ||  | ||||| || ||||||||||| ||||||||||| || || ||||||||||| || ||||||||||| || ||||| || ||||||||
gtaatctttttcctacatgtcggtttgcatctttt--tcctatattttatttacacatgtgcttcatacttgtagtttgtgccgttattgatgtttaggattctctaataaataagatttgtg-----gttccagCCGACTCTTTAACGGTGGAATCATTGTTGGAACTCTTGGATGAGGATAGCTTGAGAAAAGACACAGCACTTCCTTCTCCGGAGTGGTCCTCTGATCATAT

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|86251336|gb|CI055469.1|CI055469
EST:     CAACTGCACACGAGATTTCACTGGAACGGTTGATTACATATTTTACACAG                         CGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTT
genomic: AAACTGCACACGAGATTTCACTGGAACGGTTGATTACATATTTTACACAGgtcagttcct ... cgtatttcagCGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTT
EST: gi|29613589|gb|CB618602.1|CB618602
EST:     AAACTGCACACGAGATTTCACTGGAACGGTTGATTACATATTTTACACAG                         CGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTT
genomic: AAACTGCACACGAGATTTCACTGGAACGGTTGATTACATATTTTACACAGgtcagttcct ... cgtatttcagCGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTT
EST: gi|88836259|gb|CI371364.1|CI371364
EST:     AACGGTTGATTACATATTTTACACAG                         CGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTT
genomic: AACGGTTGATTACATATTTTACACAGgtcagttcct ... cgtatttcagCGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTT
EST: gi|86537140|gb|CI177346.1|CI177346
EST:     AAACTGCACACGAGATTTCACTGGAACGGTTGATTACATATTTTACACAG                         CGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTT
genomic: AAACTGCACACGAGATTTCACTGGAACGGTTGATTACATATTTTACACAGgtcagttcct ... cgtatttcagCGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTT
EST: gi|29627416|gb|CB632427.1|CB632427
EST:     AAACTGCACACGAGATTTCACTGGAACGGTTGATTACATATTTTACACAG                         CGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTT
genomic: AAACTGCACACGAGATTTCACTGGAACGGTTGATTACATATTTTACACAGgtcagttcct ... cgtatttcagCGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTT
EST: gi|88320509|gb|CI523252.1|CI523252
EST:     CACTGGAACGGTTGATTACATATTTTACACAG                         CGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTT
genomic: CACTGGAACGGTTGATTACATATTTTACACAGgtcagttcct ... cgtatttcagCGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTT
EST: gi|89180086|gb|CI044365.1|CI044365
EST:     TGATTACATATTTTACACAG                         CGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTT
genomic: TGATTACATATTTTACACAGgtcagttcct ... cgtatttcagCGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTT
EST: gi|88219644|gb|CI219204.1|CI219204
EST:     AGACTGCACACGAGATTTCACTGGAACGGTTGATTACATATTTTACACAG                         CGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTT
genomic: AAACTGCACACGAGATTTCACTGGAACGGTTGATTACATATTTTACACAGgtcagttcct ... cgtatttcagCGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTT
EST: gi|88268411|gb|CI378346.1|CI378346
EST:     AAACTGCACACGAGATTTCACTGGAACGGTTGATTACATATTTTACACAG                         CGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTT
genomic: AAACTGCACACGAGATTTCACTGGAACGGTTGATTACATATTTTACACAGgtcagttcct ... cgtatttcagCGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTT
EST: gi|29676248|gb|CB672523.1|CB672523
EST:     AAACTGCACACGAGATTTCACTGGAACGGTTGATTACATATTTTACACAG                         CGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTT
genomic: AAACTGCACACGAGATTTCACTGGAACGGTTGATTACATATTTTACACAGgtcagttcct ... cgtatttcagCGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTT
EST: gi|29630215|gb|CB635224.1|CB635224
EST:     AAACTGCACACGAGATTTCACTGGAACGGTTGATTACATATTTTACACAG                         CGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTT
genomic: AAACTGCACACGAGATTTCACTGGAACGGTTGATTACATATTTTACACAGgtcagttcct ... cgtatttcagCGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTT
EST: gi|29623249|gb|CB628260.1|CB628260
EST:     AAACTGCACACGAGATTTCACTGGAACGGTTGATTACATATTTTACACAG                         CGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTT
genomic: AAACTGCACACGAGATTTCACTGGAACGGTTGATTACATATTTTACACAGgtcagttcct ... cgtatttcagCGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTT
EST: gi|89179877|gb|CI044156.1|CI044156
EST:     AAACTGCACACGAGATTTCACTGGAACGGTTGATTACATATTTTACACAG                         CGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTT
genomic: AAACTGCACACGAGATTTCACTGGAACGGTTGATTACATATTTTACACAGgtcagttcct ... cgtatttcagCGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTT

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: 71 (upstream exon), 65 (downstream exon)
Score: 30

GAGCACCAGCGGAGGAGGATGGACCCTGCAACAAATGAACCACTTTTCACAAACTGCACACGAGATTTCACTGGAACGGTTGATTACATATTTTACACAGgtcagttcct ... cgtatttcagCGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTTTAAGAAAAGACACGGCCCTTCCTTCTCCTGAATGGTCTTCGGATCATAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagctagtgtcatgaaacatttaatgatggcccacacttgctttcgtatttcagCGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTTTAAGAAAAGACACGGCCCTTCCTTCTCCTGAATGGTCTTCGGATCATAT
                   atttaat  putative branch site (score: 30)
                                     cttgctttc  putative PPT
            atgaaacatttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagttcctggaccagtttatatctgtatgctttgatattataattttgtagcttcagtaaacatcttttaaggattacacagctagtgtcatgaaacatttaatgatggcccacacttgctttcgtatttcagCGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTTTAAGAAAAGACACGGCCCTTCCTTCTCCTGAATGGTCTTCGGATCATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA