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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttacatcaacggataatcacatgaacctttttcttggtttccacctaactggtattgtctttccccagAGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAGCAAGAACCCTTATGGATACGGGTCACTTGACTCCACCAAGCAGAACGGA

Basic information

species Oryza sativa
transcript LOC_Os08g28730.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g28730.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G469523_T01 (Zea mays), 3'ss of exon 3
gtaagttttacatcaacggataatca-----catga----acctttttcttggtttccacctaactggtattgtctttccccagAGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAGCAAGAACCCTTATGGATACGGGTCACTTGACTCCACCAAGCAGAACGGA
||||||  || ||| | | |||||       |||||    |    ||| |||  |   |  | |      | ||||| | | ||||| ||||  || || || || |||||  | || |||||||||||||| ||||||||||||||||| || || |||| |||||| | ||||||||| || 
gtaagtcatatatcgaggtataatatgttatcatgacaaaatggctttattgtatattatatgatcaacttcgtcttcctctagAGCAAAATACGGTATTGAAGAGATGTGCCGCGACCAATGGAACTGGGCCAGCAAGAACCCTTATGGCTATGGATCACCTGACTCTATCAAGCAGAATGGT

upper sequence: LOC_Os08g28730.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA11G01940.2 (Glycine max), 3'ss of exon 5
-------------gtaagttttacatcaacggataatcacatgaacctttttcttggtttccacctaact----------ggtattgtctttccc--cagAGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAGCAAGAACCCTTATGGATACGGG--TCACTTG-ACTCCACCAAGCAGAACGGA
              |   |||||| | ||   ||  |   ||  || | |||     |||     |   |            | |  |||| |     || || |||| |||||| ||||| |||||  | ||||||||||| ||||||||||| ||||||||||| || ||   |||   | | ||||||  |   |||   
ttgtagtactttcatgcattttactttaaaaaattcttttattcacttcttttccaattttgtttttttttctttctcaaaatttcatcttacgtggtagGGCAAAATATGGCATTGATGAGATGTGCCGCGATCAATGGAATTGGGCTAGCAAAAACCCTTATGGCTATGGAGATCAGGAGGATTCCACC--GTTTAACTA-

upper sequence: LOC_Os08g28730.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA05G36850.1 (Glycine max), 3'ss of exon 8
--------------------------------gtaagttttacatcaacggataatcacatgaacctttttcttggtttccacctaactggtattgtctttccccagAGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAGCAAGAACCCTTATGGATACGGGTCACTTG---ACTCCACCAAGCAGAACGGA
                                | ||| ||| |   ||  | || |  |     ||||||||||  ||||   | || |  ||| | | | |   ||  | |||| | |||||||||| |||||  | ||||||||||| ||||||||||| ||||||||||| || ||  ||  ||   | ||| ||||          
atgttttcgtcttctgataaataaaaaaatgggcaaggttt-ctctaattgttatttccgctc-cctttttctttttttctcacaaatt--tatcgccgtgc---agGACTAAATATAGCATCGATGATATGTGCCGCGATCAATGGAATTGGGCTAGCAAAAACCCTTATGGCTATGGTGCATCTGCAGATTCCTCCAATTGATGT---

upper sequence: LOC_Os08g28730.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA01G43540.2 (Glycine max), 3'ss of exon 7
-----------------------------------------------------------------------------------------------------------gtaagttttacatcaacgga-----taatcacatga-----acctttttcttggtttccacctaactggtattgtctttccccagAGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAGCAAGAACCCTTATGGATACGGGTCACTTGACTCCACCAAGCAGAACGGA-
                                                                                                            |   |||||| |  |   |     || |||| |       |  ||| | ||  ||| |  ||||    |  | |       ||| || |||| |||||| ||||| |||||  | ||||||||||| ||||||||||| ||||||||||| || ||    |  | ||||||| |  | | |    
gtaagtgttaattggctcctcctcctgaatatcctagatagataataaaagcttaatagtatgaaacaagtttttcttgataaattctggttttgtgtagtactttcatgcattttacttttaaaaaacttttattcacttcttttccaattttgttttttttttcttctaaaaattcatcttacgtggcagGGCAAAATATGGCATTGATGAGATGTGCCGTGATCAATGGAATTGGGCTAGCAAAAACCCTTATGGCTATGGAGATCAGGGCTCCACCGATTA-ACCACTT

upper sequence: LOC_Os08g28730.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT1G64440.1 (Arabidopsis thaliana), 3'ss of exon 8
----------------gtaagt-tttacatcaacggataatcacatgaaccttttt---cttggtttccacctaactggtatt-----gtctttccccagAGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAGCAAGAACCCTTATGGATACGGGTCACTTGACTCCACCAAGCAGAACGGA--
                   | | |||  || || | ||  |  |||| |||| |||   | | || || |   |    | |        ||| |   ||| || || ||||| ||||| ||||||||||||||||| ||||||||||| ||||| || ||||  || ||||| ||  || ||   ||  | || |||| |  
gtaagtaaaagacccaacgaatgtttttattaa-gtatg-tatcatggacctgttttggcatagtctctaagaatgaagaaactcaaaatctgtggacagGGCAAATTTTGGAATCGAAGAAATGTGTAGGGATCAGTGGAACTGGGCAAGCAACAATCCTTTCGGTTACGGTTC--TTCACCAAACTCAACATAACGAAGC

upper sequence: LOC_Os08g28730.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv02s0025g01580.t01 (Vitis vinifera), 3'ss of exon 8
----------------------gtaagttttacatcaacgg--ataatca--catgaacctttttcttggtttccacctaactggtattgtctttccccagAGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAGCAAGAACCCTTATGGATACGGGTCACTTGACTCCACCAAGCAGAACGGA-
                       |  |||| | |     ||   ||| ||  ||||||  |   ||||  | ||     || | || |  | |  |  ||| || || | |||||||   || |||||| |||| |||||||| ||||| ||||||||||| ||||| ||||  ||  |   |  ||| |  |  || |   
aattagaacataagtgggaagatttggtttgaaaatcttggttgtaaccatacatgaaaatgagtctta-tgtcacttcaatttgtgtgatgtccctgcagGGCCAAGTATGGCATCAGCGAGATGTGTCGGGACCAATGGAATTGGGCCAGCAAGAACCCCTATGGCTACGAATCG-TCCCCAACACAAGACTAAAGGCTG

upper sequence: LOC_Os08g28730.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv02s0025g01560.t01 (Vitis vinifera), 3'ss of exon 8
------------gtaagttttacatcaacggataatcacatgaacctttttcttggtttccacctaactgg----tattgtcttt---------ccccagAGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAGCAAGAACCCTTATGGATACGGGTCACTTGACTCCACCAAGCAGAACGGA
            | |||| ||   |  |||  ||| ||  | |    |        | || |   |  |||     ||| | |||         |  ||| || || |  || |||  ||| |||||| |||| || ||||||||||| ||||||||||| ||||| ||||  |||       | ||  |  | |||   
tgattttgtttggaaagtcttggttgtacgtgtaaccatgtaagatgtgggaaaaatatcaatgaacatggaaatcattctttttgtgatgtccctgcagGGCAAAGTACGGGATCAGTGAGATGTGTCGGGACCAGTGGAACTGGGCCAGCAAGAACCCATATGGCTACGAATCATCCCCAACAACAGACTAAAACATC

upper sequence: LOC_Os08g28730.1 (Oryza sativa), 3'ss of exon 8
lower sequence: EFJ35039 (Selaginella moellendorffii), 3'ss of exon 8
gtaagttttacatcaacggataatcacatgaacctttttcttggtttccacctaactggtat-tgtctttccccagAGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAGCAAGAACCCTTATGGATACGGGTCACTTGACTCCACCAAGCAGAACGGA
||||||     |||      ||      |   | ||||  |||| || ||  |   ||       ||    | ||| || |  | ||| ||||||||||||   |||||||||||||||||||| |||||||| || || || ||||  |     ||    | ||| || | ||  
gtaagt-----atctttcattagaactgttccctttttgtttggcttacaagttcatgtcccacttcgcatcgcagGGCCAGGTATGGTATCGATGAAATGGCCAGGGATCAATGGAACTGGGCCAGCAAGAATCCATACGGCTACGTCTACGAAGAGGAGAACAATCACACCGAG

upper sequence: LOC_Os08g28730.1 (Oryza sativa), 3'ss of exon 8
lower sequence: EFJ17435 (Selaginella moellendorffii), 3'ss of exon 8
gtaagttttacatcaacggataatcacatgaacctttttcttggtttccacctaactggtat-tgtctttccccagAGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAGCAAGAACCCTTATGGATACGGGTCACTTGACTCCACCAAGCAGAACGGA
||||||     |||      ||      | | | ||||  |||| || ||  |   ||       ||    | ||| || |  | ||| ||||||||||||   |||||||||||||||||||| |||||||| || || || ||||  |     ||    | ||| || | ||  
gtaagt-----atctttcattagaactgttacctttttgtttggcttacaagttcatgtcccacttcgcatcgcagGGCCAGGTATGGTATCGATGAAATGGCCAGGGATCAATGGAACTGGGCCAGCAAGAATCCATACGGCTACGTCTACGAAGAGGAGAACAATCACACCGAG

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|29676236|gb|CB672511.1|CB672511
EST:     GAGATTCTATTTTCATTACCTGCTAAAGCAGAGAAGGAACTCAACTGGAA                         AGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAG
genomic: GAGATTCTATTTTCATTACCTGCTAAAGCAGAGAAGGAACTCAACTGGAAgtaagtttta ... ctttccccagAGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAG
EST: gi|86256062|gb|CI007778.1|CI007778
EST:     GAGATTCTATTTTCATTACCTGCTAAAGCAGAGAAGGAACTCAACTGGAA                         AGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAG
genomic: GAGATTCTATTTTCATTACCTGCTAAAGCAGAGAAGGAACTCAACTGGAAgtaagtttta ... ctttccccagAGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAG
EST: gi|29644199|gb|CB649206.1|CB649206
EST:     GAGATTCTATTTTCATTACCTGCTAAAGCAGAGAAGGAACTCAACTGGAA                         AGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAG
genomic: GAGATTCTATTTTCATTACCTGCTAAAGCAGAGAAGGAACTCAACTGGAAgtaagtttta ... ctttccccagAGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAG
EST: gi|29673347|gb|CB669622.1|CB669622
EST:     GAGATTCTATTTTCATTACCTGCTAAAGCAGAGAAGGAACTCAACTGGAA                         AGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAG
genomic: GAGATTCTATTTTCATTACCTGCTAAAGCAGAGAAGGAACTCAACTGGAAgtaagtttta ... ctttccccagAGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAG
EST: gi|88974332|gb|CI020005.1|CI020005
EST:     TTTCATTACCTGCTAAAGCAGAGAAGGAACTCAACTGGAA                         AGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAG
genomic: TTTCATTACCTGCTAAAGCAGAGAAGGAACTCAACTGGAAgtaagtttta ... ctttccccagAGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAG
EST: gi|58657907|gb|CK046587.1|CK046587
EST:     GAGATTCTATTTTCATTACCTGCTAAAGCAGAGAAGGAACTCAACTGGAA                         AGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAG
genomic: GAGATTCTATTTTCATTACCTGCTAAAGCAGAGAAGGAACTCAACTGGAAgtaagtttta ... ctttccccagAGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAG
EST: gi|87024689|gb|CI259404.1|CI259404
EST:     AGAGAAGGAACTCAACTGGAA                         AGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAG
genomic: AGAGAAGGAACTCAACTGGAAgtaagtttta ... ctttccccagAGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAG
EST: gi|58686188|gb|CK074875.1|CK074875
EST:     GAGATTCTATTTTCATTACCTGCTAAAGCAGAGAAGGAACTCAACTGGAA                         AGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAG
genomic: GAGATTCTATTTTCATTACCTGCTAAAGCAGAGAAGGAACTCAACTGGAAgtaagtttta ... ctttccccagAGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAG
EST: gi|51946130|gb|CV152471.1|CV152471
EST:     GAGATTCTATTTTCATTACCTGCTAAAGCAGAGAAGGAACTCAACTGGAA                         AGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAG
genomic: GAGATTCTATTTTCATTACCTGCTAAAGCAGAGAAGGAACTCAACTGGAAgtaagtttta ... ctttccccagAGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAG
EST: gi|86423405|gb|CI062166.1|CI062166
EST:     GAGATTCTATTTTCATTACCTGCTAAAGCAGAGAAGGAACTCAACTGGAA                         AGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAG
genomic: GAGATTCTATTTTCATTACCTGCTAAAGCAGAGAAGGAACTCAACTGGAAgtaagtttta ... ctttccccagAGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAG
EST: gi|29682808|gb|CB679083.1|CB679083
EST:     GAGATTCTATTTTCATTACCTGCTAAAGCAGAGAAGGAACTCAACTGGAA                         AGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAG
genomic: GAGATTCTATTTTCATTACCTGCTAAAGCAGAGAAGGAACTCAACTGGAAgtaagtttta ... ctttccccagAGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAG
EST: gi|29673348|gb|CB669623.1|CB669623
EST:     GAGATTCTATTTTCATTACCTGCTAAAGCAGAGAAGGAACTCAACTGGAA                         AGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAG
genomic: GAGATTCTATTTTCATTACCTGCTAAAGCAGAGAAGGAACTCAACTGGAAgtaagtttta ... ctttccccagAGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAG
EST: gi|7332395|gb|AU085741.1|AU085741
EST:     GATTCTATTTTTCATTACCTGCTAAAGCAGAGAAGGAACTCCAACTGGAA                         AGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTA
genomic: GATTCTA-TTTTCATTACCTGCTAAAGCAGAGAAGGAACT-CAACTGGAAgtaagtttta ... ctttccccagAGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTA

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: 50 (upstream exon), 46 (downstream exon)
Score: 11

AAAATTCCTCTGATTATTGGCCCAAGACGCCCTGGTGATGCGGAGATTCTATTTTCATTACCTGCTAAAGCAGAGAAGGAACTCAACTGGAAgtaagtttta ... ctttccccagAGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAGCAAGAACCCTTATGGATACGGGTCACTTGACTCCACCAAGCAGAACGGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatcacatgaacctttttcttggtttccacctaactggtattgtctttccccagAGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAGCAAGAACCCTTATGGATACGGGTCACTTGACTCCACCAAGCAGAACGGA
                             acctaac  putative branch site (score: 11)
                                       tattgtctttcccc  putative PPT
              tttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttttacatcaacggataatcacatgaacctttttcttggtttccacctaactggtattgtctttccccagAGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAGCAAGAACCCTTATGGATACGGGTCACTTGACTCCACCAAGCAGAACGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC