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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagattgctagactacttacaaacattcttgcactttccatgaacatttgacatgctgcagataacatcatttctaaacattgttgcttgcatttttcagGGACATAACAACCACATTTCCCAGTTTTGTATTCAATTCTGAGGTTGATGATCTCGTCACATGATCGTGTTTCTGTTACCGGTGTACAGTTAACAAAAAC

Basic information

species Oryza sativa
transcript LOC_Os10g41510.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g41510.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G015324_T05 (Zea mays), 3'ss of exon 7
tagattgctagactacttacaaacattcttgcactttccatgaacatttgacatgctgcagataac-atcatttctaaacattgttgcttgcatttttcagGGACATAAC-AACCACATTTCCCAGTTTTGTATTCAATTCTGAGGTTGATGATCTCGTCACATGATCGTGTTTCTGTTACCGGTGTACAGTTAACAAAAAC---------
           |  | | |   ||||     ||   | |   | | ||     |    | ||   | || || ||   || |     |     | | || |    |||   ||| |      || ||   |  ||       ||| ||  |   ||| |  ||| || |  |    | ||      | | | || ||  ||          
---------caataattcagggacatcacaacaacattccccagctttgtgtttaactctgaagtcgatgatctcgtcacgtgaccacgattttctctccgatgtatagTTAACAAGGAGAACCTGTCGAGGGTTACGACTGGAGATTTCTAGCCTC-TGGCATTAT-GAATGGAGGGTATATTCATGCGGCTACCAGGAAGGGTGCGTCA

upper sequence: LOC_Os10g41510.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G015324_T04 (Zea mays), 3'ss of exon 1
tagattgctagactacttacaaacattcttgcactttccatgaacatttgacatgctgcagataacatcatttctaaacattgttgcttgc---atttttcagGGACATAACAACCACATTTCCCAGTTTTGTATTCAATTCTGAGGTTGATGATCTCGTCACATGATCGTGTTTCTGTTACCGGTGTACAGTTAACAAAAAC
   | ||    ||     |   |   | |||  |||| ||||||| || ||  ||  |||   || |  |  |   |||| | |  ||||    ||  ||||||||||| ||||| ||||| ||||| ||||| || || ||||| || |||||||||||||| ||| |  | || | |  ||| |||| |||||||||  | 
-gaactggccaacatgaaatttatgct-ttgtgctttgcatgaac-ttcgagttgaagcaacaaaaaaaacctgctaacagtttatcttggtcaataattcagGGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGATCTCGTCACGTGACCACGATTTTCTCTCCGATGTATAGTTAACAAGGAG
















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|88276214|gb|CI396818.1|CI396818
EST:     GTCTCAAGG-ATCCCTCTTTATTGAAGATAATGACTCTTCCGTACCTC-A                         GGACATAACAACCACATTTCCCAGTTTTGTATTCAATTCTGAGGTTGATGA
genomic: GTCTCAAGGAATCCCTCTTTATTGAAGATAATGACTCTTCCGTACCTCAAgtgagtataa ... catttttcagGGACATAACAACCACATTTCCCAGTTTTGTATTCAATTCTGAGGTTGATGA
EST: gi|88485363|gb|CI422634.1|CI422634
EST:     GTCTCAAGGAATCCCTCTTTATTGAAGATAATGACTCTTCCGTACCTCAA                         GGACATAACAACCACATTTCCCAGTTTTGTATTCAATTCTGAGGTTGATGA
genomic: GTCTCAAGGAATCCCTCTTTATTGAAGATAATGACTCTTCCGTACCTCAAgtgagtataa ... catttttcagGGACATAACAACCACATTTCCCAGTTTTGTATTCAATTCTGAGGTTGATGA
EST: gi|2796254|gb|AA749548.1|AA749548
EST:     TTCCGTACCTCAA                         GGACATAACAACCACATTTCCCAGTTTTGTATTCAATTCTGAGGTTGATGA
genomic: TTCCGTACCTCAAgtgagtataa ... catttttcagGGACATAACAACCACATTTCCCAGTTTTGTATTCAATTCTGAGGTTGATGA
EST: gi|112785549|gb|EE590928.1|EE590928
EST:     GTCTCAAGGAATCCCTCTTTATTGAAGATAATGACTCTTCCGTACCTCAA                         GGACATAACAACCACATTTCCCAGTTTTGTATTCAATTCTGAGGTTGATGA
genomic: GTCTCAAGGAATCCCTCTTTATTGAAGATAATGACTCTTCCGTACCTCAAgtgagtataa ... catttttcagGGACATAACAACCACATTTCCCAGTTTTGTATTCAATTCTGAGGTTGATGA
EST: gi|88442238|gb|CI541445.1|CI541445
EST:     TCCGTACCTCAA                         GGACATAACAACCACATTTCCCAGTTTTGTATTCAATTCTGAGGTTGATGA
genomic: TCCGTACCTCAAgtgagtataa ... catttttcagGGACATAACAACCACATTTCCCAGTTTTGTATTCAATTCTGAGGTTGATGA
EST: gi|29657603|gb|CB653878.1|CB653878
EST:     GTCTCAAGGAATCCCTCGTTATTGAAGATAATGACTCTTCCGTACCTCAA                         GGACATAACAACCACATTTCCCAGTTTTGTATTCAATTCTGAGGTTGATGA
genomic: GTCTCAAGGAATCCCTCTTTATTGAAGATAATGACTCTTCCGTACCTCAAgtgagtataa ... catttttcagGGACATAACAACCACATTTCCCAGTTTTGTATTCAATTCTGAGGTTGATGA
EST: gi|88490044|gb|CI427316.1|CI427316
EST:     GTCTCAAGGAATCCCTCTTTATTGAAGATAATGACTCTTCCGTACCTCAA                         GGACATAACAACCACATTTCCCAGTTTTGTATTCAATTCTGAGGTTGATGA
genomic: GTCTCAAGGAATCCCTCTTTATTGAAGATAATGACTCTTCCGTACCTCAAgtgagtataa ... catttttcagGGACATAACAACCACATTTCCCAGTTTTGTATTCAATTCTGAGGTTGATGA
EST: gi|2799518|gb|AA752507.1|AA752507
EST:     GTCTCAAGGAATCCCTCTTTATTGAAGATAATGACTCTTCCGTACCTCAA                         GGACATAACAACCACATTTCCCAGTTTTGTATTCAATTCTGRGGTTGATGA
genomic: GTCTCAAGGAATCCCTCTTTATTGAAGATAATGACTCTTCCGTACCTCAAgtgagtataa ... catttttcagGGACATAACAACCACATTTCCCAGTTTTGTATTCAATTCTGAGGTTGATGA
EST: gi|89176813|gb|CI013386.1|CI013386
EST:     GTCTCAAGGAATCCCTCTTTATTGAAGATAATGACTCTTCCGTACCTCAA                         GGACATAACAACCACATTTCCCAGTTTTGTATTCAATTCTGAGGTTGATGA
genomic: GTCTCAAGGAATCCCTCTTTATTGAAGATAATGACTCTTCCGTACCTCAAgtgagtataa ... catttttcagGGACATAACAACCACATTTCCCAGTTTTGTATTCAATTCTGAGGTTGATGA

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: 74 (upstream exon), 73 (downstream exon)
Score: 38

CTGATACTAATCAGGATGGGAGAATAGATAGAACAGAGTGGGAGAATTTTGTCTCAAGGAATCCCTCTTTATTGAAGATAATGACTCTTCCGTACCTCAAgtgagtataa ... catttttcagGGACATAACAACCACATTTCCCAGTTTTGTATTCAATTCTGAGGTTGATGATCTCGTCACATGATCGTGTTTCTGTTACCGGTGTACAGTTAACAAAAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgacatgctgcagataacatcatttctaaacattgttgcttgcatttttcagGGACATAACAACCACATTTCCCAGTTTTGTATTCAATTCTGAGGTTGATGATCTCGTCACATGATCGTGTTTCTGTTACCGGTGTACAGTTAACAAAAAC
                          ttctaaa  putative branch site (score: 38)
                                             catttttc  putative PPT
                        atttctaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagattgctagactacttacaaacattcttgcactttccatgaacatttgacatgctgcagataacatcatttctaaacattgttgcttgcatttttcagGGACATAACAACCACATTTCCCAGTTTTGTATTCAATTCTGAGGTTGATGATCTCGTCACATGATCGTGTTTCTGTTACCGGTGTACAGTTAACAAAAAC

- gattgct
- - - - - - - - - acaaaca
- - - - - - - - - - - - - tcttgca
- - - - - - - - - - - - - - - - - - - catgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgct