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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagccacattttccatgattgcaattgaaaaacttctgttttaatgtaaatcagttctaactcgtgtcatctttaacagGTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATGTGCCTTCTCCTGTACTATCATGATGTGATGAACAGGATTGAGAAGGCAA

Basic information

species Oryza sativa
transcript LOC_Os05g10810.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g10810.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G130749_T02 (Zea mays), 3'ss of exon 14
gttagccacattttccatgattgcaattgaaaaacttctgttttaatgtaaatcagttctaactcgtgtcatctttaacagGTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATGTGCCTTCTCCTGTACTATCATGATGTGATGAACAGGATTGAGAAGGCAA
|| ||||| ||||| | |  |||  | |    |   ||  |||| |||  || | || |||| | |||  || || || |||||||||| ||||| |||||||| ||||||||||| || ||||||||||||||  ||||  |||| || ||||||||||||||| ||| |||||||||||
gtgagccatatttttcttagttgatacttgctaggatcgttttttatgggaacctgt-ctaatttgtggtatattcaatagGTTGGCAATATGATCTTTTGGTTTTTTTTCTGCATATACGGGCAGCCAATGTGTGTTCTATTGTATTACCATGATGTGATGAACCGGACTGAGAAGGCAA

upper sequence: LOC_Os05g10810.1 (Oryza sativa), 3'ss of exon 15
lower sequence: PP1S66_164V6.1 (Physcomitrella patens), 3'ss of exon 14
---------------------gttagccacattttccatgattgcaattgaaaaacttctgttttaatgtaaatcagttctaactcgtgtcatctttaacagGTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATGTGCCTTCTCCTGTACTATCATGATGTGATGAACAGGATTGAGAAGGCAA
                     || |   | ||| |   | ||| || | | | |        ||  ||||||  || |  || |   | | |   |   |||||||| || ||| ||||||||||||||||||||||    ||||| || |||||| | ||| ||||||| || |||||  | |||    |  || |    |
taaagcataacgtgatatattgtcatttaaattgttgtttatt-cagtcgcatagtacaatgttagatgtaagacattaatatcgact-tgaatgtgcccagGTTGGAAATATGGTATTTTGGTTCTTTTTCTGCATTGTGGGGCAACCCATGTGCTTGCTCTTGTACTACCACGATGTTGTCAACTTT-TCCAGCAACTGA
















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|88515663|gb|CI443317.1|CI443317
EST:     CCCTTATCGTATTGACAGCATACCTCCAAAGTGAATTCAGAGATACCATG                         GTTGGCGACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATN
genomic: CCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATGgttagccaca ... tctttaacagGTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
EST: gi|29664361|gb|CB660636.1|CB660636
EST:     CCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATG                         GTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
genomic: CCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATGgttagccaca ... tctttaacagGTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
EST: gi|29615462|gb|CB620474.1|CB620474
EST:     CCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATG                         GTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
genomic: CCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATGgttagccaca ... tctttaacagGTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
EST: gi|29664325|gb|CB660600.1|CB660600
EST:     CCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATG                         GTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
genomic: CCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATGgttagccaca ... tctttaacagGTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
EST: gi|25803480|gb|CA759449.1|CA759449
EST:     CCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATG                         GTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
genomic: CCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATGgttagccaca ... tctttaacagGTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
EST: gi|88521128|gb|CI448787.1|CI448787
EST:     CCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATG                         GTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
genomic: CCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATGgttagccaca ... tctttaacagGTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
EST: gi|29641508|gb|CB646515.1|CB646515
EST:     CCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATG                         GTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
genomic: CCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATGgttagccaca ... tctttaacagGTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
EST: gi|29634262|gb|CB639271.1|CB639271
EST:     CCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATG                         GTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
genomic: CCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATGgttagccaca ... tctttaacagGTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
EST: gi|16578658|gb|BI812753.1|BI812753
EST:     CCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATG                         GTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
genomic: CCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATGgttagccaca ... tctttaacagGTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
EST: gi|88469648|gb|CI406919.1|CI406919
EST:     TCAAAAGTAAATTCAGAGATACAATG                         GTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
genomic: TCAAAAGTAAATTCAGAGATACAATGgttagccaca ... tctttaacagGTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
EST: gi|88282976|gb|CI404224.1|CI404224
EST:     CCTCGAAAGTAAATTCAGAGAAACAATG                         GTTGGCAACATGATATTTTGGTTCTTTTTCGGCATCTATGGCCAGCCCATG
genomic: CCTCAAAAGTAAATTCAGAGATACAATGgttagccaca ... tctttaacagGTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
EST: gi|88510251|gb|CI437757.1|CI437757
EST:     TACCTCAAAAGTAAATTCAGAGATACAATG                         GTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
genomic: TACCTCAAAAGTAAATTCAGAGATACAATGgttagccaca ... tctttaacagGTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
EST: gi|29664324|gb|CB660599.1|CB660599
EST:     CCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATG                         GTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
genomic: CCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATGgttagccaca ... tctttaacagGTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
EST: gi|29664362|gb|CB660637.1|CB660637
EST:     CCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATG                         GTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
genomic: CCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATGgttagccaca ... tctttaacagGTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
EST: gi|29646484|gb|CB651491.1|CB651491
EST:     CCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATG                         GTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
genomic: CCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATGgttagccaca ... tctttaacagGTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
EST: gi|88477472|gb|CI414743.1|CI414743
EST:     CCTTATCGGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATG                         GTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
genomic: CCTTATC-GTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATGgttagccaca ... tctttaacagGTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
EST: gi|88486834|gb|CI424105.1|CI424105
EST:     TATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACCATG                         GTTGGCGACATGATATTTTGGGTCTTTTTCTGCATCTATGGGCAGCCGATG
genomic: TATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATGgttagccaca ... tctttaacagGTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
EST: gi|88504163|gb|CI431669.1|CI431669
EST:     CCCTTATGGTATTGACAGCATACCTCAAAAGTAAATTCAGAAATACAATG                         GTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
genomic: CCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATGgttagccaca ... tctttaacagGTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
EST: gi|88520579|gb|CI448233.1|CI448233
EST:     CCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATG                         GTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
genomic: CCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATGgttagccaca ... tctttaacagGTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
EST: gi|29614065|gb|CB619078.1|CB619078
EST:     CCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATG                         GTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
genomic: CCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATGgttagccaca ... tctttaacagGTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
EST: gi|88553690|gb|CI483820.1|CI483820
EST:     TCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATG                         GTTGGCNACATGATATTNTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
genomic: TCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATGgttagccaca ... tctttaacagGTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
EST: gi|27548811|gb|CA766770.2|CA766770
EST:     GTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATG                         GTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
genomic: GTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATGgttagccaca ... tctttaacagGTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
EST: gi|66928227|gb|CX115075.1|CX115075
EST:     CCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATG                         GTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
genomic: CCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATGgttagccaca ... tctttaacagGTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
EST: gi|29615460|gb|CB620472.1|CB620472
EST:     CCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATG                         GTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG
genomic: CCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATGgttagccaca ... tctttaacagGTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATG

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: 54 (upstream exon), 46 (downstream exon)
Score: 31

ATCCCCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATGgttagccaca ... tctttaacagGTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATGTGCCTTCTCCTGTACTATCATGATGTGATGAACAGGATTGAGAAGGCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaaaaacttctgttttaatgtaaatcagttctaactcgtgtcatctttaacagGTTGGCAACATGATATTTTGGTTCTTTTTCTGCATCTATGGGCAGCCAATGTGCCTTCTCCTGTACTATCATGATGTGATGAACAGGATTGAGAAGGCAA
                              ttctaac  putative branch site (score: 31)
                                          tcatcttt  putative PPT
            tgttttaatgtaaat  TA-rich tract