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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTTCCCCCTGGTGAAGAATCAGGAGTTTGACGACGCTGCGAAAGTTATTGATAAAGCATTAACAACAGCAGGCATCTCGCATATTATTGACACTACTGgtacgtatataatatgaaaatagcttctcccactgttgcttgaagatattattaacatctaattgacaataaagaaaaacatctgagttaaaaattattaccatgttgggaagtgtaatatgcaaattcatgctagtttatgcattactctatgagcttatgtatgtcatgtgcttgtgcag

Basic information

species Oryza sativa
transcript LOC_Os08g42560.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g42560.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM5G821551_T03 (Zea mays), 5'ss of exon 8
GTGTTCCCCCTGGTGAAGAATCAGGAGTTTGACGACGCTGCGAAAGTTATTGATAAAGCATTAACAACAGCAGGCATCTCGCATATTATTGACACTACTGgtacgtatataatatgaaaatagcttctcccactgttgcttgaagatattattaacatctaattgacaataaagaaaaacatctgagttaaaaattattaccatgttgggaagtgtaatatgcaaattcatgctagtttatgcattactctatgagcttatgtatgtcatgtgcttgtgcag
||||||||||| || |||||||| ||||||||||| ||||| ||||| || |  || ||||||||||| || || ||||| || ||||||||||||||||||||||  |  |||  |   ||  | | ||||||   |  | | |  | |||  | || |||                     | || |     || ||  | ||  |                                                                          
GTGTTCCCCCTTGTTAAGAATCAAGAGTTTGACGATGCTGCCAAAGTAATCGCCAAGGCATTAACAACTGCTGGTATCTCCCACATTATTGACACTACTGgtacgtgca--atacaatcttaaatac-cccact-ccgtataacgtaactatatatatgtaagca------------------taagctcgtggttgttctcttgcag--------------------------------------------------------------------------
















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|29626190|gb|CB631201.1|CB631201
EST:     TGATAAAGCATTAACAACAGCAGGCATCTCGCATATTATTGACACTACTG                         CCATTTCTATTGGGAGGAGGTATGCAAGGACAGATGAGATCGGTGTTCCAT
genomic: TGATAAAGCATTAACAACAGCAGGCATCTCGCATATTATTGACACTACTGgtacgtatat ... gcttgtgcagCCATTTCTATTGGGAGGAGGTATGCAAGGACAGATGAGATCGGTGTTCCAT
EST: gi|86477656|gb|CI120289.1|CI120289
EST:     TGATAAAGCATTAACAACAGCAGGCATCTCGCATATTATTGACACCACTG                         CCATTTCTATTGGGAGGAGGTATGCAAGGACAGATGAGATCGGTGTTCCAT
genomic: TGATAAAGCATTAACAACAGCAGGCATCTCGCATATTATTGACACTACTGgtacgtatat ... gcttgtgcagCCATTTCTATTGGGAGGAGGTATGCAAGGACAGATGAGATCGGTGTTCCAT
EST: gi|4715425|gb|AU056542.1|AU056542
EST:     TGATAAAGCATTAACAACAGCAGGCATCTCGCATATTATTGACACTACTG                         C
genomic: TGATAAAGCATTAACAACAGCAGGCATCTCGCATATTATTGACACTACTGgtacgtatat ... gcttgtgcag-
EST: gi|4715425|gb|AU056542.1|AU056542
EST:     TGATAAAGCATTAACAACAGCAGGCATCTCGCATATTATTGACACTACTG                         C
genomic: TGATAAAGCATTAACAACAGCAGGCATCTCGCATATTATTGACACTACTGgtacgtatat ... gcttgtgcag-
EST: gi|27576165|gb|CA998859.1|CA998859
EST:     TGATAAAGCATTAACAACAGCAGGCATCTCGCATATTATTGACACTACTG                         CCATTTCTATTGGGAGGAGGTATGCAAGGACAGATGAGATCGGTGTTCCAT
genomic: TGATAAAGCATTAACAACAGCAGGCATCTCGCATATTATTGACACTACTGgtacgtatat ... gcttgtgcagCCATTTCTATTGGGAGGAGGTATGCAAGGACAGATGAGATCGGTGTTCCAT
EST: gi|87041266|gb|CI195888.1|CI195888
EST:     TGATAAAGCATTAACGACAGCAGGCATCTCGCATATTATTGACACTACTG                         CCATTTCTATTGGGAGGAGGTATGCAAGGACAGATGAGATCGGTGTTCCAT
genomic: TGATAAAGCATTAACAACAGCAGGCATCTCGCATATTATTGACACTACTGgtacgtatat ... gcttgtgcagCCATTTCTATTGGGAGGAGGTATGCAAGGACAGATGAGATCGGTGTTCCAT
EST: gi|89176277|gb|CI043298.1|CI043298
EST:     TGATAAAGCATTAACAACAGCAGGCATCTCGCATATTATTGACACTACTG                         CCATTTCTATTGGGAGGAGGTATGCAAGGACAGATGAGATCGGTGTTCCAT
genomic: TGATAAAGCATTAACAACAGCAGGCATCTCGCATATTATTGACACTACTGgtacgtatat ... gcttgtgcagCCATTTCTATTGGGAGGAGGTATGCAAGGACAGATGAGATCGGTGTTCCAT
EST: gi|88269105|gb|CI380403.1|CI380403
EST:     TGATAAAGCATTAACAACAGCAGGCATCTCGCATATTATTGACAGTACTG                         CCATTTCTATTGGGAGGAGTTATGCAAGGACAGATGAGATCGGTGTTCCAT
genomic: TGATAAAGCATTAACAACAGCAGGCATCTCGCATATTATTGACACTACTGgtacgtatat ... gcttgtgcagCCATTTCTATTGGGAGGAGGTATGCAAGGACAGATGAGATCGGTGTTCCAT
EST: gi|58611439|gb|CK039151.1|CK039151
EST:     TGATAAAGCATTAACAACAGCAGGCATCTCGCATATTATTGACACTACTG                         CCATTTCTATTGGGAGGAGGTATGCAAGGACAGATGAGATCGGTGTTCCAT
genomic: TGATAAAGCATTAACAACAGCAGGCATCTCGCATATTATTGACACTACTGgtacgtatat ... gcttgtgcagCCATTTCTATTGGGAGGAGGTATGCAAGGACAGATGAGATCGGTGTTCCAT
EST: gi|86844757|gb|CI338672.1|CI338672
EST:     ATTATTGACACTACTG                         CCATTTCTATTGGGAGGAGGTATGCAAGGACAGATGAGATCGGTGTTCCAT
genomic: ATTATTGACACTACTGgtacgtatat ... gcttgtgcagCCATTTCTATTGGGAGGAGGTATGCAAGGACAGATGAGATCGGTGTTCCAT
EST: gi|218494535|gb|FG968925.1|FG968925
EST:     TGATAAAGCATTAACAACAGCAGGCATCTCGCATATTATTGACACTACTG                         CCATTTCTATTG
genomic: TGATAAAGCATTAACAACAGCAGGCATCTCGCATATTATTGACACTACTGgtacgtatat ... gcttgtgcagCCATTTCTATTG
EST: gi|33682737|gb|CF310976.1|CF310976
EST:     TGATAAAGCATTAACAACAGCAGGCATCTCGCATATTATTGACACTACTG                         CCATTTCTATTGGGAGGAGGTATGCAAGGACAGATGAGATCGGTGTTCCAT
genomic: TGATAAAGCATTAACAACAGCAGGCATCTCGCATATTATTGACACTACTGgtacgtatat ... gcttgtgcagCCATTTCTATTGGGAGGAGGTATGCAAGGACAGATGAGATCGGTGTTCCAT
EST: gi|33677376|gb|CF305615.1|CF305615
EST:     TGATAAAGCATTAACAACAGCAGGCATCTCGCATATTATTGACACTACTG                         CCATTTCTATT
genomic: TGATAAAGCATTAACAACAGCAGGCATCTCGCATATTATTGACACTACTGgtacgtatat ... gcttgtgcagCCATTTCTATT
EST: gi|2797213|gb|AA750507.1|AA750507
EST:     TGATAAAGCATTAACAACAGCAGGCATCTCGCATATTATTGACACTACTG                         CCATTTCTATTGGGAGGAGGTATGCAAGGACAGATGAGATCGGTGTTCCAT
genomic: TGATAAAGCATTAACAACAGCAGGCATCTCGCATATTATTGACACTACTGgtacgtatat ... gcttgtgcagCCATTTCTATTGGGAGGAGGTATGCAAGGACAGATGAGATCGGTGTTCCAT
EST: gi|86496384|gb|CI139017.1|CI139017
EST:     TGATAAAGCATTAACAACAGCAGGCATCTCGCATATTATTGACACTACTG                         CCATTTCTATTGGGAGGAGGTATGCAAGGACAGATGAGATCGGTGTTCCAT
genomic: TGATAAAGCATTAACAACAGCAGGCATCTCGCATATTATTGACACTACTGgtacgtatat ... gcttgtgcagCCATTTCTATTGGGAGGAGGTATGCAAGGACAGATGAGATCGGTGTTCCAT
EST: gi|58601879|gb|CK012407.1|CK012407
EST:     GCAGGCATCTCGCATATTATTGACACTACTG                         CCATTTCTATTGGGAGGAGGTATGCAAGGACAGATGAGATCGGTGTTCCAT
genomic: GCAGGCATCTCGCATATTATTGACACTACTGgtacgtatat ... gcttgtgcagCCATTTCTATTGGGAGGAGGTATGCAAGGACAGATGAGATCGGTGTTCCAT
EST: gi|33682738|gb|CF310977.1|CF310977
EST:     TGATAAAGCATTAACAACAGCAGGCATCTCGCATATTATTGACACTACTG                         CCATTTCTATTGGGAAGGAGGTATGCAAGGACAGATG
genomic: TGATAAAGCATTAACAACAGCAGGCATCTCGCATATTATTGACACTACTGgtacgtatat ... gcttgtgcagCCATTTCTATTGGGA-GGAGGTATGCAAGGACAGATG
EST: gi|87041889|gb|CI196511.1|CI196511
EST:     TGACACTACTG                         CCATTTCTATTGGGAGGAGGTATGCAAGGACAGATGAGATCGGTGTTCCAT
genomic: TGACACTACTGgtacgtatat ... gcttgtgcagCCATTTCTATTGGGAGGAGGTATGCAAGGACAGATGAGATCGGTGTTCCAT

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), 75 (downstream exon)
Score: 28

GTGTTCCCCCTGGTGAAGAATCAGGAGTTTGACGACGCTGCGAAAGTTATTGATAAAGCATTAACAACAGCAGGCATCTCGCATATTATTGACACTACTGgtacgtatat ... gcttgtgcagCCATTTCTATTGGGAGGAGGTATGCAAGGACAGATGAGATCGGTGTTCCATTCGCGGTAACAGTTGACTCTGCGACAAGCGTGACAATCCGGGAGAGGGA




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