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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGAGGTACATTGTTACATATAACCCAACAAAGGACAAGGTATATGCTTTGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCCATgtaagtattgataacaaggttaacaactttggcaatgccatactggtcaaatttgtttgcattatatcatcctaatcaaatgtgttttggtttacag

Basic information

species Oryza sativa
transcript LOC_Os05g34650.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g34650.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM5G833124_T01 (Zea mays), 5'ss of exon 11
TGAGAGGTACATTGTTACATATAACCCAACAAAGGACAAGGTATATGCTTTGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCCATgtaagtattgataacaaggttaacaactttggcaatgccatactggtcaaatttgtttgcattatatcatcctaatcaaatgtgttttg-gtttacag
||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||| |||||||| ||||| || ||||| | |||| | ||| || || || || | | ||||| |||| |||||| || ||||
TGAGAGGTATATTGTTACATATAACCCAACAAAGGACAAGGTATATGCTTTGCTCAAGGACCAAGCAAAGCCAGATGACATTCTCAAAGCTGCTTTTCATgtaagcgttgattg------tattctatttggtaggattccactgct-aaagttcttcgcgttttcttatcctcgtcaaccatgttttttattaacag

upper sequence: LOC_Os05g34650.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA17G00580.1 (Glycine max), 5'ss of exon 8
TGAGAGGTACATTGTTACATATAACCCAACAAAGGACAAGGTATATGCTTTGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCCATgtaagtattgata-acaaggtta----acaactttggcaatgccatactggtcaaatttgtttgcattatatcatcctaatcaaatgtgttttggtttacag
||||| || ||||| ||||||||||| |||| ||||||| |||||| |||||||||| || || ||| ||||||| ||||| ||||| || ||||| || || ||||| | | | || || |||| ||| || | | | ||| || | | | | || | || || | | ||| |||
GGAGAGATATATTGTGACATATAACCCCTCAAAACACAAGGTTTATGCTGTGCTCAAGGATCAGGCGAAGTCAGATGACATTCTGAAAGCAGCATTCCACgtgag-attgagatatatggctatcttacaaaattgtcagaac-agattgggaaattcttaatttgaaaaatacttaaaagttaaaaaacctcgttttgcag

upper sequence: LOC_Os05g34650.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA07G40210.1 (Glycine max), 5'ss of exon 9
TGAGAGGTACATTGTTACATATAACCCAACAAAGGACAAGGTATATGCTTTGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCCATgtaagtattgataacaaggttaacaactttggcaatgccatactggtcaaatttgtttgcattatatcatcctaatcaaatgtgttttggtttacag
||||| || ||||| ||||||||||| |||| ||||||| ||||| |||||||||| || |||||| ||||||| ||||| ||||| || |||||||| || ||||| | | || ||| ||| || | | | ||| || | | | | | | || || | | ||| |||
GGAGAGATATATTGTAACATATAACCCCTCAAAACACAAGGTTTATGCGGTGCTCAAGGATCAGGCAAAGTCAGATGACATTCTGAAAGCAGCATTCCATgtgag-attgagatatataata-caaaattgtcagaac-agattgggaaattcttaatttgaaaagtacttaaaacttaaataacctcgttttgcag

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|33381296|gb|CF196639.1|CF196639
EST:     TGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCNNNGCCGCTTTCCAT                         GCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAANGCN
genomic: TGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCCATgtaagtattg ... tggtttacagGCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCA
EST: gi|33666778|gb|CF297745.1|CF297745
EST:     TGCTCAAGGACTAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCCAT                         GCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCA
genomic: TGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCCATgtaagtattg ... tggtttacagGCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCA
EST: gi|29645587|gb|CB650594.1|CB650594
EST:     TGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCCAT                         GCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCA
genomic: TGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCCATgtaagtattg ... tggtttacagGCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCA
EST: gi|117223389|gb|CT846265.1|CT846265
EST:     TGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCCAT                         GCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCA
genomic: TGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCCATgtaagtattg ... tggtttacagGCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCA
EST: gi|218496920|gb|FG952344.1|FG952344
EST:     TGCTCAAGGACCAAGCAAAGCCGGATGATATTCTCAAAGCCGCTTTCCAT                         GCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCA
genomic: TGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCCATgtaagtattg ... tggtttacagGCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCA
EST: gi|86910785|gb|CI294785.1|CI294785
EST:     TGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCCAT                         GCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCA
genomic: TGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCCATgtaagtattg ... tggtttacagGCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCA
EST: gi|58593357|gb|CF991665.1|CF991665
EST:     TGCTCAAGGACCAAGCAAAGCCGGATGATATTCTCAAAGCCGCTTTCCAT                         GCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCA
genomic: TGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCCATgtaagtattg ... tggtttacagGCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCA
EST: gi|58675486|gb|CK064173.1|CK064173
EST:     TGCTCAAGGACCAAGCAAAGCCGGATGATATTCTCAAAGCCGCTTTCCAT                         GCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCA
genomic: TGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCCATgtaagtattg ... tggtttacagGCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCA
EST: gi|58600585|gb|CK011113.1|CK011113
EST:     TGCTCAAGGACCAAGCAAAGCCGGATGATATTCTCAAAGCCGCTTTCCAT                         GCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCA
genomic: TGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCCATgtaagtattg ... tggtttacagGCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCA

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: 72 (upstream exon), 71 (downstream exon)
Score: 34

TGAGAGGTACATTGTTACATATAACCCAACAAAGGACAAGGTATATGCTTTGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCCATgtaagtattg ... tggtttacagGCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCACGGAAGCGGATGAACTCCAATCGGTCATACCAAAATGCAAACCCACTGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAGAGGTACATTGTTACATATAACCCAACAAAGGACAAGGTATATGCTTTGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCCATgtaagtattgataacaaggttaacaactttggcaatgccatactggtcaaatttgtttgcattatatcatcctaatcaaatgtgttttggtttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG