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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAGgtattcataattgctcttcttttgcccttcccccatatttgtatctcccctttttcagataatggattaaaccgacctcgatatccataacggatgtacgcatccacatatttgtatctcccgtagttgttatataactgaaagcttaaagatttctaaatgcttataacatatatgttctttactag

Basic information

species Oryza sativa
transcript LOC_Os11g03380.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g03380.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G410155_T01 (Zea mays), 5'ss of exon 4
CTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAGgtattcataattgctcttcttttgcccttcccccatatttgtatctcccctttttcagataatggattaaaccgacctcgatatccataacggatgtacgcatccacatatttgtatctcccgtagttgttatataactgaaagcttaaagatttctaaatgcttataacatatatgttctttactag
|| |||||||||||||| |||||||||||||||| |||| |  |||||| |||||| ||||||||| |||||    ||| ||| |     | |     ||| || ||      |  || || || |       ||      |  || | | |  |||                                                                                              
CTGCAATCGTCAGACATATCTAAAGATAAGCAAGTTGATCCAGCTTTAGCAGACACACTGAAGgtaatcataggcactcatctctcaga-tactgttctatatgcatgg----tacttgagttattctgcgctactactgacacta-ctaaattggag---------------------------------------------------------------------------------------------

upper sequence: LOC_Os11g03380.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G179737_T02 (Zea mays), 5'ss of exon 5
CTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAGgtattcataattgctcttcttttgcccttcccccatatttgtatctcccctttttcagataatggattaaaccgacctcgatatccataacggatgtacgcatccacatatttgtatctcccgtagttgttatataactgaaagcttaaagatttctaaatgcttataacatatatgttctttactag
|| |||||||||||||| |||||||||||||||| |||| |  |||||| |||||| ||||||||| |||||    ||| ||| |  |   || |   || | | | |  |    | |||   | ||  |  ||||  | |||    |  || | |                                                                                               
CTGCAATCGTCAGACATATCTAAAGATAAGCAAGTTGATCCAGCTTTAGCAGACACACTGAAGgtaatcataggcactcatctctctcagatctcgtttact-ggagcatcaaagtgtca---actgcttataacccgcttcg---cctctaccag-----------------------------------------------------------------------------------------------
















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|4715628|gb|AU056744.1|AU056744
EST:     ACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAG                         AACTCGTTTGCAAAGCTCCGANTTTTCGATGGGCAT-CCCCTA
genomic: ACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAGgtattcataa ... tctttactagAACTCGTTTGCAA-GCTCCGAGTTTTCGATGG-CATTCCCCTA
EST: gi|33658304|gb|CF280918.1|CF280918
EST:     ACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAG                         AACTCGTTTGCAAGCTCCGAGTTTTCGATGGCATTCCCCTACATTGCCATG
genomic: ACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAGgtattcataa ... tctttactagAACTCGTTTGCAAGCTCCGAGTTTTCGATGGCATTCCCCTACATTGCCATG
EST: gi|33658126|gb|CF280740.1|CF280740
EST:     ACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAG                         AACTCGTTTGCAAGCTCCGAGTTTTCGATGGCATTCCCCTACATTGCCATG
genomic: ACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAGgtattcataa ... tctttactagAACTCGTTTGCAAGCTCCGAGTTTTCGATGGCATTCCCCTACATTGCCATG
EST: gi|33690612|gb|CF318851.1|CF318851
EST:     ACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAG                         AACTCGTTTGCAAGCTCCGAGTTTTCGATGGCATTCCCCTACATTGCCATG
genomic: ACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAGgtattcataa ... tctttactagAACTCGTTTGCAAGCTCCGAGTTTTCGATGGCATTCCCCTACATTGCCATG
EST: gi|29672707|gb|CB668982.1|CB668982
EST:     ACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAG                         AACTCGTTTGCAAGCTCCGAGTTTTCGATGGCATTCCCCTACATTGCCATG
genomic: ACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAGgtattcataa ... tctttactagAACTCGTTTGCAAGCTCCGAGTTTTCGATGGCATTCCCCTACATTGCCATG
EST: gi|14714076|gb|AU198016.1|AU198016
EST:     ACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAG                         AACTCGTTTGCAAGCTCCGAGTTTTCGATGGCATTCCCCTA
genomic: ACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAGgtattcataa ... tctttactagAACTCGTTTGCAAGCTCCGAGTTTTCGATGGCATTCCCCTA
EST: gi|29663528|gb|CB659803.1|CB659803
EST:     ACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAG                         AACTCGTTTGCAAGCTCCGAGTTTTCGATGGCATTCCCCTACATTGCCATG
genomic: ACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAGgtattcataa ... tctttactagAACTCGTTTGCAAGCTCCGAGTTTTCGATGGCATTCCCCTACATTGCCATG
EST: gi|33679537|gb|CF307776.1|CF307776
EST:     ACATTTCTAAAGATAAGCAAGCTGATTCTACCTTAGTAGACACGCTGAAG                         AACTCGTTTGCAAGCTCCGAGTTTTCGATGGCATTCCCCTACATTGCCATG
genomic: ACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAGgtattcataa ... tctttactagAACTCGTTTGCAAGCTCCGAGTTTTCGATGGCATTCCCCTACATTGCCATG
EST: gi|29658170|gb|CB654445.1|CB654445
EST:     ACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAG                         AACTCGTTTGCAAGCTCCGAGTTTTCGATGGCATTCCCCTACATTGCCATG
genomic: ACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAGgtattcataa ... tctttactagAACTCGTTTGCAAGCTCCGAGTTTTCGATGGCATTCCCCTACATTGCCATG
EST: gi|58664366|gb|CK053052.1|CK053052
EST:     ACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAG                         AACTCGTTTGCAAGCTCCGAGTTTTCGATGGCATTCCCCTACATTGCCATG
genomic: ACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAGgtattcataa ... tctttactagAACTCGTTTGCAAGCTCCGAGTTTTCGATGGCATTCCCCTACATTGCCATG
EST: gi|58677950|gb|CK066637.1|CK066637
EST:     ACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAG                         AACTCGTTTGCAAGCTCCGAGTTTTCGATGGCATTCCCCTACATTGCCATG
genomic: ACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAGgtattcataa ... tctttactagAACTCGTTTGCAAGCTCCGAGTTTTCGATGGCATTCCCCTACATTGCCATG
EST: gi|29678424|gb|CB674699.1|CB674699
EST:     ACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAG                         AACTCGTTTGCAAGCTCCGAGTTTTCGATGGCATTCCCCTACATTGCCATG
genomic: ACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAGgtattcataa ... tctttactagAACTCGTTTGCAAGCTCCGAGTTTTCGATGGCATTCCCCTACATTGCCATG
EST: gi|33822526|gb|CF337070.1|CF337070
EST:     ACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAG                         AACTCGTTTGCAAGCTCCGA
genomic: ACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAGgtattcataa ... tctttactagAACTCGTTTGCAAGCTCCGA
EST: gi|33658022|gb|CF280636.1|CF280636
EST:     ACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAG                         AACTCGTTTGCAAGCTCCGAGTTTTCGATGGCATTCCCCTACATTGCCATG
genomic: ACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAGgtattcataa ... tctttactagAACTCGTTTGCAAGCTCCGAGTTTTCGATGGCATTCCCCTACATTGCCATG
EST: gi|58598104|gb|CK008632.1|CK008632
EST:     ACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAG                         AACTCGTTTGCAAGCTCCGAGTTTTCGATGGCATTCCCCTACATTGCCATG
genomic: ACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAGgtattcataa ... tctttactagAACTCGTTTGCAAGCTCCGAGTTTTCGATGGCATTCCCCTACATTGCCATG
EST: gi|88445308|gb|CI587202.1|CI587202
EST:     ACATTTCTAAAGATAAGCAAGCTGATTCTACTTTACTAGACACGCTGAAG                         AACTCGTTTGCACGCTC-GAGTTTTCGATGGCATTCCCCTACATTGGCATG
genomic: ACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAGgtattcataa ... tctttactagAACTCGTTTGCAAGCTCCGAGTTTTCGATGGCATTCCCCTACATTGCCATG
EST: gi|29624905|gb|CB629916.1|CB629916
EST:     ACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAG                         AACTCGTTTGCAAGCTCCGAGTTTTCGATGGCATTCCCCTACATTGCCATG
genomic: ACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAGgtattcataa ... tctttactagAACTCGTTTGCAAGCTCCGAGTTTTCGATGGCATTCCCCTACATTGCCATG
EST: gi|2428191|gb|C72654.1|C72654
EST:     TTTCTAAAGATAAGCAAGCTGATTCTAACTTTTAGTAAGACACGCTGAAG                         A-CTCCGNTTGCAAGCTCCGAGTNTTCGATGG
genomic: TTTCTAAAGATAAGCAAGCTGATTCTA-CTTT-AGTA-GACACGCTGAAGgtattcataa ... tctttactagAACTC-GTTTGCAAGCTCCGAGTTTTCGATGG
EST: gi|58694105|gb|CK082792.1|CK082792
EST:     CATTTCTAAANGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAG                         AACTCGTTTGCAAGCTCCGAGTTTTCGATGGCATTCCCCTACATTGCCATG
genomic: CATTTCTAAA-GATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAGgtattcataa ... tctttactagAACTCGTTTGCAAGCTCCGAGTTTTCGATGGCATTCCCCTACATTGCCATG

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: 63 (upstream exon), 60 (downstream exon)
Score: 22

CTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAGgtattcataa ... tctttactagAACTCGTTTGCAAGCTCCGAGTTTTCGATGGCATTCCCCTACATTGCCATGTCAGATGATGACAAATTGGAGAAGTCATTGCTATCTGGGTTTGCTGAGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAGgtattcataattgctcttcttttgcccttcccccatatttgtatctcccctttttcagataatggattaaaccgacctcgatatccataacggatgtacgcatccacatatttgtatctcccgtagttgttatataactgaaagcttaaagatttctaaatgcttataacatatatgttctttactag

- - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG