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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAAATGCTGGCTTTCCTGCGGTAGTTACTGCACACTTTGTGCCAATTGAGGGCCAACAAAGGCCAAGGACAACAATCTTGATAAAATTTGCTGAAGAGgtaggagatgcttgtatttgtttttctttctttagaactatttaatataataggcacagttgactgttactgaacaatacttattagacttaaccaaata...

Basic information

species Oryza sativa
transcript LOC_Os01g51220.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g51220.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G439457_T01 (Zea mays), 5'ss of exon 7
GGAAAATGCTGGCTTTCCTGCGGTAGTTACTGCACACTTTGTGCCAATTGAGGGCCAACAAAGGCCAAGGACAACAATCTTGATAAAATTTGCTGAAGAGgtaggagatgcttgtatttgtttttc------tttctttagaactatttaatataataggcacagttgactgttactgaacaatacttattagacttaaccaaata
 || ||||| ||||||||||| |||||||||||||| |||||||||||||| ||||| ||||||||||| || |||||| ||||||| |||||||||||||||| || |  || |  || | |  |      | |||||     |   |||| ||| |   | ||   | | ||     ||    |||  || ||  |        
AGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTGCCAATTGAAGGCCAGCAAAGGCCAAGAACGACAATCCTGATAAAGTTTGCTGAAGAGgtagaagttttttatccttttataccgtcagttctcttttagtgttgctaatttaacaataataggctaat-ttgtgtgacctccctttctaaacacattt-----

upper sequence: LOC_Os01g51220.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA11G34840.1 (Glycine max), 5'ss of exon 8
GGAAAATGCTGGCTTTCCTGCGGTAGTTACTGCACACTTTGTGCCAATTGAGGGCCAACAAAGGCCAAGGACAACAATCTTGATAAAATTTGCTGAAGAGgtaggagatgcttgtatttgtttttctt-tctttagaactatttaatataataggcacagttgactgttactgaacaatacttattagacttaaccaaata
|||   |||||| ||||| || || || || || || |||||||| || || || |||||| | ||  |||||||||| ||||||||||||||||||||||||      |||   | | ||||||||| || |  | ||| || | || | |    || | | | | |   |      |   |||    |           
GGATGGTGCTGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTGCCCATGGAAGGTCAACAACGACCGCGGACAACAATTTTGATAAAATTTGCTGAAGAGgta-----cgctgtcagtggtttttcttgtcatgtgtactgttaactacattctatactgataatt-tcctttcggggtttctatcttccag---------

upper sequence: LOC_Os01g51220.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA18G03480.1 (Glycine max), 5'ss of exon 8
GGAAAATGCTGGCTTTCCTGCGGTAGTTACTGCACACTTTGTGCCAATTGAGGGCCAACAAAGGCCAAGGACAACAATCTTGATAAAATTTGCTGAAGAGgtaggagatgcttgtatttgtttttctt-tctttaga-actatttaatataataggcacagttgact--gttactgaacaa-tacttattagacttaaccaaata
 ||   ||| || ||||| || || || || || || ||||| || || || || |||||| | ||| |||||||||| ||||||||||||||||||||||||     |   ||  ||||||| || | | |  | | ||| ||   || | |    || | |   |  ||| |||      ||  |   ||             
-GATGGTGCCGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTCCCCATGGAAGGTCAACAACGACCACGGACAACAATTTTGATAAAATTTGCTGAAGAGGtatactgtcagtggttttgtttgtcatgtgtgcacatactgttagctacattctaaactgatagtttcgtttctgggtttctatcttccagg------------

upper sequence: LOC_Os01g51220.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv11s0037g00110.t01 (Vitis vinifera), 5'ss of exon 7
GGAAAATGCTGGCTTTCCTGCGGTAGTTACTGCACACTTTGTGCCAATTGAGGGCCAACAAAGGCCAAGGACAACAATCTTGATAAAATTTGCTGAAGAGgtaggagatgcttgtatttgtttttctttctttagaactatttaatata-ataggcac-agttgactgttactgaacaatacttattagacttaaccaaata-
||| | ||| || ||||| || || || || || |||||||| || || ||||| |||||| | ||  ||||||| || ||||| ||||||||||||||||||    |    |||  |   |||||| |   | | ||  || |  | | ||   ||  |  | |      |  ||| |   ||       ||       |  
GGATAGTGCAGGTTTTCCAGCTGTGGTAACAGCTCACTTTGTACCTATGGAGGGTCAACAACGACCTCGGACAACTATTTTGATTAAATTTGCTGAAGAGgta---aacatatgttatcccttttctgttacttgcacatttgatcacagatccacatgaactaaacacctccaaaccaccttttcctcttttcctttggtta

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|88661963|gb|CI460991.1|CI460991
EST:     AGGGCCAACAAAGGCCAAGGACAACAATCTTGATAAAATTTGCTGAAGAG                         GTTTTACAGCGAGAAGCTAGATTTGGCTAAATTTTATCATATGTTCACACT
genomic: AGGGCCAACAAAGGCCAAGGACAACAATCTTGATAAAATTTGCTGAAGAGgtaggagatg ... tttttttcagGTTTTACAGCGAGAAGCTAGATTTGGCTAAATTTTATCATATGTTCACACT
EST: gi|87031904|gb|CI268133.1|CI268133
EST:     AGGGCCAACAAAGGCCAAGGACAACAATCTTGATAAAATTTGCTGAAGAG                         GTTTTACAGCGAGAAGCTAGATTTGGCTAAATTTTATCATATGTTCACACT
genomic: AGGGCCAACAAAGGCCAAGGACAACAATCTTGATAAAATTTGCTGAAGAGgtaggagatg ... tttttttcagGTTTTACAGCGAGAAGCTAGATTTGGCTAAATTTTATCATATGTTCACACT
EST: gi|88488420|gb|CI425691.1|CI425691
EST:     AGGGCCAACAAAGGCCAAGGACAACAATCTTGATAAAATTTGCTGAAGAG                         GTTTTACAGCGAGAAGCTAGATTTGGCTAAATTTTATCATATGTTCACACT
genomic: AGGGCCAACAAAGGCCAAGGACAACAATCTTGATAAAATTTGCTGAAGAGgtaggagatg ... tttttttcagGTTTTACAGCGAGAAGCTAGATTTGGCTAAATTTTATCATATGTTCACACT
EST: gi|88484151|gb|CI421422.1|CI421422
EST:     AGGGCCAACAAAGGCCAAGGACAACAATCTTGATAAAATTTGCTGAAGAG                         GTTTTACAGCGAGAAGCTAGATTTGGCTAAATTTTATCATATGTTCACACT
genomic: AGGGCCAACAAAGGCCAAGGACAACAATCTTGATAAAATTTGCTGAAGAGgtaggagatg ... tttttttcagGTTTTACAGCGAGAAGCTAGATTTGGCTAAATTTTATCATATGTTCACACT
EST: gi|88243947|gb|CI243069.1|CI243069
EST:     AGGGCCAACAAAGGCCAAGGACAACAATCTTGATAAAATTTGCTGAAGAG                         GTTTTACAGCGAGAAGCTAGATTTGGCTAGATTTTATCATATGTTCACACT
genomic: AGGGCCAACAAAGGCCAAGGACAACAATCTTGATAAAATTTGCTGAAGAGgtaggagatg ... tttttttcagGTTTTACAGCGAGAAGCTAGATTTGGCTAAATTTTATCATATGTTCACACT
EST: gi|88516373|gb|CI444027.1|CI444027
EST:     AGGGCCAACAAAGGCCAAGGACAACAATCTTGATAAAATTTGCTGAAGAG                         GTTTTACAGCGAGAAGCTAGATTTGGCTAAATTTTATCATATGTTCACACT
genomic: AGGGCCAACAAAGGCCAAGGACAACAATCTTGATAAAATTTGCTGAAGAGgtaggagatg ... tttttttcagGTTTTACAGCGAGAAGCTAGATTTGGCTAAATTTTATCATATGTTCACACT
EST: gi|88520758|gb|CI446414.1|CI446414
EST:     AGGGCCAACAAAGGCCAAGGACAACAATCTTGATAAAATTTGCTGAAGAG                         GTTTTACAGCGAGAAGCTAGATTTGGCTAAATTTTATCATATGTTCACACT
genomic: AGGGCCAACAAAGGCCAAGGACAACAATCTTGATAAAATTTGCTGAAGAGgtaggagatg ... tttttttcagGTTTTACAGCGAGAAGCTAGATTTGGCTAAATTTTATCATATGTTCACACT
EST: gi|88281784|gb|CI403180.1|CI403180
EST:     AGGGCCAACAAAGGCCAAGGACAACAATCTTGATAAAATTTGCTGAAGAG                         GTTTTACAGCGAGAAGCTAGATTTGGCTAAATTTTATCATATGTTCACACT
genomic: AGGGCCAACAAAGGCCAAGGACAACAATCTTGATAAAATTTGCTGAAGAGgtaggagatg ... tttttttcagGTTTTACAGCGAGAAGCTAGATTTGGCTAAATTTTATCATATGTTCACACT
EST: gi|12622960|gb|AU173173.1|AU173173
EST:     AGGGCCAACAAAGGCCAAGGACAACAATCTTGATAAAATTTGCTGAAGAG                         GTTTTACAGCGAGAAGCTAGATTTGGCTAAATTTTATCATATGTTCACACT
genomic: AGGGCCAACAAAGGCCAAGGACAACAATCTTGATAAAATTTGCTGAAGAGgtaggagatg ... tttttttcagGTTTTACAGCGAGAAGCTAGATTTGGCTAAATTTTATCATATGTTCACACT
EST: gi|88281957|gb|CI403353.1|CI403353
EST:     AGGGCCAACAAAGGCCAAGGACAACAATCTTGATAAAATTTGCTGAAGAG                         GTTTTACAGCGAGAAGCTAGATTTGGCTAAATTTTATCATATGTTCACACT
genomic: AGGGCCAACAAAGGCCAAGGACAACAATCTTGATAAAATTTGCTGAAGAGgtaggagatg ... tttttttcagGTTTTACAGCGAGAAGCTAGATTTGGCTAAATTTTATCATATGTTCACACT
EST: gi|88489179|gb|CI426451.1|CI426451
EST:     AGGGCCAACAAAGGCCAAGGACAACAATCTTGATAAAATTTGCTGAAGAG                         GTTTTACAGCGAGAAGCTAGATTTGGCTAAATTTTATCATATGTTCACACT
genomic: AGGGCCAACAAAGGCCAAGGACAACAATCTTGATAAAATTTGCTGAAGAGgtaggagatg ... tttttttcagGTTTTACAGCGAGAAGCTAGATTTGGCTAAATTTTATCATATGTTCACACT
EST: gi|88519872|gb|CI447526.1|CI447526
EST:     AGGGCCAACAAAGGCCAAGGACAACAATCTTGATAAAATTTGCTGAAGAG                         GTTTTACAGCGAGAAGCTAGATTTGGCTAAATTTTATCATATGTTCACACT
genomic: AGGGCCAACAAAGGCCAAGGACAACAATCTTGATAAAATTTGCTGAAGAGgtaggagatg ... tttttttcagGTTTTACAGCGAGAAGCTAGATTTGGCTAAATTTTATCATATGTTCACACT

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: 68 (upstream exon), 66 (downstream exon)
Score: 28

GGAAAATGCTGGCTTTCCTGCGGTAGTTACTGCACACTTTGTGCCAATTGAGGGCCAACAAAGGCCAAGGACAACAATCTTGATAAAATTTGCTGAAGAGgtaggagatg ... tttttttcagGTTTTACAGCGAGAAGCTAGATTTGGCTAAATTTTATCATATGTTCACACTTCTTTCTGATCAATTGGTGAAGATACTGTTGAAATGTTTTTTTGTGGCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAAAATGCTGGCTTTCCTGCGGTAGTTACTGCACACTTTGTGCCAATTGAGGGCCAACAAAGGCCAAGGACAACAATCTTGATAAAATTTGCTGAAGAGgtaggagatgcttgtatttgtttttctttctttagaactatttaatataataggcacagttgactgttactgaacaatacttattagacttaaccaaata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA