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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCATATAACCAGAGGTGAATATGATGAGGATGCTCGTTACCCAGAGACTAAGACACTTACTATTGGTCAGTTCAAGCTAGGGCTGTGCCATGGTCATCAGgtttgcttttgactctagaactattacttgccttgttagtatgagcttcatgaccatgaatcagggatactagacttttaatatgctacttttttagaac...

Basic information

species Oryza sativa
transcript LOC_Os02g16550.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g16550.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G068489_T02 (Zea mays), 5'ss of exon 1
CCATATAACCAGAGGTGAATATGATGAGGATGCTCGTTACCCAGAGACTAAGACACTTACTATTGGTCAGTTCAAGCTAGGGCTGTGCCATGGTCATCAGgtttgcttttgactctagaactat-tacttgccttgttagtatgagcttcatgaccatgaatcagggatactagacttttaatatgctacttttt-tagaac-
|||||| |||||||||||| |||||||||||||||| ||||||||||||||||||||||| ||||||||||| ||||| |||||||||||||| ||||||||||| |||||||||   || | | ||   | || |    ||| || |||||| |||||    |   ||| ||   |||  |  |||| ||| |   | ||  
CCATATTACCAGAGGTGAACATGATGAGGATGCTCGATACCCAGAGACTAAGACACTTACAATTGGTCAGTTTAAGCTTGGGCTGTGCCATGGCCATCAGgtttgtttttgactcagaaaatgtataggaggctaggagctattagtttcatgcccatgg--taataataatat-ttttacaggtgctccttgtcacacaaaa

upper sequence: LOC_Os02g16550.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G109315_T02 (Zea mays), 5'ss of exon 2
CCATATAACCAGAGGTGAATATGATGAGGATGCTCGTTACCCAGAGACTAAGACACTTACTATTGGTCAGTTCAAGCTAGGGCTGTGCCATGGTCATCAGgtttgcttttgactctagaactattacttg---ccttgttagtatgagcttcatgaccatgaatcagggatac-tagacttttaatatgctacttttttagaac
||| || ||  ||||||||||||||||| ||||||| ||||||||||||||||||||||| ||||||||||| ||||| |||||||||||||||||||||||||| |||||||||   || | |   |     || || || ||  ||  |  | ||      ||   |   |  | |       ||||||  |||| |     
CCACATTACTGGAGGTGAATATGATGAGTATGCTCGATACCCAGAGACTAAGACACTTACAATTGGTCAGTTTAAGCTTGGGCTGTGCCATGGTCATCAGgtttgtttttgactcagcaaatgtctttcatgcccatggtaataatagtattcttacaggtgctccttggcgcacaaaaggaacctatgcttgttttatg----

upper sequence: LOC_Os02g16550.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv01s0026g01860.t01 (Vitis vinifera), 5'ss of exon 3
CCATATAACCAGAGGTGAATATGATGAGGATGCTCGTTACCCAGAGACTAAGACACTTACTATTGGTCAGTTCAAGCTAGGGCTGTGCCATGGTCATCAGgtttgcttt-tgactctagaactattacttgccttgttagtatgagcttcatgaccatgaatcagggatactagacttttaatatgctacttt---tttagaac
 ||| | ||| |||||||||||||||| ||| | |||||||  ||||| ||||||||||| || ||||| || ||||| ||  | ||||||||||||||||| ||  |  |    ||    || ||   || | |||  |  |||  || | |      ||  |    |  || | |  |||| || |   ||   ||   | |
GCATGTCACCCGAGGTGAATATGATGAAGATTCACGTTACCTGGAGACCAAGACACTTACAATCGGTCAATTTAAGCTTGGAGTATGCCATGGTCATCAGgtctgtctggttttcctctgtctgtt--ctgacatgt-ggcttgatttttaaggattgcaaataaatgtgttaca-taataatttgatgaattggattccaatc

upper sequence: LOC_Os02g16550.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv17s0000g05880.t01 (Vitis vinifera), 5'ss of exon 2
CCATATAACCAGAGGTGAATATGATGAGGATGCTCGTTACCCAGAGACTAAGACACTTACTATTGGTCAGTTCAAGCTAGGGCTGTGCCATGGTCATCAGgtttgcttttgactctagaactattacttgccttgttagtatgagcttcatgaccatgaatcagggatactagacttttaatatgctacttttttagaac---
 ||||| ||| |||||||||||||||||||  | |||||||||||||| || |||||||| |||||||| |||||||| || || ||||||||||||||||||   |||| | ||   |       |||  |||| |  |   |  | | ||  ||||  ||    | | || |   |  | || ||||    |    |    
GCATATTACCCGAGGTGAATATGATGAGGAGACACGTTACCCAGAGACCAAAACACTTACCATTGGTCAATTCAAGCTTGGACTATGCCATGGTCATCAGgttcaattttcattccctattggcatcttttcttgatgattacaaatccgtg--catgtttcttaca-agtaaaacatcgagattctacaggatatagatgga

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|58686250|gb|CK074937.1|CK074937
EST:     AGACACTTACTATTGGTCAGTTCAAGCTAGGGCTGTGCCATGGTCATCAG                         GTTGTTCCATGGGGCGATTTGGACTCCCTGGCGATGCTCCAACGGCAGCTG
genomic: AGACACTTACTATTGGTCAGTTCAAGCTAGGGCTGTGCCATGGTCATCAGgtttgctttt ... caatcatcagGTTGTTCCATGGGGCGATTTGGACTCCCTGGCGATGCTCCAACGGCAGCTG
EST: gi|88204867|gb|CI202718.1|CI202718
EST:     AGACACTTACTATTGGTCAGTTCAAGCTAGGGCTGTGCCATGGTCATCAG                         GTTGTTCCATGGGGCGATTTGGACTCCCTGGCGATGCTCCAACGGCAGCTG
genomic: AGACACTTACTATTGGTCAGTTCAAGCTAGGGCTGTGCCATGGTCATCAGgtttgctttt ... caatcatcagGTTGTTCCATGGGGCGATTTGGACTCCCTGGCGATGCTCCAACGGCAGCTG
EST: gi|88839485|gb|CI005273.1|CI005273
EST:     TTCAAGCTAGGGCTGTGCCATGGTCATCAG                         GTTGTTCCATGGGGCGATTTGGACTCCCTGGCGATGCTCCAACGGCAGCTG
genomic: TTCAAGCTAGGGCTGTGCCATGGTCATCAGgtttgctttt ... caatcatcagGTTGTTCCATGGGGCGATTTGGACTCCCTGGCGATGCTCCAACGGCAGCTG
EST: gi|27576125|gb|CA998819.1|CA998819
EST:     AGACACTTACTATTGGTCAGTTCAAGCTAGGGCTGTGCCATGGTCATCAG                         GTTGTTCCATGGGGCGATTTGGACTCCCTGGCGATGCTCCAACGGCAGCTG
genomic: AGACACTTACTATTGGTCAGTTCAAGCTAGGGCTGTGCCATGGTCATCAGgtttgctttt ... caatcatcagGTTGTTCCATGGGGCGATTTGGACTCCCTGGCGATGCTCCAACGGCAGCTG
EST: gi|86859026|gb|CI276969.1|CI276969
EST:     AGACACTTACTATTGGTCAGTTCAAGCTAGGGCTGTGCCATGGTCATCAG                         GTTGTTCCATGGGGCGATTTGGACTCCCTGGCGATGCTCCAACGGCAGCTG
genomic: AGACACTTACTATTGGTCAGTTCAAGCTAGGGCTGTGCCATGGTCATCAGgtttgctttt ... caatcatcagGTTGTTCCATGGGGCGATTTGGACTCCCTGGCGATGCTCCAACGGCAGCTG
EST: gi|89180305|gb|CI044584.1|CI044584
EST:     AGACACTTACTATTGGTCAGTTCAAGCTAGGTCTGTGCCATGGTCATCAG                         GTTGTTCCATGGGGCGATTTGGACTCCCTGGCGATGCTCCAACGGCAGCTG
genomic: AGACACTTACTATTGGTCAGTTCAAGCTAGGGCTGTGCCATGGTCATCAGgtttgctttt ... caatcatcagGTTGTTCCATGGGGCGATTTGGACTCCCTGGCGATGCTCCAACGGCAGCTG
EST: gi|87026474|gb|CI252428.1|CI252428
EST:     AGACACTTACTATTGGTCAGTTCAAGCTAGGGCTGTGCCATGGTCATCAG                         GTTGTTCCATGGGGCGATTTGGACTCCCTGGCGATGCTCCAACGGCAGCTG
genomic: AGACACTTACTATTGGTCAGTTCAAGCTAGGGCTGTGCCATGGTCATCAGgtttgctttt ... caatcatcagGTTGTTCCATGGGGCGATTTGGACTCCCTGGCGATGCTCCAACGGCAGCTG
EST: gi|87018528|gb|CI252282.1|CI252282
EST:     AGACACTTACTATTGGTCAGTTCAAGCTAGGGCTGTGCCATGGTCATCAG                         GTTGTTCCATGGGGCGATTTGGACTCCCTGGCGATGCTCCAACGGCAGCTG
genomic: AGACACTTACTATTGGTCAGTTCAAGCTAGGGCTGTGCCATGGTCATCAGgtttgctttt ... caatcatcagGTTGTTCCATGGGGCGATTTGGACTCCCTGGCGATGCTCCAACGGCAGCTG
EST: gi|569224|gb|D40073.1|D40073
EST:     AGACACTTACTATTGGTCAGTTCAAGCTAGGGCTGTGCCATGGTCATCAG                         GTTGTTCCATGGGGCGATTTGGACTCCCTGGCGATGCTCCAACGGCAGCTG
genomic: AGACACTTACTATTGGTCAGTTCAAGCTAGGGCTGTGCCATGGTCATCAGgtttgctttt ... caatcatcagGTTGTTCCATGGGGCGATTTGGACTCCCTGGCGATGCTCCAACGGCAGCTG
EST: gi|87035741|gb|CI190363.1|CI190363
EST:     AGACACTTACTATTGGTCAGTTCAAGCTAGGGCTGTGCCATGGTCATCAG                         GTTGTTCCATGGGGCGATTTGGACTCCCTGGCGATGCTCCAACGGCAGCTG
genomic: AGACACTTACTATTGGTCAGTTCAAGCTAGGGCTGTGCCATGGTCATCAGgtttgctttt ... caatcatcagGTTGTTCCATGGGGCGATTTGGACTCCCTGGCGATGCTCCAACGGCAGCTG

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: 75 (upstream exon), 68 (downstream exon)
Score: 73

CCATATAACCAGAGGTGAATATGATGAGGATGCTCGTTACCCAGAGACTAAGACACTTACTATTGGTCAGTTCAAGCTAGGGCTGTGCCATGGTCATCAGgtttgctttt ... caatcatcagGTTGTTCCATGGGGCGATTTGGACTCCCTGGCGATGCTCCAACGGCAGCTGGACGTGGACATCCTCGTCACAGGGCACACCCACCAGTTCAAGGCGTACA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCATATAACCAGAGGTGAATATGATGAGGATGCTCGTTACCCAGAGACTAAGACACTTACTATTGGTCAGTTCAAGCTAGGGCTGTGCCATGGTCATCAGgtttgcttttgactctagaactattacttgccttgttagtatgagcttcatgaccatgaatcagggatactagacttttaatatgctacttttttagaac

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