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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCACCGCTCCGGAGGAGGGTGGGCAAGATGATCGGCGTCGGGAAGGCGAAGCAGTACGCCAACGTGCTCGACAAGCCCCTCAGCCGCGGCAGGCAGGAGgtactcactggctcgccttccctccccacacacacctccagcctctctcagatctgtgcacgcacgggccccgatccgtgctagaggtttagatctcgct...

Basic information

species Oryza sativa
transcript LOC_Os01g51220.1
intron # 1
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 1
lower sequence: GRMZM2G439457_T02 (Zea mays), 5'ss of exon 2
GCCACCGCTCCGGAGGAGGGTGGGCAAGATGATCGGCGTCGGGAAGGCGAAGCAGTACGCCAACGTGCTCGACAAGCCCCTCAGCCGCGGCAGGCAGGAGgtactcactggctcgccttccctccccacacacacctccagcctctctcagatctgtgcacgcacgggcccc---gatccgtgctagaggtttagatctcgct---------------
         |  || | |||  ||||||||||||||||| |||||||||||||||||||||||||| || ||||||||||||||||| |||||||||||||||    ||| |||                  | |||  |  |||  ||||||||| || ||| | | | ||   |||| || || ||| | | ||| |   |               
---------CTTGAAG-GGGCTGGCAAGATGATCGGCGTAGGGAAGGCGAAGCAGTACGCCAACGTCCTTGACAAGCCCCTCAGCCGTGGCAGGCAGGAGgtatgtgctgtctc------------------cgccttgaatctccatcagatctgcgcgcgcgctgcctccctagatcagtcctcgagatgtcgatatttttctgccatgtatctca
















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|88382318|gb|CI633176.1|CI633176
EST:     AGCAGTACGCCAACGTGCTCGACAAGCCCCTCAGCCGCGGCAGGCAGGAG                         GTCAGTTTGAGTGCATTTGCGTTCCTGTTCTCAGAGTTGGTTCAATACAAC
genomic: AGCAGTACGCCAACGTGCTCGACAAGCCCCTCAGCCGCGGCAGGCAGGAGgtactcactg ... tatttgatagGTCAGTTTGAGTGCATTTGCGTTCCTGTTCTCAGAGTTGGTTCAATACAAC
EST: gi|88303013|gb|CI668859.1|CI668859
EST:     AGCAGTACGCCAACGTGCTCGACAAGCCCCTCAGCCGCGGCAGGCAGGAG                         GTCAGTTTGAGTGCATTTGCGTTCCTGTTCTCAGAGTTGGTTCAATACAAC
genomic: AGCAGTACGCCAACGTGCTCGACAAGCCCCTCAGCCGCGGCAGGCAGGAGgtactcactg ... tatttgatagGTCAGTTTGAGTGCATTTGCGTTCCTGTTCTCAGAGTTGGTTCAATACAAC
EST: gi|88347620|gb|CI634305.1|CI634305
EST:     AGCAGTACGCCAACGTGCTCGACAAGCCCCTCAGCCGCGGCAGGCAGGAG                         GTCAGTTTGAGTGCATTTGCGTTCCTGTTCTCAGAGTTGGTTCAATACAAC
genomic: AGCAGTACGCCAACGTGCTCGACAAGCCCCTCAGCCGCGGCAGGCAGGAGgtactcactg ... tatttgatagGTCAGTTTGAGTGCATTTGCGTTCCTGTTCTCAGAGTTGGTTCAATACAAC
EST: gi|88336811|gb|CI644238.1|CI644238
EST:     AGCAGTACGCCAACGTGCTCGACAAGCCCCTCAGCCGCGGCAGGCAGGAG                         GTCAGTTTGAGTGCATTTGCGTTCCTGTTCTCAGAGTTGGTTCAATACAAC
genomic: AGCAGTACGCCAACGTGCTCGACAAGCCCCTCAGCCGCGGCAGGCAGGAGgtactcactg ... tatttgatagGTCAGTTTGAGTGCATTTGCGTTCCTGTTCTCAGAGTTGGTTCAATACAAC
EST: gi|88356314|gb|CI652718.1|CI652718
EST:     AGCAGTACGCCAACGTGCTCGACAAGCCCCTCAGCCGCGGCAGGCAGGAG                         GTCAGTTTGAGTGCATTTGCGTTCCTGTTCTCAGAGTTGGTTCAATACAAC
genomic: AGCAGTACGCCAACGTGCTCGACAAGCCCCTCAGCCGCGGCAGGCAGGAGgtactcactg ... tatttgatagGTCAGTTTGAGTGCATTTGCGTTCCTGTTCTCAGAGTTGGTTCAATACAAC
EST: gi|88338206|gb|CI633325.1|CI633325
EST:     AGCAGTACGCCAACGTGCTCGACAAGCCCCTCAGCCGCGGCAGGCAGGAG                         GTCAGTTTGAGTGCATTTGCGTTCCTGTTCTCAGAGTTGGTTCAATACAAC
genomic: AGCAGTACGCCAACGTGCTCGACAAGCCCCTCAGCCGCGGCAGGCAGGAGgtactcactg ... tatttgatagGTCAGTTTGAGTGCATTTGCGTTCCTGTTCTCAGAGTTGGTTCAATACAAC
EST: gi|88575096|gb|CI666865.1|CI666865
EST:     AGCAGTACGCCAACGTGCTCGACAAGCCCCTCAGCCGCGGCAGGCAGGAG                         GTCAGTTTGAGTGCATTTGCGTTCCTGTTCTCAGAGTTGGTTCAATACAAC
genomic: AGCAGTACGCCAACGTGCTCGACAAGCCCCTCAGCCGCGGCAGGCAGGAGgtactcactg ... tatttgatagGTCAGTTTGAGTGCATTTGCGTTCCTGTTCTCAGAGTTGGTTCAATACAAC
EST: gi|88305183|gb|CI651980.1|CI651980
EST:     AGCAGTACGCCAACGTGCTCGACAAGCCCCTCAGCCGCGGCAGGCAGGAG                         GTCAGTTTGAGTGCATTTGCGTTCCTGTTCTCAGAGTTGGTTCAATACAAC
genomic: AGCAGTACGCCAACGTGCTCGACAAGCCCCTCAGCCGCGGCAGGCAGGAGgtactcactg ... tatttgatagGTCAGTTTGAGTGCATTTGCGTTCCTGTTCTCAGAGTTGGTTCAATACAAC
EST: gi|109974426|gb|DT806902.1|DT806902
EST:     GCCAACGTGTTCTACAAGCCCCTCAGCCGCGGCAAGCAGGAG                         GTCAGTTTGAGTGCATTTGCGCTCCTGTTCTCAGAGTTGGCTCAATACAAC
genomic: GCCAACGTGCTCGACAAGCCCCTCAGCCGCGGCAGGCAGGAGgtactcactg ... tatttgatagGTCAGTTTGAGTGCATTTGCGTTCCTGTTCTCAGAGTTGGTTCAATACAAC
EST: gi|88575793|gb|CI669938.1|CI669938
EST:     AGCAGTACGCCAACGTGCTCGACAAGCCCCTCAGCCGCGGCAGGCAGGAG                         GTCAGTTTGAGTGCATTTGCGTTCCTGTTCTCAGAGTTGGTTCAATACAAC
genomic: AGCAGTACGCCAACGTGCTCGACAAGCCCCTCAGCCGCGGCAGGCAGGAGgtactcactg ... tatttgatagGTCAGTTTGAGTGCATTTGCGTTCCTGTTCTCAGAGTTGGTTCAATACAAC
EST: gi|163929185|gb|EG713058.1|EG713058
EST:     AGCAGTACGCCAACGTGCTCGACAAGCCCCTCAGCCGCGGCAGGCAGGAG                         GTCAGTTTGAGTGCATTTGCGTTCCTGTTCTCAGAGTTGGTTCAATACAAC
genomic: AGCAGTACGCCAACGTGCTCGACAAGCCCCTCAGCCGCGGCAGGCAGGAGgtactcactg ... tatttgatagGTCAGTTTGAGTGCATTTGCGTTCCTGTTCTCAGAGTTGGTTCAATACAAC
EST: gi|88719072|gb|CI742582.1|CI742582
EST:     AGCAGTACGCCAACGTGCTCGACAAGCCCCTCAGCCGCGGCAGGCAGGAG                         GTCAGTTTGAGTGCATTTGCGTTCCTGTTCTCAGAGTTGGTTCAATACAAC
genomic: AGCAGTACGCCAACGTGCTCGACAAGCCCCTCAGCCGCGGCAGGCAGGAGgtactcactg ... tatttgatagGTCAGTTTGAGTGCATTTGCGTTCCTGTTCTCAGAGTTGGTTCAATACAAC
EST: gi|88381600|gb|CI682265.1|CI682265
EST:     AGCAGTACGCCAACGTGCTCGACAAGCCCCTCAGCCGCGGCAGGCAGGAG                         GTCAGTTTGAGTGCATTTGCGTTCCTGTTCTCAGAGTTGGTTCAATACAAC
genomic: AGCAGTACGCCAACGTGCTCGACAAGCCCCTCAGCCGCGGCAGGCAGGAGgtactcactg ... tatttgatagGTCAGTTTGAGTGCATTTGCGTTCCTGTTCTCAGAGTTGGTTCAATACAAC
EST: gi|88327973|gb|CI648377.1|CI648377
EST:     AGCAGTACGCCAACGTGCTCGACAAGCCCCTCAGCCGCGGCAGGCAGGAG                         GTCAGTTTGAGTGCATTTGCGTTCCTGTTCTCAGAGTTGGTTCAATACAAC
genomic: AGCAGTACGCCAACGTGCTCGACAAGCCCCTCAGCCGCGGCAGGCAGGAGgtactcactg ... tatttgatagGTCAGTTTGAGTGCATTTGCGTTCCTGTTCTCAGAGTTGGTTCAATACAAC
EST: gi|88308467|gb|CI650876.1|CI650876
EST:     AGCAGTACGCCAACGTGCTCGACAAGCCCCTCAGCCGCGGCAGGCAGGAG                         GTCAGTTTGAGTGCATTTGCGTTCCTGTTCTCAGAGTTGGTTCAATACAAC
genomic: AGCAGTACGCCAACGTGCTCGACAAGCCCCTCAGCCGCGGCAGGCAGGAGgtactcactg ... tatttgatagGTCAGTTTGAGTGCATTTGCGTTCCTGTTCTCAGAGTTGGTTCAATACAAC

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: 65 (upstream exon), 69 (downstream exon)
Score: 8

GCCACCGCTCCGGAGGAGGGTGGGCAAGATGATCGGCGTCGGGAAGGCGAAGCAGTACGCCAACGTGCTCGACAAGCCCCTCAGCCGCGGCAGGCAGGAGgtactcactg ... tatttgatagGTCAGTTTGAGTGCATTTGCGTTCCTGTTCTCAGAGTTGGTTCAATACAACCAGACACAGGTTGATAACATTGCTGAGCTGGAAAGAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCACCGCTCCGGAGGAGGGTGGGCAAGATGATCGGCGTCGGGAAGGCGAAGCAGTACGCCAACGTGCTCGACAAGCCCCTCAGCCGCGGCAGGCAGGAGgtactcactggctcgccttccctccccacacacacctccagcctctctcagatctgtgcacgcacgggccccgatccgtgctagaggtttagatctcgct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggccccg