Sequence
atgc intronic sequence ATGC exonic sequenceAGCCATAGAAGGGCTACGAATCACAGGTGAAGCTTTTCCTGGAAGAGAGCTTCAAGCAAGTGGCTACTCTATCAATGGGACCACAAGTTGTAATTTTGAGgtgtgcttcataactgttctcctcattccaatataccatcaaatttgttcaccattttgaatttgatcttagctcactacaatgttccattttgcaatttctttttgtgcatacag
Basic information
| species | Oryza sativa |
| transcript | LOC_Os05g01060.2 |
| intron # | 13 |
| splice site | 5' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g01060.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G104377_T03 (Zea mays), 5'ss of exon 12
AGCCATAGAAGGGCTACGAATCACAGGTGAAGCTTTTCCTGGAAGAGAGCTTCAAGCAAGTGGCTACTCTATCAATGGGACCACAAGTTGTAATTTTGAGgtgtgcttcataac---tgttctcctcattcca-atataccatcaaatttgttcaccattttgaatttgatcttagctcactacaat-gttccattttgcaatttctttttgtgcatacag
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AGCCATAGAAGGACTGCGAATCACAGGTGAAGCCTTTCCTGGAAGAGAACTTCAAGCAAGTGGGTACTCTATCCATGGAACCACAAGTTGTAATTTTGAGgtgcgctctattgcctttgttatccatgtcttagatattcaactaaattcatttgtactcatgaat--aatttcagttttgtgttttcattataatctgtgttttgtttttgtgctcacag
upper sequence: LOC_Os05g01060.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA20G35770.1 (Glycine max), 5'ss of exon 15
AGCCATAGAAGGGCTACGAATCACAGGTGAAGCTTTTCCTGGAAGAGAGCTTCAAGCAAGTGGCTACTCTATCAATGGGACCACAAGTTGTAATTTTGAGgtgtgcttcat---------------aactgttctcctcattcca-atatacc-atcaaatttgttcaccattttgaa---tttgat--cttagctcactac--aatgttccattttgcaatttctttttgtgcatacag
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GGCTATAGAGGGTCTTCAAATTTCAGGAGAAGCCTTTCCTGGAAGGGAACTTCAAGCATGTGGATACTCCATCAATGGCACTACTAGTTGTAATTTTGAGgtgcattttatttgtgtataatttggaacttgtttcttcttgctttatgtacttaaaagagtttttcattatatggtaatgcttgatatctttcctaaacatttgacattaccttgtgtcccttcttgttggactaccag
upper sequence: LOC_Os05g01060.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA10G31880.1 (Glycine max), 5'ss of exon 14
AGCCATAGAAGGGCTACGAATCACAGGTGAAGCTTTTCCTGGAAGAGAGCTTCAAGCAAGTGGCTACTCTATCAATGGGACCACAAGTTGTAATTTTGAGgtgtgcttcat---------------aactgttctcctcattcca-atatacc-atcaaatttgttcaccattttgaatttgatcttagctcactacaatgttccattttgca----atttctttttgt--gcatacag-
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GGCTATAGAGGGTCTCCAAATTTCAGGAGAAGCCTTTCCTGGAAGGGAACTTAAGGCAGGCGGATACTCCATCAATGGCACTACTAGTTGTAATTTTGAGgtgcattttatttgtgtataatttggaacttgtttcttcttgctttatgtacttaaaagagtttttcattatatggtaatgtttgatatctttcctaaacatttgacattaccttgtgtcccttcttgtcggaataccag
upper sequence: LOC_Os05g01060.1 (Oryza sativa), 5'ss of exon 13
lower sequence: AT5G23510.1 (Arabidopsis thaliana), 5'ss of exon 2
AGCCATAGAAGGGCTACGAATCACAGGTGAAGCTTTTCCTGGAAGAGAGCTTCAAGCAAGTGGCTACTCTATCAATGGGACCACAAGTTGTAATTTTGAGgtgtgcttcataactgttctcctcattccaatataccatcaaatttgttcaccattttgaatttgatcttagctcactacaatgttccattttgcaatttctttttgtgcatacag
||| |||| || | ||| |||| ||| ||| ||||||| || ||||| || |||| ||||| || ||||| || ||||||||||||||||||||||| | ||| | | || || | || ||| || || ||||||| || || | | ||||||||| ||
AGCTTTAGAGAACCTCCAAATTTCAGGAGAACCTTATCCTGGACATGAACTTCAGGCTTGTGGTTACTCCATTAATGGAACAACAAGTTGTAATTTTGAGgtgtgtactaaaacag--------acaacagaatcgcttcc--tttcttacttatgttgaatt--gctctatcttcttctgttcttccatttt-cag-------------------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|163928384|gb|EG714704.1|EG714704EST: TTCAAGCAAGTGGCTACTCTATCAATGGGACCACAAGTTGTAATTTTGAG TGGGTACGGCATTTGGAGGATGGATCAGTAAATTACATAGAAG
genomic: TTCAAGCAAGTGGCTACTCTATCAATGGGACCACAAGTTGTAATTTTGAGgtgtgcttca ... gtgcatacagTGGGTACGGCATTTGGAGGATGGATCAGTAAATTACATAGAAG
EST:
gi|163919906|gb|EG714908.1|EG714908EST: TTCAAGCAAGTGGCTACTCTATCAATGGGACCACAAGTTGTAATTTTGAG TGGGTACGGCATTTGGAGGATGGATCAGTAAATTACATAGAAG
genomic: TTCAAGCAAGTGGCTACTCTATCAATGGGACCACAAGTTGTAATTTTGAGgtgtgcttca ... gtgcatacagTGGGTACGGCATTTGGAGGATGGATCAGTAAATTACATAGAAG
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:
73 (upstream exon),
65 (downstream exon)
Score:
9AGCCATAGAAGGGCTACGAATCACAGGTGAAGCTTTTCCTGGAAGAGAGCTTCAAGCAAGTGGCTACTCTATCAATGGGACCACAAGTTGTAATTTTGAGgtgtgcttca ... gtgcatacagTGGGTACGGCATTTGGAGGATGGATCAGTAAATTACATAGAAG
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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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AGCCATAGAAGGGCTACGAATCACAGGTGAAGCTTTTCCTGGAAGAGAGCTTCAAGCAAGTGGCTACTCTATCAATGGGACCACAAGTTGTAATTTTGAGgtgtgcttcataactgttctcctcattccaatataccatcaaatttgttcaccattttgaatttgatcttagctcactacaatgttccattttgcaatttctttttgtgcatacag
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
