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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAACGGAATCATTAGAACTCCACAAGATTAAGAGCCGTCAATGGGCGATTTTCAAAACATCTGCCATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTGgtaagtcacatgaaattttcttttctctacggaacaaatgaaataatggctaaaatgtttatgctggtaaaatcctgtactatcctgtttcttgtagtga...

Basic information

species Oryza sativa
transcript LOC_Os08g15040.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g15040.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G147726_T03 (Zea mays), 5'ss of exon 5
TAACGGAATCATTAGAACTCCACAAGATTAAGAGCCGTCAATGGGCGATTTTCAAAACATCTGCCATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTGgtaagtcacatgaaattttcttttctctacggaa---caaatgaaataatggctaaaatgtttatgctggtaaaatcctgtactatcctgtttcttgtagtga
| || || ||||||||||| ||||| ||||||||||| |||||||||||||||||||||||||| ||||| |||||||| || || |||||||||||||||||||| | |||||||| | || | || | | |||||| | | | | ||| | | | | | || | |
TTACAGAGTCATTAGAACTACACAAAATTAAGAGCCGCCAATGGGCGATTTTCAAAACATCTGCAATAAAGGGAGAGGGGCTCTTCGAAGGTTTGGACTGgtaagtggggtcaaattttcatgtcctaagcgatgtttctgtaagataatgacaagtggatgaacttctttaataaaccat-tcgtatcatcagttaaaat--

upper sequence: LOC_Os08g15040.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA17G07390.1 (Glycine max), 5'ss of exon 6
TAACGGAATCATTAGAACTCCACAAGATTAAGAGCCGTCAATGGGCGATTTTCAAAACATCTGCCATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTGgtaagtcacatgaaattttcttttctctacggaacaaatgaaataatggctaaaatgtttatgctggtaaaatcctgtactatcctgtttcttgtagtga------
| ||||| | |||| | |||||||| || | || |||||||| ||||||||||| ||||||||||||||||| || |||||||| || ||||||||||||||| || ||||| | | | || || | || || || || ||| | | || ||| | |||| | || ||| | ||
TGACGGAGGCTCTAGAGTTACACAAGATCAAAAATCGCCAATGGGCTATTTTCAAAACTTCTGCCATAAAAGGAGAAGGACTTTTTGAGGGCCTGGACTGgtaagtcaaataaaattgaaggctgttt-cgagggaatt---atgattttaaatatcctta-gataataggtacctttgctatattattgcttttt-tgttttcgt

upper sequence: LOC_Os08g15040.2 (Oryza sativa), 5'ss of exon 7
lower sequence: AT2G24765.1 (Arabidopsis thaliana), 5'ss of exon 7
TAACGGAATCATTAGAACTCCACAAGATTAAGAGCCGTCAATGGGCGATTTTCAAAACATCTGCCATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTGgtaagtcacat---gaaatt---ttcttttctctacggaacaaatgaaataatgg-ctaaaatgtttatgctggtaaaatcctgtactatcctgt--ttcttgtagtga-------
| || ||| | || || | || ||||| ||||| ||||||||||| || |||||||| | ||| | ||||| ||||| ||||| || || ||||||||||||| ||||| |||| |||||| | | ||||| | || | | | ||||||| | || || | | || | || | |||
TTACAGAAGCCTTGGAGTTGCATAAGATAAAGAGTCGTCAATGGGCAATCTTCAAAACTTGTGCTGTGAAAGGCGAGGGACTTTTCGAGGGATTGGACTGgtaag-cacattctgaaaccgaaccattttcttggtcccattattgaaacactgaacccatttctttatgcatttcttctcaaatattcttctctcatttccatcttgatcttcag

upper sequence: LOC_Os08g15040.2 (Oryza sativa), 5'ss of exon 7
lower sequence: AT2G24765.2 (Arabidopsis thaliana), 5'ss of exon 7
TAACGGAATCATTAGAACTCCACAAGATTAAGAGCCGTCAATGGGCGATTTTCAAAACATCTGCCATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTGgtaagtcacat---gaaatt---ttcttttctctacggaacaaatgaaataatgg-ctaaaatgtttatgctggtaaaatcctgtactatcctgt--ttcttgtagtga-------
|| | || || | || ||||| ||||| ||||||||||| || |||||||| | ||| | ||||| ||||| ||||| || || ||||||||||||| ||||| |||| |||||| | | ||||| | || | | | ||||||| | || || | | || | || | |||
------AAGCCTTGGAGTTGCATAAGATAAAGAGTCGTCAATGGGCAATCTTCAAAACTTGTGCTGTGAAAGGCGAGGGACTTTTCGAGGGATTGGACTGgtaag-cacattctgaaaccgaaccattttcttggtcccattattgaaacactgaacccatttctttatgcatttcttctcaaatattcttctctcatttccatcttgatcttcag

upper sequence: LOC_Os08g15040.2 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv11s0052g01720.t01 (Vitis vinifera), 5'ss of exon 8
TAACGGAATCATTAGAACTCCACAAGATTAAGAGCCGTCAATGGGCGATTTTCAAAACATCTGCCATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTGgtaagtcacatgaaattttcttttctctacggaacaa-atgaaataat--ggcta--aaatgtttatgctggtaaaatcctgtactatcctgtttcttgtagtga
| || || | ||||| | ||||||||||| | |||||||||||| ||||| ||||| |||||||||||||| || || || ||||| || |||||||||||||||| | | ||| | | || | | |||| || || | | | |||| | | || || | || || | |
TGACTGAGGCCTTAGAGTTGCACAAGATTAAAAACCGTCAATGGGCAATTTTTAAAACTTCTGCCATAAAAGGGGAAGGTCTCTTTGAGGGCTTGGACTGgtaagtca----acacttttaatgataaacatgttagtgttggttaataaggttaccaggcatctgtgctt-tcagattttgagttgctctattgttcaccattt

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|88838029|gb|CI372597.1|CI372597
EST:     TTCAAAACATCTGCCATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTG                         GCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
genomic: TTCAAAACATCTGCCATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTGgtaagtcaca ... cttgctgcagGCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
EST: gi|88560826|gb|CI491521.1|CI491521
EST:     CATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTG                         GCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
genomic: CATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTGgtaagtcaca ... cttgctgcagGCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
EST: gi|88906338|gb|CI375410.1|CI375410
EST:     TTCAAAACATCTGCCATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTG                         GCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
genomic: TTCAAAACATCTGCCATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTGgtaagtcaca ... cttgctgcagGCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
EST: gi|86844287|gb|CI337645.1|CI337645
EST:     TTCAAAACATCTGCCATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTG                         GCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
genomic: TTCAAAACATCTGCCATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTGgtaagtcaca ... cttgctgcagGCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
EST: gi|86527922|gb|CI168128.1|CI168128
EST:     AGGAGAGGGCCTTTTTGAAGGTTTGGACTG                         GCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
genomic: AGGAGAGGGCCTTTTTGAAGGTTTGGACTGgtaagtcaca ... cttgctgcagGCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
EST: gi|89162128|gb|CI103664.1|CI103664
EST:     TTCAAAACATCTGCCATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTG                         GCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
genomic: TTCAAAACATCTGCCATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTGgtaagtcaca ... cttgctgcagGCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
EST: gi|88239417|gb|CI240579.1|CI240579
EST:     TTCAAAACATCTGCCATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTG                         GCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
genomic: TTCAAAACATCTGCCATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTGgtaagtcaca ... cttgctgcagGCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
EST: gi|86879835|gb|CI339947.1|CI339947
EST:     TTCAAAACATCTGCCATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTG                         GCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
genomic: TTCAAAACATCTGCCATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTGgtaagtcaca ... cttgctgcagGCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
EST: gi|88243558|gb|CI243955.1|CI243955
EST:     TTCAAAACATCTGCCATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTG                         GCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
genomic: TTCAAAACATCTGCCATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTGgtaagtcaca ... cttgctgcagGCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
EST: gi|2800167|gb|AA753156.1|AA753156
EST:     GAGAGGGCCTTTTTGAANGTTTGGACTG                         GCTCNTTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
genomic: GAGAGGGCCTTTTTGAAGGTTTGGACTGgtaagtcaca ... cttgctgcagGCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
EST: gi|88465078|gb|CI514850.1|CI514850
EST:     TTCAAAACATCTGCCATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTG                         GCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
genomic: TTCAAAACATCTGCCATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTGgtaagtcaca ... cttgctgcagGCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
EST: gi|86434337|gb|CI094680.1|CI094680
EST:     TTCAAAACATCTGCCATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTG                         GCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
genomic: TTCAAAACATCTGCCATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTGgtaagtcaca ... cttgctgcagGCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
EST: gi|88502850|gb|CI430356.1|CI430356
EST:     TTCAAAACATCTGCCATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTG                         GCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
genomic: TTCAAAACATCTGCCATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTGgtaagtcaca ... cttgctgcagGCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
EST: gi|27547712|gb|CA765788.2|CA765788
EST:     TTCAAAACATCTGCCATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTG                         GCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
genomic: TTCAAAACATCTGCCATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTGgtaagtcaca ... cttgctgcagGCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
EST: gi|86511016|gb|CI153649.1|CI153649
EST:     TTCAAAACATCTGCCATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTG                         GCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
genomic: TTCAAAACATCTGCCATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTGgtaagtcaca ... cttgctgcagGCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
EST: gi|88200314|gb|CI200164.1|CI200164
EST:     TTCAAAACATCTGCCATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTG                         GCTCAGTAATGCACTGAAATCCGAAAGCAGCTAATTTAGGAGCCTCTGTTC
genomic: TTCAAAACATCTGCCATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTGgtaagtcaca ... cttgctgcagGCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
EST: gi|88459095|gb|CI514376.1|CI514376
EST:     GAGGGCCTTTTTGAAGGTTTGGACTG                         GCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
genomic: GAGGGCCTTTTTGAAGGTTTGGACTGgtaagtcaca ... cttgctgcagGCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
EST: gi|88319099|gb|CI513163.1|CI513163
EST:     TTCNAAACATCTGCCATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTG                         GCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
genomic: TTCAAAACATCTGCCATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTGgtaagtcaca ... cttgctgcagGCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
EST: gi|33682863|gb|CF311102.1|CF311102
EST:     TGAAGGTTTGGACTG                         GCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
genomic: TGAAGGTTTGGACTGgtaagtcaca ... cttgctgcagGCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
EST: gi|88468492|gb|CI514974.1|CI514974
EST:     TTCAAAACATCTGCCATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTG                         GCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC
genomic: TTCAAAACATCTGCCATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTGgtaagtcaca ... cttgctgcagGCTCAGTAATGCACTGAAATCCAAAAGCAGCTAATTTAGGAGCCTCTGTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAACGGAATCATTAGAACTCCACAAGATTAAGAGCCGTCAATGGGCGATTTTCAAAACATCTGCCATAAAAGGAGAGGGCCTTTTTGAAGGTTTGGACTGgtaagtcacatgaaattttcttttctctacggaacaaatgaaataatggctaaaatgtttatgctggtaaaatcctgtactatcctgtttcttgtagtga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG