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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGAGTACGTCATTTGCAATGGTTGCAAAAGCCCTGATACCATTCTATCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaatgccgtctgattatctgcttgtgcatgttcagttacatccagtttgcttcggcatgagcgatcactcctctgtgaaaacattagttaattgcctt...

Basic information

species Oryza sativa
transcript LOC_Os07g48300.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g48300.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G030646_T02 (Zea mays), 5'ss of exon 7
ATGAGTACGTCATTTGCAATGGTTGCAAAAGCCCTGATACCATTCTATCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaatgccgtctgattatctgcttgtgcatgttcagttacatccagtttgcttcggcatgagcgatcactcctctgtgaaaacattagttaattgcctt-------
||||||| ||||| |||||||| ||||| ||||||||||| ||| | ||||| ||||||||||||||||||||||||||||||||||||||    ||||    |     |   | ||||   |  ||  |   | || |  |  ||   |  | ||  ||||| |  |   |  |||| |    ||       
ATGAGTATGTCATCTGCAATGGATGCAAGAGCCCTGATACTATTTTGTCCAAAGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaa--atgtcttgcaaaacaatgtaggatgt--ggggactgctgttctgatgtgatattttc--taacggctctg-ggcactttcggttactcctgtttcataca

upper sequence: LOC_Os07g48300.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G080048_T01 (Zea mays), 5'ss of exon 8
ATGAGTACGTCATTTGCAATGGTTGCAAAAGCCCTGATACCATTCTATCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaatgccgtctgattatctgcttgtgcatgttcagttacatccagtttgcttcggcatgagcga-tcactcctctgtgaaaacattagttaattgcctt-
||||||||||||| |||||||| ||||| ||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||| |  | | ||   || |  || || | || |  |     |     |  | |||   |   ||| ||| || | | |  |||| ||  ||      
ATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaatgtctgcagttttggtg-tgatgtatttccaatagctctaggcactttcagtcattcccatctcattcccctat-acatgattattttgttatacat

upper sequence: LOC_Os07g48300.1 (Oryza sativa), 5'ss of exon 9
lower sequence: PP1S280_23V6.1 (Physcomitrella patens), 5'ss of exon 7
ATGAGTACGTCATTTGCAATGGTTGCAAAAGCCCTGATACCATTCTATCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaatgccgtctgattatctgcttgtgcatgttcagttacatccagtttgcttcggcatgagcga-tcactcctctgtgaaaacattagttaattgcctt------------------------------------------------------------------------------
| ||||||||||| |||||||||||||| ||||||||||||||||| |||||||| ||||| |||||||||||||| || |||||||||| |        ||| | ||  | |   | ||  | |   |    | | |||   ||    | | |  ||  | | |  | || |   ||   |||  |                                                                              
ACGAGTACGTCATGTGCAATGGTTGCAAGAGCCCTGATACCATTCTTTCCAAGGAGAATCGGCTGTTCTTCCTTCGTTGTGAACAGgtaagtaattctcaattttgtggctttttctatttcggtg-gttgtttatacttgtacaatttctactttcttttatttagacacctctattttgtgctcttcttttttaatgcaagacacagtctttgtttcgtgatattatttatacggacatgaccgatgggttgcttgtcaacag

upper sequence: LOC_Os07g48300.1 (Oryza sativa), 5'ss of exon 9
lower sequence: PP1S81_161V6.1 (Physcomitrella patens), 5'ss of exon 5
ATGAGTACGTCATTTGCAATGGTTGCAAAAGCCCTGATACCATTCTATCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaatg-ccgtctgattatctgcttgtgcatgttc-agttaca--tccagtttgcttcggcatgagcgatc-actcctctgtgaaaac----------attagttaattgcctt------------------------------------------------------------------------------
||||||| || || |||||||||||||| || || || || || || |||||||| ||||| |||||||| ||||| || |||||||| |       |||  ||   |   ||||  | ||   ||| ||  | ||||     || ||    ||  |  ||     ||  |  ||          ||| |||| |||| |                                                                               
ATGAGTATGTTATGTGCAATGGTTGCAAGAGTCCAGACACTATCCTTTCCAAGGAGAATCGGCTGTTCTTTCTTCGTTGTGAACAGgttagcaattatctatttgcgtctgtgtggttcttttggtttcagtttcagtggttctctgctcttgcagttgaccagcttggcaggacctttttacaaattggttatttgcatcttcgaagaacgacgtcagtcttgtttcatggtggttgtgttgtgctgacgtagtctcttggtttttgtacgttgacag

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|33824940|gb|CF338274.1|CF338274
EST:     ATACCATTCTATCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGN-CAG                         TGTGGATCGTCGAGGTCTGTTGCTCCAATCAAGGCTGGATTTGTCGCACAA
genomic: ATACCATTCTATCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaatgccg ... ttctgtctagTGTGGATCGTCGAGGTCTGTTGCTCCAATCAAGGCTGGATTTGTCGCACAA
EST: gi|89163018|gb|CI099908.1|CI099908
EST:     ATACCATTCTATCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG                         TGTGGATCGTCGAGGTCTGTTGCTCCAATCAAGGCTGGATTTGTCGCACAA
genomic: ATACCATTCTATCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaatgccg ... ttctgtctagTGTGGATCGTCGAGGTCTGTTGCTCCAATCAAGGCTGGATTTGTCGCACAA
EST: gi|33658199|gb|CF280813.1|CF280813
EST:     ATACCATTCTATCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG                         TGTGGATCGTCGAGGTCTGTTGCTCCAATCAAGGCTGGATTTGTCGCACAA
genomic: ATACCATTCTATCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaatgccg ... ttctgtctagTGTGGATCGTCGAGGTCTGTTGCTCCAATCAAGGCTGGATTTGTCGCACAA
EST: gi|25803992|gb|CA759953.1|CA759953
EST:     ATACCATTCTATCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG                         TGTGGATCGTCGAGGTCTGTTGCTCCAATCAAGGCTGGATTTGTCGCACAA
genomic: ATACCATTCTATCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaatgccg ... ttctgtctagTGTGGATCGTCGAGGTCTGTTGCTCCAATCAAGGCTGGATTTGTCGCACAA
EST: gi|55409065|gb|CV721441.1|CV721441
EST:     ATACCATTCTATCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG                         TGTGGATCGTCGAGGTCTGTTGCTCCAATCAAGGCTGGATTTGTCGCACAA
genomic: ATACCATTCTATCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaatgccg ... ttctgtctagTGTGGATCGTCGAGGTCTGTTGCTCCAATCAAGGCTGGATTTGTCGCACAA
EST: gi|88990737|gb|CI108124.1|CI108124
EST:     ATACCATTCTATCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG                         TGTGGATCGTCGAGGTCTGTTGCTCCAATCAAGGCTGGATTTGTCGCACAA
genomic: ATACCATTCTATCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaatgccg ... ttctgtctagTGTGGATCGTCGAGGTCTGTTGCTCCAATCAAGGCTGGATTTGTCGCACAA
EST: gi|88238682|gb|CI238531.1|CI238531
EST:     ATACCATTCTATCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG                         TGTGGATCGTCGAGGTCTGTTGCTCCAATCAAGGCTGGATTTGTCGCACAA
genomic: ATACCATTCTATCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaatgccg ... ttctgtctagTGTGGATCGTCGAGGTCTGTTGCTCCAATCAAGGCTGGATTTGTCGCACAA
EST: gi|38481420|gb|CF965509.1|CF965509
EST:     ATACCATTCTATCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG                         TGTGGATCGTCGAGGTCTGTTGCTCCAATCAAGGCTGGATTTGTCGCACAA
genomic: ATACCATTCTATCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaatgccg ... ttctgtctagTGTGGATCGTCGAGGTCTGTTGCTCCAATCAAGGCTGGATTTGTCGCACAA
EST: gi|66923189|gb|CX110037.1|CX110037
EST:     ATACCATTCTATCCAAGGAAAATCGTCTGTTCTTACTTCGCTGCGAACAG                         TGTGGATCGTC
genomic: ATACCATTCTATCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaatgccg ... ttctgtctagTGTGGATCGTC

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: 50 (upstream exon), 58 (downstream exon)
Score: 2

ATGAGTACGTCATTTGCAATGGTTGCAAAAGCCCTGATACCATTCTATCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaatgccg ... ttctgtctagTGTGGATCGTCGAGGTCTGTTGCTCCAATCAAGGCTGGATTTGTCGCACAAGTTGGTCGGCGGAAGGCCTGAACATAAGTCGAAGCTTTGGATTTGTCTA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGAGTACGTCATTTGCAATGGTTGCAAAAGCCCTGATACCATTCTATCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAGgtaaatgccgtctgattatctgcttgtgcatgttcagttacatccagtttgcttcggcatgagcgatcactcctctgtgaaaacattagttaattgcctt

- - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA