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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTTTGTAATCGCCTTCTCCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAGgtatagcttcatggctcataatcatacggccttggaatttagctgaagagcattcacatggccatgatttttggagcatttgtcagatggtctgaagactcacttccaacttgtatattttcag

Basic information

species Oryza sativa
transcript LOC_Os05g49270.1
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g49270.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G077546_T01 (Zea mays), 5'ss of exon 15
GCTTTTGTAATCGCCTTCTCCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAGgtatagcttcatggctcataatcatacggccttggaatttagctgaagagcattcacatg--gccatgatttttggagcatttgtcagatggtctgaagactcacttccaacttgtatattttcag
|||| ||| || ||||||| |||||| ||||||||||||||||||||||| ||||| |||||||||   |    | ||| |       || |  ||     ||||||     |    | |  |  || ||| | | | | |||| || || | | |                              
GCTTATGTCATTGCCTTCTGCTTCGGCATGGGTGCCATTCCATGGATCATTATGTCTGAGgtatagtacctcaacacatga----gatgcttgagacacatgctgaaagctctctgaacgaagggattattctcgaaac-tttg-catatcgacag------------------------------

upper sequence: LOC_Os05g49270.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G160460_T02 (Zea mays), 5'ss of exon 15
GCTTTTGTAATCGCCTTCTCCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAGgtatagcttcatggctcata----------atca-tacggccttggaatttagctgaagag---cattcacatggccatgatttttggagcatttgtcagatggtctgaagactcacttccaactt-gtatattttcag
|||| ||| || ||||||||||||||||||||||||||||| |||||||||||||| |||||||||   | |    || |          |||| |||   | |       || |  ||     || | |   |    || | || ||   ||  |    |  || ||||| || ||||| ||||| | || |||  ||
GCTTATGTCATTGCCTTCTCCTTCGGTATGGGTGCCATTCCTTGGATCATAATGTCTGAGgtatagtaccttaatgcacagcgaagatatatcaatacatgcctctctcccagttttaggtttccactgaagagcaagtgctcttaggcatataggctttaaagtttgaaggcttacttcaaactttgcatttttgtag

upper sequence: LOC_Os05g49270.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G160504_T02 (Zea mays), 5'ss of exon 15
GCTTTTGTAATCGCCTTCTCCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAGgtata--gcttcatggctcata-atcatacggcct-tggaatt-----tagctgaagagcattcacatggccatgatttttggagcatttgtcagatg----gtctgaagactcacttccaacttgtatattttcag---------------------------------------
 ||||||| ||  ||||||| || ||||||||||||||||||||| |||| ||||| ||||||     |||| | || ||      |||  || | |  |||      | ||     ||  || ||||  | | ||     | |  || ||    ||     ||||||||   ||  ||      |||   |   |                                        
TCTTTTGTCATTACCTTCTCGTTTGGTATGGGTGCCATTCCATGGCTCATGATGTCTGAGgtacgctacttctttgcacacctgatataaagcttgtataatgcctcattgcctcctagttttgacatcccaacgaagg--gaactatctgcacaatcaactgtctgaagctacagctcaggaacgtactgtaagaaatatctgaatgtatagttcaaactttgtgcgtttttcag

upper sequence: LOC_Os05g49270.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G028570_T01 (Zea mays), 5'ss of exon 8
GCTTTTGTAATCGCCTTCTCCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAGgtatagcttcatggctcataatcatacggccttggaatttagctgaagagcattcacatggccatgatttttggagcatttgtcagatggtctgaagactcacttccaa---cttgtatattttcag
|||| ||| |  || | |||||| |||||||||||||||||||||||||||||| | |||||||||     |  || || | ||||  ||     ||||||||| |     |  | ||||  ||||   ||   || |  ||    |||     ||  |||| |  |||    ||| |||||  |||
GCTTGTGTCACTGCTTACTCCTTTGGTATGGGTGCCATTCCATGGATCATAATGGCTGAGgtatag-----taccttatca-catatagct----aatttagctcatagtaagcctcatgcacatg---ttgaaagga--tgctgaatg-----aaagctcattctcaaaactttgcatattgacag

upper sequence: LOC_Os05g49270.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G098679_T01 (Zea mays), 5'ss of exon 15
GCTTTTGTAATCGCCTTCTCCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAGgtatagcttcatggctcataatcatacggccttggaatttagctgaagagcattcacatggccatgatttttggagcatttgtcagatggtctgaagactcacttccaacttgtatattttcag
|||| ||| |  |||| |||||| |||||||||||||||||||||||||||||| | |||||||||   |||     ||||  |      ||   ||  |   ||| |      ||||||   |     ||   |      |     |  |||  | |||          ||| |||||  |||
GCTTATGTCACTGCCTACTCCTTTGGTATGGGTGCCATTCCATGGATCATAATGGCTGAGgtatagtcacat-----ataactaatttagctcataagatgcttgagg------cacatgatgaaaggattctaaatgaaggct---taatctcgaaact----------ttgcatattggcag

upper sequence: LOC_Os05g49270.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G160430_T04 (Zea mays), 5'ss of exon 14
GCTTTTGTAATCGCCTTCTCCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAGgtatagcttcatggctcataatcatacggccttggaatttagctgaagagcattcacatggccatgatttttggagcatttgtcagatggtctgaagactcacttccaacttgtatattttcag
|||| ||| |  ||||||||||||||||||||| |||||||||||||||||||||| ||||||||    | |   ||| |   |||    ||   ||| || || |  ||       |||   |     ||  ||      | | |||  ||||   |||   | || | |   |         
GCTTATGTCACTGCCTTCTCCTTCGGTATGGGTTCCATTCCATGGATCATAATGTCTGAGgtataataccctta-tcaca--tatataagct---aatataactcataag-------atgctgaaagcattctgaatgaaaggctgat--tctgggaactt--tgcctattgacag--------

upper sequence: LOC_Os05g49270.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G160430_T03 (Zea mays), 5'ss of exon 1
----------------------------------------GCTTTTGTAATCGCCTTCTCCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAGgtatagcttcatggctcataatcatacggccttggaatttagctgaagagcattcacatggccatgatttttggagcatttgtcagatggtctgaagactcacttccaacttgtatattttcag
                                        |||| ||| |  ||||||||||||||||||||| |||||||||||||||||||||| ||||||||    | |   ||| |   |||    ||   ||| || || |  ||       |||   |     ||  ||      | | |||  ||||   |||   | || | |   |         
TGTGGAATCTGTAAGTTTTTTGCCCAACTACTTTGTTCAGGCTTATGTCACTGCCTTCTCCTTCGGTATGGGTTCCATTCCATGGATCATAATGTCTGAGgtataataccctta-tcaca--tatataagct---aatataactcataag-------atgctgaaagcattctgaatgaaaggctgat--tctgggaactt--tgcctattgacag--------

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|87009920|gb|CI277421.1|CI277421
EST:     TCGCCTTCTCCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAG                         ATCCTCCCGGTTAGTATCAAGAGTCTCGCAGGAAGCTTTGCGACGCTCGCC
genomic: TCGCCTTCTCCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAGgtatagcttc ... atattttcagATCCTCCCGGTTAGTATCAAGAGTCTCGCAGGAAGCTTTGCGACGCTCGCC
EST: gi|88956974|gb|CI095026.1|CI095026
EST:     CCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAG                         ATCCTCCCGGTTAGTATCAAGAGTCTCGCAGGAAGCTTTGCGACGCTCGCC
genomic: CCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAGgtatagcttc ... atattttcagATCCTCCCGGTTAGTATCAAGAGTCTCGCAGGAAGCTTTGCGACGCTCGCC
EST: gi|58682760|gb|CK071447.1|CK071447
EST:     TCGCCTTCTCCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAG                         ATCCTCCCGGTTAGTATCAAGAGTCTCGCAGGAAGCTTTGCGACGCTCGCC
genomic: TCGCCTTCTCCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAGgtatagcttc ... atattttcagATCCTCCCGGTTAGTATCAAGAGTCTCGCAGGAAGCTTTGCGACGCTCGCC
EST: gi|88257732|gb|CI360318.1|CI360318
EST:     TTCCATGGATCATAATGTCAGAG                         ATCCTCCCGGTTAGTATCAAGAGTCTCGCAGGAAGCTTTGCGACGCTCGCC
genomic: TTCCATGGATCATAATGTCAGAGgtatagcttc ... atattttcagATCCTCCCGGTTAGTATCAAGAGTCTCGCAGGAAGCTTTGCGACGCTCGCC
EST: gi|86541299|gb|CI181505.1|CI181505
EST:     TCGCCTTCTCCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAG                         ATCCTCCCGGTTAGTATCAAGAGTCTCGCAGGAAGCTTTGCGACGCTCGCC
genomic: TCGCCTTCTCCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAGgtatagcttc ... atattttcagATCCTCCCGGTTAGTATCAAGAGTCTCGCAGGAAGCTTTGCGACGCTCGCC
EST: gi|86501749|gb|CI144382.1|CI144382
EST:     TCGCCTTCTCCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAG                         ATCCTCCCGGTTAGTATCAAGAGTCTCGCAGGAAGCTTTGCGACGCTCGCC
genomic: TCGCCTTCTCCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAGgtatagcttc ... atattttcagATCCTCCCGGTTAGTATCAAGAGTCTCGCAGGAAGCTTTGCGACGCTCGCC
EST: gi|87021810|gb|CI277977.1|CI277977
EST:     TCGCCTTCTCCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAG                         ATCCTCCCGGTTAGTATCAAGAGTCTCGCAGGAAGCTTTGCGACGCTCGCC
genomic: TCGCCTTCTCCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAGgtatagcttc ... atattttcagATCCTCCCGGTTAGTATCAAGAGTCTCGCAGGAAGCTTTGCGACGCTCGCC
EST: gi|86890215|gb|CI321392.1|CI321392
EST:     TCGCCTTCTCCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAG                         ATCCTCCCGGTTAGTATCAAGAGTCTCGCAGGAAGCTTTGCGACGCTCGCC
genomic: TCGCCTTCTCCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAGgtatagcttc ... atattttcagATCCTCCCGGTTAGTATCAAGAGTCTCGCAGGAAGCTTTGCGACGCTCGCC
EST: gi|88281786|gb|CI403182.1|CI403182
EST:     TCGCCTTCTCCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAG                         ATCCTCCCGGTTAGTATCAAGAGTCTCGCAGGAAGCTTTGCGACGCTCGCC
genomic: TCGCCTTCTCCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAGgtatagcttc ... atattttcagATCCTCCCGGTTAGTATCAAGAGTCTCGCAGGAAGCTTTGCGACGCTCGCC
EST: gi|29687040|gb|CB683315.1|CB683315
EST:     TCGCCTTCTCCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAG                         ATCCTCCCGGTTAGTATCAAGAGTCTCGCAGGAAGCTTTGCGACGCTCGCC
genomic: TCGCCTTCTCCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAGgtatagcttc ... atattttcagATCCTCCCGGTTAGTATCAAGAGTCTCGCAGGAAGCTTTGCGACGCTCGCC
EST: gi|88502203|gb|CI429709.1|CI429709
EST:     TCGCCTTCTCCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAG                         ATCCTCCCGGTTAGTATCAAGAGTCTCGCAGGAAGCTTTGCGACGCTCGCC
genomic: TCGCCTTCTCCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAGgtatagcttc ... atattttcagATCCTCCCGGTTAGTATCAAGAGTCTCGCAGGAAGCTTTGCGACGCTCGCC
EST: gi|86887575|gb|CI294209.1|CI294209
EST:     TCGCCTTCTCCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAG                         ATCCTCCCGGTTAGTATCAAGAGTCTCGCAGGAAGCTTTGCGACGCTCGCC
genomic: TCGCCTTCTCCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAGgtatagcttc ... atattttcagATCCTCCCGGTTAGTATCAAGAGTCTCGCAGGAAGCTTTGCGACGCTCGCC
EST: gi|88975788|gb|CI024039.1|CI024039
EST:     TCGCCTTCTCCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAG                         ATCCTCCCGGTTAGTATCAAGAGTCTCGCAGGAAGCTTTGCGACGCTCGCC
genomic: TCGCCTTCTCCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAGgtatagcttc ... atattttcagATCCTCCCGGTTAGTATCAAGAGTCTCGCAGGAAGCTTTGCGACGCTCGCC
EST: gi|86903200|gb|CI313563.1|CI313563
EST:     TCGCCTTCTCCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAG                         ATCCTCCCGGTTAGTATCAAGAGTCTCGCAGGAAGCTTTGCGACGCTCGCC
genomic: TCGCCTTCTCCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAGgtatagcttc ... atattttcagATCCTCCCGGTTAGTATCAAGAGTCTCGCAGGAAGCTTTGCGACGCTCGCC
EST: gi|86890239|gb|CI321416.1|CI321416
EST:     TCGCCTTCTCCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAG                         ATCCTCCCGGTTAGTATCAAGAGTCTCGCAGGAAGCTTTGCGACGCTCGCC
genomic: TCGCCTTCTCCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAGgtatagcttc ... atattttcagATCCTCCCGGTTAGTATCAAGAGTCTCGCAGGAAGCTTTGCGACGCTCGCC

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: 60 (upstream exon), 56 (downstream exon)
Score: 8

GCTTTTGTAATCGCCTTCTCCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAGgtatagcttc ... atattttcagATCCTCCCGGTTAGTATCAAGAGTCTCGCAGGAAGCTTTGCGACGCTCGCCAACTGGCTTACATCCTTTGGAATAACAATGACAGCAAACTTGATGCTTA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTTTGTAATCGCCTTCTCCTTCGGTATGGGTGCCATTCCATGGATCATAATGTCAGAGgtatagcttcatggctcataatcatacggccttggaatttagctgaagagcattcacatggccatgatttttggagcatttgtcagatggtctgaagactcacttccaacttgtatattttcag

- - - - - - - - - - - - - - - - - - - - CATGGA