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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTATAGGAAGCTTGCTAGGAGCTACCATCCTGATGTGAACAAgtaagtactaaccattatatgggaattgtgtttcagctacactcgatatattgcttctttttctcctttcgatccattataaacctgagtactagttgttgcattacctttttcataactacataatcaaataagcaattgttatgcttgtgtatttttctttag

Basic information

species Oryza sativa
transcript LOC_Os05g26914.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g26914.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G091811_T01 (Zea mays), 5'ss of exon 5
CCTATAGGAAGCTTGCTAGGAGCTACCATCCTGATGTGAACAAgtaagtactaaccattatatgggaattgtgtttcagctacactcgatatattgcttctttttctcctttcgatccattataaacctgagtactagttgttgcattacctttttcataactacataatcaaataagcaattgttatgcttgtgtatttttctttag
||||| ||||||||||||||||||| ||||| ||||| |||||||||||  |  | |||  |    |||    ||||||||||  ||     ||  |   | |||  | |||||     ||| | |    |   | ||| || || | |    |                                                      
CCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAAgtaagt--tggctattgca--ataatcacttttcagctactatc-----atcaccattcttttgcttttcggatgcttagaga----aactccagtagtcgcctaaagaatcc----------------------------------------------------

upper sequence: LOC_Os05g26914.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM5G856084_T01 (Zea mays), 5'ss of exon 5
CCTATAGGAAGCTTGCTAGGAGCTACCATCCTGATGTGAACAAgtaagtactaaccattatat--gggaattgtgtttcagctac----ac--tcgatatattgcttctttttc--tcctttcgatccattataa-acctgagtactagttgttg--catta--cctttttcataactacataatcaaataagcaattgttatgcttgtgtatttttctttag
||||| ||||||||||||||||||| ||||| ||||| ||||||| |||  |  | |||  |   | ||||    ||||||||||    ||  ||   || ||| | |||||    | |||     |   | ||   ||||  || |  |  |||  |||||  | | | ||  |  ||   | ||||||||  ||    |||   | | |  | |  |||||
CCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAAgtgagt--tggctattgcaatagagaatcacttttcagctactatcaccatcatcattttgttgcttttcgggtgcttatagccagctgtactgcctgtatattcttctttgtacattagacatctctctcatttagtcagtcaaataatgaa--agtatctatttatgatctattttag

upper sequence: LOC_Os05g26914.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT4G39960.1 (Arabidopsis thaliana), 5'ss of exon 5
CCTATAGGAAGCTTGCTAGGAGCTACCATCCTGATGTGAACAAgtaagtactaaccattatatgggaattgtgtttcagctacactcgatatattgcttctttttctcctttcgatccattataaacctgagtactagttgttgcattacctttttcataactacataatcaaataagcaattgttatgcttgtgtatttttctttag
| ||| ||||||| |||||||| || ||||| |||||||||||||||||   ||   ||   |     |||| |      ||   ||    |  || || | ||  |    |   | ||| | | |   | ||  |  ||||| ||                                                              
CTTATCGGAAGCTCGCTAGGAGTTATCATCCAGATGTGAACAAgtaagtg--aagggtttagtttactttgtatccagtataaggtcttcgt-ctgtttatattatttaccttcctgcatca-agattggtgtgtttcttgttacaa-------------------------------------------------------------

upper sequence: LOC_Os05g26914.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT2G22360.1 (Arabidopsis thaliana), 5'ss of exon 5
CCTATAGGAAGCTTGCTAGGAGCTACCATCCTGATGTGAACAAgtaagtactaaccattatatgggaattgtgtttcagctacactcgatatattgcttctttttctcctttcgatccattataaacctgagtactagttgttgcattacctttttcataactacataatcaaataagcaattgttatgcttgtgtatttttctttag
| ||| ||||||| |||||||  |||||||| |||||||||||||||||   || | | |  ||   |   |  |  |  || |        ||       |    ||    |  || | || | |   ||    || |   ||                                                                
CTTATCGGAAGCTGGCTAGGAATTACCATCCGGATGTGAACAAgtaagtgaaaaacttcacttgatgacgatagtggatgtatatcttgagaataagaagataggatcga--cagtcaagtagagataagaagcttaatatctgt---------------------------------------------------------------

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|58608089|gb|CK036122.1|CK036122
EST:     CCTATCGGAAGCTTGCTAGGAGCTACCATCCTGATGTGAACAA                         AGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG
genomic: CCTATAGGAAGCTTGCTAGGAGCTACCATCCTGATGTGAACAAgtaagtacta ... ttttctttagAGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG
EST: gi|29685207|gb|CB681482.1|CB681482
EST:     CCTATAGGAAGCTTGCTAGGAGCTACCATCCTGATGTGAACAA                         AGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG
genomic: CCTATAGGAAGCTTGCTAGGAGCTACCATCCTGATGTGAACAAgtaagtacta ... ttttctttagAGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG
EST: gi|29620923|gb|CB625934.1|CB625934
EST:     CCTATCGGAAGCTTGCTAAGAGCTACCATCCTGATGTGAACAA                         AGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG
genomic: CCTATAGGAAGCTTGCTAGGAGCTACCATCCTGATGTGAACAAgtaagtacta ... ttttctttagAGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG
EST: gi|58673732|gb|CK062418.1|CK062418
EST:     GCTAGGAGCTACCATCCTGATGTGAACAA                         AGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG
genomic: GCTAGGAGCTACCATCCTGATGTGAACAAgtaagtacta ... ttttctttagAGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG
EST: gi|29680449|gb|CB676724.1|CB676724
EST:     CCTATAGGAAGCTTGCTAGGAGCTACCATCCTGATGTGAACAA                         AGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG
genomic: CCTATAGGAAGCTTGCTAGGAGCTACCATCCTGATGTGAACAAgtaagtacta ... ttttctttagAGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG
EST: gi|29681007|gb|CB677282.1|CB677282
EST:     CCTATAGGAAGCTTGCTAGGAGCTACCATCCTGATGTGAACAA                         AGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG
genomic: CCTATAGGAAGCTTGCTAGGAGCTACCATCCTGATGTGAACAAgtaagtacta ... ttttctttagAGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG
EST: gi|58660788|gb|CK049468.1|CK049468
EST:     CCTATCGGAGGCTTGCTAGGAGCTACCATCCTGATGTGAACAA                         AGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG
genomic: CCTATAGGAAGCTTGCTAGGAGCTACCATCCTGATGTGAACAAgtaagtacta ... ttttctttagAGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG
EST: gi|29680374|gb|CB676649.1|CB676649
EST:     CCTATAGGAAGCTTGCTAGGAGCTACCATCCTGATGTGAACAA                         AGATCCTGGTGCTGAACAAAAGTTCAAGGATATTACCAATGCTTATGAA
genomic: CCTATAGGAAGCTTGCTAGGAGCTACCATCCTGATGTGAACAAgtaagtacta ... ttttctttagAGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG
EST: gi|58676612|gb|CK065299.1|CK065299
EST:     GAGTGCCTATCGGAAGCTTGCTAGGAGCTACCATCCTGATGTGAACAA                         AGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG
genomic: GAGTGCCTATAGGAAGCTTGCTAGGAGCTACCATCCTGATGTGAACAAgtaagtacta ... ttttctttagAGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG

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: 69 (upstream exon), 75 (downstream exon)
Score: 50

CCTATAGGAAGCTTGCTAGGAGCTACCATCCTGATGTGAACAAgtaagtacta ... ttttctttagAGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTATAGGAAGCTTGCTAGGAGCTACCATCCTGATGTGAACAAgtaagtactaaccattatatgggaattgtgtttcagctacactcgatatattgcttctttttctcctttcgatccattataaacctgagtactagttgttgcattacctttttcataactacataatcaaataagcaattgttatgcttgtgtatttttctttag

- - - - - - - - - GGAGCT