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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaagacctgaacatatgctttttatagtctttttttcttatatttgatgggggtcaacattacttgggggcgctaactgtttgtttcactctccaaatccagACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTTAATATTGCCCTTGATGATGTGTCCATCACAAGCCTGAGCTTCGGAAAGG

Basic information

species Oryza sativa
transcript LOC_Os07g15880.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g15880.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G352289_T01 (Zea mays), 3'ss of exon 2
gttaagacctgaacatatgctttttatagtctttttttcttatatttgatgggggtcaacattacttgggggcg---ctaactgtttgtttcactctccaaatccagACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTTAATATTGCCCTTGATGATGTGTCCATCACAAGCCTGAGCTTCGGAAAGG
                                |    |   |  | ||| |  | |    | |||||    ||    ||   |  |  ||||   | |||| | ||| | |||||||||||||| || ||||||||||| |||||||| ||    |  || ||||| ||||||||||| |||||||||||||| |||||||| | ||
-------------------------------gtacgattgaacgtatgaagttgctagtaactacttaatagcaattctgtttactcttttccgccaccaatttcagGCTGTGAGTAGGGAGATTAGGAAGATACTGACCGAGAGGGCTAGATTCTCCAACATTGCTCTTGATGATGTCTCCATCACAAGCCTAAGCTTCGGGAGGG
















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|55431838|gb|CV728939.1|CV728939
EST:     ACAATGCGAGTCAGCTAATCACACAGAGAGAG                         ACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
genomic: ACAATGCGAGTCAGCTAATCACACAGAGAGAGgttaagacct ... ccaaatccagACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
EST: gi|86498079|gb|CI140712.1|CI140712
EST:     AAGCTGTTGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAG                         ACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
genomic: AAGCTGTTGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAGgttaagacct ... ccaaatccagACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
EST: gi|32948492|gb|BP185064.1|BP185064
EST:     AAGCTGTTGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAG                         ACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
genomic: AAGCTGTTGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAGgttaagacct ... ccaaatccagACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
EST: gi|218492050|gb|FG952147.1|FG952147
EST:     CTAATCACACAGAGAGAG                         ACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
genomic: CTAATCACACAGAGAGAGgttaagacct ... ccaaatccagACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
EST: gi|58693615|gb|CK082302.1|CK082302
EST:     AAGCTGTTGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAG                         ACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
genomic: AAGCTGTTGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAGgttaagacct ... ccaaatccagACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
EST: gi|218496989|gb|FG950832.1|FG950832
EST:     AAGCTGTTGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAG                         ACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
genomic: AAGCTGTTGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAGgttaagacct ... ccaaatccagACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
EST: gi|86594738|gb|CI255814.1|CI255814
EST:     AAGCTGTTGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAG                         ACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
genomic: AAGCTGTTGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAGgttaagacct ... ccaaatccagACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
EST: gi|33803697|gb|CF327723.1|CF327723
EST:     AAGCTGTTGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAG                         ACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
genomic: AAGCTGTTGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAGgttaagacct ... ccaaatccagACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
EST: gi|86594799|gb|CI255875.1|CI255875
EST:     AAGCTGTTGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAG                         ACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
genomic: AAGCTGTTGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAGgttaagacct ... ccaaatccagACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
EST: gi|218494609|gb|FG957575.1|FG957575
EST:     CACACAGAGAGAG                         A-CGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
genomic: CACACAGAGAGAGgttaagacct ... ccaaatccagACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
EST: gi|89180747|gb|CI009655.1|CI009655
EST:     CACACAGAGAGAG                         ACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
genomic: CACACAGAGAGAGgttaagacct ... ccaaatccagACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
EST: gi|8335502|gb|BE040419.1|BE040419
EST:     AAGCTGTTGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAG                         ACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
genomic: AAGCTGTTGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAGgttaagacct ... ccaaatccagACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
EST: gi|117233393|gb|CT848123.1|CT848123
EST:     AAGCTGTTGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAG                         ACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
genomic: AAGCTGTTGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAGgttaagacct ... ccaaatccagACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
EST: gi|218488311|gb|FG953544.1|FG953544
EST:     AAGCTGTTGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAG                         ACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
genomic: AAGCTGTTGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAGgttaagacct ... ccaaatccagACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
EST: gi|11118161|gb|AU163349.1|AU163349
EST:     AGCTAATCACCNCAGAGAGAAG                         NCCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTT
genomic: AGCTAATCA-CACAGAGAG-AGgttaagacct ... ccaaatccagACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTT
EST: gi|8335500|gb|BE040418.1|BE040418
EST:     AAGCTGTTGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAG                         ACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
genomic: AAGCTGTTGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAGgttaagacct ... ccaaatccagACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
EST: gi|58694784|gb|CK083471.1|CK083471
EST:     AAGCTG-TGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAG                         ACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
genomic: AAGCTGTTGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAGgttaagacct ... ccaaatccagACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
EST: gi|218489869|gb|FG943959.1|FG943959
EST:     CAGCTAATCACACAGAGAGAG                         ACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
genomic: CAGCTAATCACACAGAGAGAGgttaagacct ... ccaaatccagACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
EST: gi|27576598|gb|CA999292.1|CA999292
EST:     AAGCTGTTGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAG                         ACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
genomic: AAGCTGTTGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAGgttaagacct ... ccaaatccagACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
EST: gi|218492453|gb|FG950899.1|FG950899
EST:     AAGCTGTTGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAG                         ACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
genomic: AAGCTGTTGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAGgttaagacct ... ccaaatccagACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
EST: gi|58686687|gb|CK075374.1|CK075374
EST:     AAGCTGTTGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAG                         ACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
genomic: AAGCTGTTGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAGgttaagacct ... ccaaatccagACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
EST: gi|11118160|gb|AU163348.1|AU163348
EST:     AAGCTGTTGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAG                         ACCGTGAGTAGGGAAGATAAGAAAG
genomic: AAGCTGTTGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAGgttaagacct ... ccaaatccagACCGTGAGTAGGGA-GATAAGAAAG
EST: gi|218497361|gb|FG953033.1|FG953033
EST:     AGCTGTTGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAG                         ACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
genomic: AGCTGTTGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAGgttaagacct ... ccaaatccagACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
EST: gi|218481986|gb|FG957221.1|FG957221
EST:     AAGCTGTTGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAG                         ACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT
genomic: AAGCTGTTGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAGgttaagacct ... ccaaatccagACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTT

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), 73 (downstream exon)
Score: 89

GGAGAACTTCAATGAGAGAGTTTTGCCTTCAATTATCCATGAAACACTTAAAGCTGTTGTCGCACAATACAATGCGAGTCAGCTAATCACACAGAGAGAGgttaagacct ... ccaaatccagACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTTAATATTGCCCTTGATGATGTGTCCATCACAAGCCTGAGCTTCGGAAAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgggggtcaacattacttgggggcgctaactgtttgtttcactctccaaatccagACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTTAATATTGCCCTTGATGATGTGTCCATCACAAGCCTGAGCTTCGGAAAGG
                       cgctaac  putative branch site (score: 89)
                                tttgtttcactctcc  putative PPT
        aacatta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaagacctgaacatatgctttttatagtctttttttcttatatttgatgggggtcaacattacttgggggcgctaactgtttgtttcactctccaaatccagACCGTGAGTAGGGAGATAAGAAAGATACTGACTGAGAGGGCCAGGAATTTTAATATTGCCCTTGATGATGTGTCCATCACAAGCCTGAGCTTCGGAAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT