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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGACAAGATTAGGAGGCCACTGATGCGGACGCGTGCCAATGATCCAGCCAAGGTGCAAGAACTCATGGACAGTATCCGTGTCATTGGCCTCCAAGTACCTgtgggtatctctagtacctttatgctttatcactttcctgtccacacaagtaccacttgtttggttaattcatgatctagcaatgaaggattctgctgaa...

Basic information

species Oryza sativa
transcript LOC_Os06g07760.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g07760.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G173911_T01 (Zea mays), 5'ss of exon 3
GGACAAGATTAGGAGGCCACTGATGCGGACGCGTGCCAATGATCCAGCCAAGGTGCAAGAACTCATGGACAGTATCCGTGTCATTGGCCTCCAAGTACCTgtgggtatctcta---gtacctttatgctttatc----actttcctgtccacacaagtaccacttgtttggttaattcatgatctagcaatgaaggattctgctgaa
                              ||| ||||||||||    ||||||||||||||||||||||||||||||||||||  |||||||||||||||||||||||| ||   ||| |||||| ||||  |    |  || |      ||| ||||| | || ||  ||| | || || |||| | | || || || | |||  
------------------------------GCGGGCCAATGATCTGATCAAGGTGCAAGAACTCATGGACAGTATCCGTGTCATCAGCCTCCAAGTACCTgtgggtatctatatgtgtatctttattcttttccttccatatttcatcatccacgagtac-agttatt--gtttagtcctggtctaccta-gatgggtttt-ctg--

upper sequence: LOC_Os06g07760.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G007683_T01 (Zea mays), 5'ss of exon 2
GGACAAGATTAGGAGGCCACTGATGCGGACGCGTGCCAATGATCCAGCCAAGGTGCAAGAACTCATGGACAGTATCCGTGTCATTGGCCTCCAAGTACCTgtgggtatctcta---gtacctttatgctttatcactttcctgtccacacaagtaccacttgtttggttaattcatgatctagcaatg-aaggattctgctgaa--
|||| | ||  |||||||||||||||| ||||| ||||||||||||| |||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||| ||   ||| ||||    || || |  |     |||||   ||||| | |   ||||||| | | ||| ||| | |    ||  ||||     |  
GGACCAAATCCGGAGGCCACTGATGCGAACGCGGGCCAATGATCCAGTCAAGGTGCAAGAACTCATGGACAGTATCCGTGTCATCGGCCTCCAAGTACCTgtgggtatctatatctgtatcttttcatttcat-atctcatcatccacg--agtacaatt--attggttagtcc-tgacctacctagatgagttttctatcagatt
















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|87031893|gb|CI268122.1|CI268122
EST:     AGGTGCAAGTACTCATGGACAGTATCCGTGTCATTGGCCTCCAAGTACCT                         ATTGACGTACTGGAGGTTGATGGAGTCTACTATG
genomic: AGGTGCAAGAACTCATGGACAGTATCCGTGTCATTGGCCTCCAAGTACCTgtgggtatct ... aatattgcagATTGACGTACTGGAGGTTGATGGAGTCTACTATG
EST: gi|88664093|gb|CI490467.1|CI490467
EST:     AGGTGCAAGAACTCATGGACAGTATCCGTGTCATTGGCCTCCAAGTACCT                         ATTGACGTACTGGAGGTTGATGGAGTCTACTATG
genomic: AGGTGCAAGAACTCATGGACAGTATCCGTGTCATTGGCCTCCAAGTACCTgtgggtatct ... aatattgcagATTGACGTACTGGAGGTTGATGGAGTCTACTATG
EST: gi|25798058|gb|CA754019.1|CA754019
EST:     AGGTGCAAGAACTCATGGACAGTATCCGTGTCATTGGCCTCCAAGTACCT                         ATTGACGTACTGGAGGTTGATGGAGTCTACTATG
genomic: AGGTGCAAGAACTCATGGACAGTATCCGTGTCATTGGCCTCCAAGTACCTgtgggtatct ... aatattgcagATTGACGTACTGGAGGTTGATGGAGTCTACTATG
EST: gi|117232192|gb|CT859987.1|CT859987
EST:     AGGTGCAAGAACTCATGGACAGTATCCGTGTCATTGGCCTCCAAGTACCT                         ATTGACGTACTGGAGGTTGATGGAGTCTACTATG
genomic: AGGTGCAAGAACTCATGGACAGTATCCGTGTCATTGGCCTCCAAGTACCTgtgggtatct ... aatattgcagATTGACGTACTGGAGGTTGATGGAGTCTACTATG
EST: gi|88273375|gb|CI393781.1|CI393781
EST:     AGGTGCAAGAACTCATGGACAGTATCCGTGTCATTGGCCTCCAAGTACCT                         ATTGACGTACTGGAGGTTGATGGAGTCTACTATG
genomic: AGGTGCAAGAACTCATGGACAGTATCCGTGTCATTGGCCTCCAAGTACCTgtgggtatct ... aatattgcagATTGACGTACTGGAGGTTGATGGAGTCTACTATG
EST: gi|88324654|gb|CI506038.1|CI506038
EST:     AGGTGCAAGAACTCATGGACAGTATCCGTGTCATTGGCCTCCAAGTACCT                         ATTGACGTACTGGAGGTTGATGGAGTCTACTATG
genomic: AGGTGCAAGAACTCATGGACAGTATCCGTGTCATTGGCCTCCAAGTACCTgtgggtatct ... aatattgcagATTGACGTACTGGAGGTTGATGGAGTCTACTATG
EST: gi|56158131|gb|C73488.2|C73488
EST:     GGTGCAAGAACTCATGGACAGTATCCGTGTCATTTGGNCTNCAAGTACCT                         ATTGACGTACTGGAGGTTGATGGAGTCTACTATG
genomic: GGTGCAAGAACTCATGGACAGTATCCGTGTCATT-GGCCTCCAAGTACCTgtgggtatct ... aatattgcagATTGACGTACTGGAGGTTGATGGAGTCTACTATG
EST: gi|86841916|gb|CI337538.1|CI337538
EST:     AGGTGCAAGAACTCATGGACAGTATCCGTGTCATTGGCCTCCAAGTACCT                         ATTGACGTACTGGAGGTTGATGGAGTCTACTATG
genomic: AGGTGCAAGAACTCATGGACAGTATCCGTGTCATTGGCCTCCAAGTACCTgtgggtatct ... aatattgcagATTGACGTACTGGAGGTTGATGGAGTCTACTATG
EST: gi|5005508|gb|AU070273.1|AU070273
EST:     AGGTGCAAGAACTCATGGACAGTATCCGTGTCATTGGCCTCCAAGTACCT                         ATTGACGTACTGGAGGTTGATGGAGTCTACTATG
genomic: AGGTGCAAGAACTCATGGACAGTATCCGTGTCATTGGCCTCCAAGTACCTgtgggtatct ... aatattgcagATTGACGTACTGGAGGTTGATGGAGTCTACTATG
EST: gi|88345020|gb|CI625866.1|CI625866
EST:     AGGTGCAAGAACTCATGGACAGTATCCGTGTCATTGGCCTCCAAGTACCT                         ATTGACGTACTGGAGGTTGATGGAGTCTACTATGGTTTTTCT
genomic: AGGTGCAAGAACTCATGGACAGTATCCGTGTCATTGGCCTCCAAGTACCTgtgggtatct ... aatattgcagATTGACGTACTGGAGGTTGATGGAGTCTACTATGGTTTTTCT
EST: gi|88567828|gb|CI498545.1|CI498545
EST:     AGGTGCAAGAACTCATGGACAGTATCCGTTTCATTGGCCTCCAAGTACCT                         ATTGACGTACTGGAGGTTGATGGAGTTTACTATG
genomic: AGGTGCAAGAACTCATGGACAGTATCCGTGTCATTGGCCTCCAAGTACCTgtgggtatct ... aatattgcagATTGACGTACTGGAGGTTGATGGAGTCTACTATG
EST: gi|88665263|gb|CI710321.1|CI710321
EST:     AGGTGCAAGAACTCATGGACAGTATCCGTGTCATTGGCCTCCAAGTACCT                         ATTGACGTACTGGAGGTTGATGGAGTCTACTATGGT
genomic: AGGTGCAAGAACTCATGGACAGTATCCGTGTCATTGGCCTCCAAGTACCTgtgggtatct ... aatattgcagATTGACGTACTGGAGGTTGATGGAGTCTACTATGGT
EST: gi|88567353|gb|CI498070.1|CI498070
EST:     AGGTGCAAGAACTCATGGACAGTATCCGTGTCATTGGCCTCCAAGTACCT                         ATTGACGTACTGGAGGTTGATGGAGTCTACTATG
genomic: AGGTGCAAGAACTCATGGACAGTATCCGTGTCATTGGCCTCCAAGTACCTgtgggtatct ... aatattgcagATTGACGTACTGGAGGTTGATGGAGTCTACTATG
EST: gi|88569011|gb|CI499728.1|CI499728
EST:     AGGTGCAAGAACTCATGGACAGTATCCGTGTCATTGGCCTCCAAGTACCT                         ATTGACGTACTGGAGGTTGATGGAGTCTACTATG
genomic: AGGTGCAAGAACTCATGGACAGTATCCGTGTCATTGGCCTCCAAGTACCTgtgggtatct ... aatattgcagATTGACGTACTGGAGGTTGATGGAGTCTACTATG
EST: gi|38477761|gb|CF961894.1|CF961894
EST:     AGGTGCAAGAACTCATGGACAGTATCCGTGTCATTGGCCTCCAAGTACCT                         ATTGACGTACTGGAGGTTGATGGAGTCTACTATG
genomic: AGGTGCAAGAACTCATGGACAGTATCCGTGTCATTGGCCTCCAAGTACCTgtgggtatct ... aatattgcagATTGACGTACTGGAGGTTGATGGAGTCTACTATG
EST: gi|58592631|gb|CF990939.1|CF990939
EST:     TCATGGACAGTATCCGTGTCATTGGCCTCCAAGTACCT                         ATTGACGTACTGGAGGTTGATGGAGTCTACTATG
genomic: TCATGGACAGTATCCGTGTCATTGGCCTCCAAGTACCTgtgggtatct ... aatattgcagATTGACGTACTGGAGGTTGATGGAGTCTACTATG

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: 64 (upstream exon), 34 (downstream exon)
Score: 12

GGACAAGATTAGGAGGCCACTGATGCGGACGCGTGCCAATGATCCAGCCAAGGTGCAAGAACTCATGGACAGTATCCGTGTCATTGGCCTCCAAGTACCTgtgggtatct ... aatattgcagATTGACGTACTGGAGGTTGATGGAGTCTACTATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGACAAGATTAGGAGGCCACTGATGCGGACGCGTGCCAATGATCCAGCCAAGGTGCAAGAACTCATGGACAGTATCCGTGTCATTGGCCTCCAAGTACCTgtgggtatctctagtacctttatgctttatcactttcctgtccacacaagtaccacttgtttggttaattcatgatctagcaatgaaggattctgctgaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA