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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACATGGGGCTCTGTTAGGGCTGCAATGGGCCACCCTGAACCATTCCCAGTGAAATATGTTGCAATAGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtaaatttaccaactacattttgttacatcctttttagagtataagtggaaaagcacttttgcacaagggcagtttctaaggaacctctcttcactagca...

Basic information

species Zea mays
transcript GRMZM2G077299_T03
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G077299_T03 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os12g03470.5 (Oryza sativa), 5'ss of exon 11
ACATGGGGCTCTGTTAGGGCTGCAATGGGCCACCCTGAACCATTCCCAGTGAAATATGTTGCAATAGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtaaatttaccaactacattt-tgttacatcctttttagagtataagtggaaaagcacttttgcacaagggcagtttctaaggaacctctcttcactagca
|||||||| |||||||| ||||||||||| ||||||||||||||||| || ||||| |||||||| ||||||||||||||||||||||||||||||||||||| |||   || | |  ||  | ||  ||||  || |   ||||| || | |||       |  |  |    | |  | | |||  | | |   | || |
ACATGGGGTTCTGTTAGAGCTGCAATGGGGCACCCTGAACCATTCCCTGTCAAATACGTTGCAATTGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtatattcctcatccaatttcatattttatccacttgaccatataactgcataagttgaagag-gcttgtctggataattaagaaggtgtatgatcgagga

upper sequence: GRMZM2G077299_T03 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os11g03730.3 (Oryza sativa), 5'ss of exon 11
ACATGGGGCTCTGTTAGGGCTGCAATGGGCCACCCTGAACCATTCCCAGTGAAATATGTTGCAATAGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtaaatttaccaactacattttgttacatcctttttagagtataagtggaaaagcacttttgcacaagggcagtttctaaggaacctctcttcactagca--
|||||||| |||||||| ||||||||||| ||||| ||||||||||| || ||||| || ||||| ||||||||||||||||||||||||||||||||||||  |||   ||| ||| || |  |     |  || |   ||||| || | ||  | |   |  |   | | |     ||  ||  | | |   | |  |  
ACATGGGGTTCTGTTAGAGCTGCAATGGGGCACCCCGAACCATTCCCTGTCAAATACGTCGCAATTGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtgcattcctcaattactttcttattttatcacttcaccatataactgcataa--attgaagagccttgtctggaataaattaaggtgtatgatcgaataaa

upper sequence: GRMZM2G077299_T03 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA03G27490.1 (Glycine max), 5'ss of exon 10
---------------------ACATGGGGCTCTGTTAGGGCTGCAATGGGCCACCCTGAACCATTCCCAGTGAAATATGTTGCAATAGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtaaatttaccaactacattttgttacatcctttttagagtataagtggaaaagcacttttgcacaagggcagtttctaaggaacctctcttcactagca
                     | |||||| ||  |||| ||  | ||||| |||||  | || ||     | ||||||||||| || |||||||||||||||||||| | |   ||||  || |   |  ||   | | ||||  |      |||| ||  | ||  | ||    |  |||||    |   ||   | |     |                
GCCAGAGGTGAGGCTACTTCAAAATGGGGTTCCCTTAGAGCATCTATGGGGCACCCAAAGCCTTTTGACCTAAAATATGTTGCTATTGGAAATGAAGATTgtgggaagacaaactaccaaggcatgctctcctttttctttttcct-----tttttaagtatttacattgagtgacttttttgagtgaacacaaagtatttacta----------------

upper sequence: GRMZM2G077299_T03 (Zea mays), 5'ss of exon 10
lower sequence: AT3G10740.1 (Arabidopsis thaliana), 5'ss of exon 11
ACATGGGGCTCTGTTAGGGCTGCAATGGGCCACCCTGAACCATTCCCAGTGAAATATGTTGCAATAGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtaaatttaccaactacattttgttacatcctttttagagtataagtggaaaagcacttttgcacaagggcagtttctaaggaacctctcttcactagca
|| ||||| |||||| | |||  |||||| | ||  ||||| ||   | | ||||| ||||| || ||||||||||||||||||||||    ||||  | | |  |||  ||  |   | |  | ||||| |   |    | |  || ||  |   ||||  ||| |    || ||  ||       || | ||      
ACTTGGGGATCTGTTCGAGCTAAAATGGGACGCCAAGAACCTTTTGAACTTAAATACGTTGCTATTGGAAATGAAGATTGTGGGAAAA---CTTACTACAG-AGgttttgcatttctctatgatcacatcttgacttagatttttgttgagcat--ctttgacactaaatgagattacaa-------ctttacag-----

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|32847594|gb|CD987275.1|CD987275
EST:     GAAATATGTTGCAATAGGAAATGAAGATTGTGGGAAAAAATTTTACCGCG                         GTAACTACCTCAAGTTCTACAATGCTATAAGACAGGCCTATCCAGACATTC
genomic: GAAATATGTTGCAATAGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtaaatttac ... tattgaacagGTAACTACCTCAAGTTCTACAATGCTATAAGACAGGCCTATCCAGACATTC
EST: gi|213170538|gb|FM181869.1|FM181869
EST:     GAAATATGTTGCAATAGGAAATGAAGATTGTGGGAAAAAATTTTACCGCG                         GTAACTACCTCAAGTTCTACAATGCTATAAGACAGGCCTATCCAGACATTC
genomic: GAAATATGTTGCAATAGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtaaatttac ... tattgaacagGTAACTACCTCAAGTTCTACAATGCTATAAGACAGGCCTATCCAGACATTC
EST: gi|116814377|gb|EC856917.1|EC856917
EST:     AAATATGTTGCAATAGGAAATGAAGATTGTGGGAAAAAATTTTTACCGCG                         GTAACTACCTCAAG-TCTACAATGCTATAAGACAGGCCTATCCAGACATTC
genomic: AAATATGTTGCAATAGGAAATGAAGATTGTGGGAAAAAA-TTTTACCGCGgtaaatttac ... tattgaacagGTAACTACCTCAAGTTCTACAATGCTATAAGACAGGCCTATCCAGACATTC
EST: gi|12045517|gb|BF727656.1|BF727656
EST:     GAAATATGTTGCAATTGGAAATGAAGATTGTGGGAAAAAATTTTACCGCG                         GTAACTACCTCAAGTTCTACAATGCTATAAGACAGGCCTATCCAGACATTC
genomic: GAAATATGTTGCAATAGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtaaatttac ... tattgaacagGTAACTACCTCAAGTTCTACAATGCTATAAGACAGGCCTATCCAGACATTC
EST: gi|32846175|gb|CD985856.1|CD985856
EST:     GAAATATGTTGCAATAGGAAATGAAGATTGTGGGAAAAAATTTTACCGCG                         GTAACTACCTCAAGTTCTACAATGCTATAAGACAGGCCTATCCAGACATTC
genomic: GAAATATGTTGCAATAGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtaaatttac ... tattgaacagGTAACTACCTCAAGTTCTACAATGCTATAAGACAGGCCTATCCAGACATTC
EST: gi|6095297|gb|AW119964.1|AW119964
EST:     GAAATATGTTGCAATTGGAAATGAAGATTGNGGGAAAAAATTTTACCGCG                         GTAACCTACCTTCAAGTTCTACAATGCTATAAGACAGGCCTATCCAGACAT
genomic: GAAATATGTTGCAATAGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtaaatttac ... tattgaacagGTAAC-TACCT-CAAGTTCTACAATGCTATAAGACAGGCCTATCCAGACAT
EST: gi|211082959|gb|FL420012.1|FL420012
EST:     GAAATATGTTGCAATAGGAAATGAAGATTGTGGGAAAAAATTTTACCGCG                         GTAACTACCTCAAGTTCTACAATGCTATAAGACAGGCCTATCCAGACATTC
genomic: GAAATATGTTGCAATAGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtaaatttac ... tattgaacagGTAACTACCTCAAGTTCTACAATGCTATAAGACAGGCCTATCCAGACATTC
EST: gi|32865761|gb|CF005443.1|CF005443
EST:     GAAATATGTTGCAATAGGAAATGAAGATTGTGGGAAAAAATTTTACCGCG                         GTAACTACCTCAAGTTCTACAATGCTATAAGACAGGCCTATCCAGACATTC
genomic: GAAATATGTTGCAATAGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtaaatttac ... tattgaacagGTAACTACCTCAAGTTCTACAATGCTATAAGACAGGCCTATCCAGACATTC
EST: gi|78179997|gb|DV550370.1|DV550370
EST:     GAAATATGTTGCAATTGGAAATGAAGATTGTGGGAAAAAATTTTACCGCG                         GTAACTACCTCAAGTTCTACAATGCTATAAGACAGGCCTATCCAGACATTC
genomic: GAAATATGTTGCAATAGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtaaatttac ... tattgaacagGTAACTACCTCAAGTTCTACAATGCTATAAGACAGGCCTATCCAGACATTC
EST: gi|211043015|gb|FL421679.1|FL421679
EST:     GAAATATGTTGCAATAGGAAATGAAGATTGTGGGAAAAAATTTTACCGCG                         GTAACTACCTCAAGTTCTACAATGCTATAAGACAGGCCTATCCAGACATTC
genomic: GAAATATGTTGCAATAGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtaaatttac ... tattgaacagGTAACTACCTCAAGTTCTACAATGCTATAAGACAGGCCTATCCAGACATTC
EST: gi|32846927|gb|CD986608.1|CD986608
EST:     GAAATATGTTGCAATAGGAAATGAAGATTGTGGGAAAAAATTTTACCGCG                         GTAACTACCTCAAGTTCTACAATGCTATAAGACAGGCCTATCCAGACATTC
genomic: GAAATATGTTGCAATAGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtaaatttac ... tattgaacagGTAACTACCTCAAGTTCTACAATGCTATAAGACAGGCCTATCCAGACATTC
EST: gi|32835529|gb|CD975207.1|CD975207
EST:     GAAATATGTTGCAATAGGAAATGAAGATTGTGGGAAAAAATTTTACCGCG                         GTAACTACCTCAAGTTCTACAATGCTATAAGACAGGCCTATCCAGACATTC
genomic: GAAATATGTTGCAATAGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtaaatttac ... tattgaacagGTAACTACCTCAAGTTCTACAATGCTATAAGACAGGCCTATCCAGACATTC
EST: gi|71441725|gb|DR822775.1|DR822775
EST:     GAAATATGTTGCAATAGGAAATGAAGATTGTGGGAAAAAATTTTACCGCG                         GTAACTACCTCAAGTTCTACAATGCTATAAGACAGGCCTATCCAGACATTC
genomic: GAAATATGTTGCAATAGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtaaatttac ... tattgaacagGTAACTACCTCAAGTTCTACAATGCTATAAGACAGGCCTATCCAGACATTC
EST: gi|32846588|gb|CD986269.1|CD986269
EST:     GAAATATGTTGCAATAGGAAATGAAGATTGTGGGAAAAAATTTTACCGCG                         GTAACTACCTCAAGTTCTACAATGCTATAAGACAGGCCTATCCAGACATTC
genomic: GAAATATGTTGCAATAGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtaaatttac ... tattgaacagGTAACTACCTCAAGTTCTACAATGCTATAAGACAGGCCTATCCAGACATTC

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 4 RNA-Seq libraries.


Block sizes: 46 (upstream exon), 43 (downstream exon)
Score: 73

ACATGGGGCTCTGTTAGGGCTGCAATGGGCCACCCTGAACCATTCCCAGTGAAATATGTTGCAATAGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtaaatttac ... tattgaacagGTAACTACCTCAAGTTCTACAATGCTATAAGACAGGCCTATCCAGACATTCAAATGATTTCAAACTGCGATGGTTCATCTACACCACTTGATCATCCTGC


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 82

ACATGGGGCTCTGTTAGGGCTGCAATGGGCCACCCTGAACCATTCCCAGTGAAATATGTTGCAATAGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtaaatttac ... tattgaacagGTAACTACCTCAAGTTCTACAATGCTATAAGACAGGCCTATCCAGACATTCAAATGATTTCAAACTGCGATGGTTCATCTACACCACTTGATCATCCTGC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 66

ACATGGGGCTCTGTTAGGGCTGCAATGGGCCACCCTGAACCATTCCCAGTGAAATATGTTGCAATAGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtaaatttac ... tattgaacagGTAACTACCTCAAGTTCTACAATGCTATAAGACAGGCCTATCCAGACATTCAAATGATTTCAAACTGCGATGGTTCATCTACACCACTTGATCATCCTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1302

ACATGGGGCTCTGTTAGGGCTGCAATGGGCCACCCTGAACCATTCCCAGTGAAATATGTTGCAATAGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtaaatttac ... tattgaacagGTAACTACCTCAAGTTCTACAATGCTATAAGACAGGCCTATCCAGACATTCAAATGATTTCAAACTGCGATGGTTCATCTACACCACTTGATCATCCTGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACATGGGGCTCTGTTAGGGCTGCAATGGGCCACCCTGAACCATTCCCAGTGAAATATGTTGCAATAGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtaaatttaccaactacattttgttacatcctttttagagtataagtggaaaagcacttttgcacaagggcagtttctaaggaacctctcttcactagca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA