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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACATTCATTGACAAGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAGgtacactttctcactcgtaaccggaatttttgtagttgtttcacttaacagatactgtatggacaaactcccaaccagaattttgatcaaggatgttgttcagtgacaaatttgatgtctgacttgaaattcttatctctgctatggcag

Basic information

species Zea mays
transcript GRMZM2G013890_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G013890_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os02g58020.1 (Oryza sativa), 5'ss of exon 9
ACATTCATTGACAAGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAGgtacactttctcactcgtaaccggaatttttgtagttgtttcacttaacagatactgtatggacaaactcccaaccagaattttgatcaaggatgttgttcagtgacaaatttgatgtctgacttgaaattcttatctctgctatggcag--
 |||||||||||||||| || ||||||||||||||||||||||||||||||||||||||||||||    || ||  |||  | ||   ||   |  | |   ||   |   || || |       | |    |    | |   |||   | |||   || || |||||| || |||  | | || ||| | |||  | | ||||   |  |    
GCATTCATTGACAAGTTCCGTTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAGgtgactttgcttgctcacatcccccatcactccattgaatt---tctgcaaatcc-----aaatattacctttgctattgtttcacttaaga--gtcgtccagtgataactttagtctgtgccttaatatttatttatctgtattcactaag

upper sequence: GRMZM2G013890_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA20G16170.1 (Glycine max), 5'ss of exon 8
ACATTCATTGACAAGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAGgtacactttctcactcgtaaccggaatttttgtagttgtttcacttaacagatactgtatggacaaactcccaaccagaattttgatcaaggatgttgttcagtgacaaatttgat-gtctgacttgaaattcttatctctgctatggcag--------------------------------------
|| |||||||||||||| || || ||||| ||||| ||||||||||||||||| |||||||||||||   || | | |   |       ||  | ||  |      |  || | ||  |||          |    |   |  | ||  | |         |    ||     |||  | || |   || ||||  |||  | || |||  | |                                      
ACCTTCATTGACAAGTTCCGTTATAATGCGAAGAGGGCATCACTTGTTCAATCTAGAATCAAGgtacttgttgttattgtcagattaccttcctataaatcaaatgcccaaaacatcatgtgaatgttgtgtgtgtatatgtgtattatttagtcgctccctggtttggttgtttttttagtttcggtttaaatcattaaatttgatatttccgtatctaaacttttttttttccctgaaaaaatattgcag

upper sequence: GRMZM2G013890_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA13G10530.1 (Glycine max), 5'ss of exon 8
ACATTCATTGACAAGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAGgtacactttctcactcgtaaccggaatttttgtagttgtttcacttaacagatactgtatggacaaactcccaaccagaattttgatcaaggatgttgttcagtgacaaatttgatgtctgac--ttgaaattcttatctctgctatggcag----------------------------
|| |||||||||||||| || || ||||| ||||| ||||||||||||||||| |||||||||||||   || | | |   |       ||  | ||  |      |  || |  |  |||    |         |     | | || |         | |||  ||    | |||    |   |   || || ||  ||| ||||       |                             
ACCTTCATTGACAAGTTCCGTTATAATGCGAAGAGGGCATCACTTGTTCAATCTAGAATCAAGgtac---ttgttattgtcagatcaccttcctataaatcaaatgcccaaaacgtcgtgtgcatatgtgtgtgtatgtgtattatttagttgctccttggtttggttgttagtttcggtttaaatcattaaatttgatatttctgtatctaaaactttttttcctgaaaaaaaatatttcag

upper sequence: GRMZM2G013890_T01 (Zea mays), 5'ss of exon 9
lower sequence: AT1G64550.1 (Arabidopsis thaliana), 5'ss of exon 9
ACATTCATTGACAAGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAGgtacactttctcactcgtaaccggaatttttgtagttg--tttcacttaacagatactgtatggacaaactcccaaccagaattttgatcaaggatgttgttcagtgacaaatttgatgtctgacttgaaattcttatctctgctatggcag
 | |||||||| || ||||| |||||||||||||| || || |||||||| ||||||||||||||        |||   || ||    |||| |||  ||   |||     | |||    ||     | |   |     | |  |||  |                                                                 
GCGTTCATTGATAAATTTCGTTACAATGCAAAGAGGGCGTCTCTTGTTCAGTCAAGAATCAAGgtg-------tcaactgttacaactatttatgtgattaaattttggccatcag-cggtgctctaatattattgtgtctatgattcag-----------------------------------------------------------------

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|60343993|gb|DN210966.1|DN210966
EST:     AGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAG                         GCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGA
genomic: AGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAGgtacactttc ... gctatggcagGCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGA
EST: gi|32930219|gb|CF035031.1|CF035031
EST:     ACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAG                         GCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGA
genomic: ACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAGgtacactttc ... gctatggcagGCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGA
EST: gi|211238345|gb|FL044423.1|FL044423
EST:     AGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAG                         GCATTGGAGCGAATGGNAACATGTTGATGCAGTTGTCAGCGATCCAGA
genomic: AGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAGgtacactttc ... gctatggcagGCATTGGAGCGAATGG-AACATGTTGATGCAGTTGTCAGCGATCCAGA
EST: gi|211429008|gb|FL174617.1|FL174617
EST:     AGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAG                         GCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGA
genomic: AGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAGgtacactttc ... gctatggcagGCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGA
EST: gi|60349362|gb|DN216335.1|DN216335
EST:     AGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAG                         GCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGA
genomic: AGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAGgtacactttc ... gctatggcagGCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGA
EST: gi|71307303|gb|DR789832.1|DR789832
EST:     AGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAG                         GCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGA
genomic: AGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAGgtacactttc ... gctatggcagGCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGA
EST: gi|32932155|gb|CF036967.1|CF036967
EST:     ACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAG                         GCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGA
genomic: ACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAGgtacactttc ... gctatggcagGCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGA
EST: gi|32932545|gb|CF037357.1|CF037357
EST:     ACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAG                         GCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGA
genomic: ACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAGgtacactttc ... gctatggcagGCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGA
EST: gi|32848242|gb|CD987923.1|CD987923
EST:     ACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAG                         GCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGA
genomic: ACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAGgtacactttc ... gctatggcagGCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGA

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: 47 (upstream exon), 49 (downstream exon)
Score: 224

ACATTCATTGACAAGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAGgtacactttc ... gctatggcagGCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 225

ACATTCATTGACAAGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAGgtacactttc ... gctatggcagGCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 219

ACATTCATTGACAAGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAGgtacactttc ... gctatggcagGCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 117

ACATTCATTGACAAGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAGgtacactttc ... gctatggcagGCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACATTCATTGACAAGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAGgtacactttctcactcgtaaccggaatttttgtagttgtttcacttaacagatactgtatggacaaactcccaaccagaattttgatcaaggatgttgttcagtgacaaatttgatgtctgacttgaaattcttatctctgctatggcag

- - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - -  AGAGCA