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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGGACCATGATCTCACCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctatccaagtacctgcagtgctttgcttaggatgtgtcatggttttatccctgatgaaatgatcttgtgatgcgtggtcttgttctag

Basic information

species Zea mays
transcript GRMZM2G019267_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G019267_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g72790.1 (Oryza sativa), 5'ss of exon 5
GTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGGACCATGATCTCACCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctatccaagtacctgcagtgctttgcttaggatgtgtcatggttttatccctgatgaaatgatcttgtgatgcgtggtctt-----gttctag
||||||||||||||| |||||||| |||||||| ||||| |||||||| || |||||||| ||| |||| || ||||||||||||||||| |||||||||||| | | | |    |   ||   || | |  || |||||||  ||  |||| |   |||   | ||||||| ||||| ||| ||||     || | ||
GTACAAGGGGAGCATCTACATGGTCTTCGAGTACATGGATCATGATCTTACTGGGCTTGCAGATAGGCCTGGGATGCGGTTCACTGTGCCTCAGATTAAGgtagaaccacctgtttgtgtgacttgttcttgtttggatgtgatata-ttttgtta-tgacagactgatcttctgatgtgtgatcttctatcgtcccag

upper sequence: GRMZM2G019267_T02 (Zea mays), 5'ss of exon 5
lower sequence: PP1S3_535V6.2 (Physcomitrella patens), 5'ss of exon 3
GTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGGACCATGATCTCACCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctatccaagtacctgcagtgctttgcttaggatgtgtcatggttttatccctgatgaaatgatcttgtgatgcgtggtcttgttctag--------------------------------------------------------------
|| ||| ||    ||||||||||| |||||||| |||||||||||||| || || ||||| ||||| || |||||||| ||| || | || || || |||||||  |      |  |  |||  |   || ||   ||||| |     |||| | | |  |    |  ||  |   |   |     ||||||                                                                
GTTCAAAGGTTCTATTTACATGGTGTTCGAGTACATGGACCATGATCTGACTGGTCTTGCAGATCGACCTGGAATGCGCTTCTCTATTCCCCAAATCAAGgtacttcgtgtagatgaattgc--ttacttcctggtgatgtatttctcttttcttcatttttccttcttcccgctctctctctctctgttctgtcttttgccttatcatttttttcgactcaatcttgaggtttaatatggtcttctataatgcag

upper sequence: GRMZM2G019267_T02 (Zea mays), 5'ss of exon 5
lower sequence: PP1S235_102V6.1 (Physcomitrella patens), 5'ss of exon 4
GTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGGACCATGATCTCACCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacc-tatccaagtacctgcagtgctttgcttaggatgtgtcatggttttatccctgatgaaatgatcttgtgatgcgtggtcttgttctag----------------------------
|| ||| ||    ||||||||||| || ||||| |||||||||||| | || || |||||||||||||| || ||||| ||| || | || || || |||||||  | |        |||| || |||||     |   |      || ||   ||| |  |    ||  || ||  |||   | |  |||| |                             
GTTCAAAGGCTCTATTTACATGGTGTTTGAGTACATGGACCATGATTTGACTGGCCTTGCTGATCGGCCTGGGATGCGCTTCTCTATTCCCCAAATCAAGgtacttcgtgggatcaaaccttcactgcttgagcgaattttctctctgtttccttccttacttttctgtcctcgttttgcacagcccagttccaagttttaacatggatcttcttcactgcag

upper sequence: GRMZM2G019267_T02 (Zea mays), 5'ss of exon 5
lower sequence: PP1S121_162V6.1 (Physcomitrella patens), 5'ss of exon 4
GTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGGACCATGATCTCACCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctatccaagtacct-gcagtgctttgcttag--gatgtgtcatggttttatccctgatgaaatgatcttgtgatgcgtggtcttgttctag--------------------------------------------
|| ||| |||   ||||||||||| |||||||| |||||||||||| | || || ||  | ||||| || || ||||| ||| || | || |||||||||||| |  |    |   | ||  | |||   ||  |    ||| |    ||  |||  |     |  | ||  | |        |  ||||||                                                 
GTTCAAAGGGTCGATTTACATGGTGTTCGAGTACATGGACCATGATTTGACTGGCCTCTCAGATCGACCTGGCATGCGTTTCTCTATTCCCCAGATTAAGgtatattttgaaagagatctcacggtgacctggctgctcgattttatttgacttttacataattttagtggacctccacatgttcttcttgtctcttcattttgtatgggacagtcttaatttgtctcttctacactgtag

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|71766382|gb|DR964319.1|DR964319
EST:     CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAG                         TGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
genomic: CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
EST: gi|71774594|gb|DR972472.1|DR972472
EST:     CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAG                         TGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
genomic: CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
EST: gi|78078029|gb|DV506444.1|DV506444
EST:     CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAG                         TGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
genomic: CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
EST: gi|29130258|gb|CB380962.1|CB380962
EST:     CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAG                         TGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
genomic: CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
EST: gi|148938174|gb|EC882457.2|EC882457
EST:     CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAG                         TGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
genomic: CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
EST: gi|149107723|gb|EE189597.2|EE189597
EST:     CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAG                         TGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
genomic: CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
EST: gi|71430764|gb|DR811814.1|DR811814
EST:     CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAG                         TGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
genomic: CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
EST: gi|149099519|gb|EE185557.2|EE185557
EST:     CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAG                         TGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
genomic: CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
EST: gi|148946782|gb|EC892051.2|EC892051
EST:     CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAG                         TGTTACATGAAGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
genomic: C-GGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
EST: gi|211438449|gb|FL012011.1|FL012011
EST:     CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAG                         TGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
genomic: CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
EST: gi|32844191|gb|CD983872.1|CD983872
EST:     CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAG                         TGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
genomic: CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
EST: gi|148942610|gb|EC887630.2|EC887630
EST:     CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAG                         TGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
genomic: CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
EST: gi|148962681|gb|EE013583.2|EE013583
EST:     CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAG                         TGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
genomic: CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
EST: gi|148969561|gb|EE020392.2|EE020392
EST:     CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAG                         TGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
genomic: CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
EST: gi|211438454|gb|FL012016.1|FL012016
EST:     CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAG                         TGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
genomic: CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
EST: gi|211325352|gb|FL255515.1|FL255515
EST:     CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAG                         TGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
genomic: CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
EST: gi|148954879|gb|EC900358.2|EC900358
EST:     CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAG                         TGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
genomic: CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
EST: gi|211438446|gb|FL012008.1|FL012008
EST:     CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAG                         TGTTACATGAGGCAGCTGCTTACAG
genomic: CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAG
EST: gi|76914973|gb|DV165773.1|DV165773
EST:     CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAG                         TGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
genomic: CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
EST: gi|32845306|gb|CD984987.1|CD984987
EST:     CCGGGCTTGCTGATCGGCCAGAAATGCGGTTCACTGTGCCGCAGATTAAG                         TGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
genomic: CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
EST: gi|149087325|gb|EE176860.2|EE176860
EST:     CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAG                         TGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
genomic: CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
EST: gi|211435854|gb|FL011998.1|FL011998
EST:     CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGAWTAAG                         TGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATG
genomic: CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATG
EST: gi|148955711|gb|EC901398.2|EC901398
EST:     CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAG                         TGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
genomic: CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
EST: gi|149106097|gb|EE291761.2|EE291761
EST:     CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAG                         TGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
genomic: CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA

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: 49 (upstream exon), 49 (downstream exon)
Score: 295

GTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGGACCATGATCTCACCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 145

GTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGGACCATGATCTCACCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 158

GTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGGACCATGATCTCACCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 221

GTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGGACCATGATCTCACCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGGACCATGATCTCACCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctatccaagtacctgcagtgctttgcttaggatgtgtcatggttttatccctgatgaaatgatcttgtgatgcgtggtcttgttctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT