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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGACGGACCTGCAGGCGCAGCTCAAGGAGCTGAAGTCTGAGCTCTCCCTCCTCCGCGTAGCCAAGGTCACCGGCGGCGCACCCAACAAGCTCTCCAAGATgtgcgtacctgcaatctctattttctcctgttattctctgctcctgaactcgactgaatcgattcgaattgtatccggcccttcttcag

Basic information

species Zea mays
transcript GRMZM2G043279_T03
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G043279_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os04g30730.1 (Oryza sativa), 5'ss of exon 2
AGACGGACCTGCAGGCGCAGCTCAAGGAGCTGAAGTCTGAGCTCTCCCTCCTCCGCGTAGCCAAGGTCACCGGCGGCGCACCCAACAAGCTCTCCAAGATgtgcgta-cctgcaatctctattttctcctgttattctctgctcctgaactcgactgaatcgattcgaattgtatccggcccttcttcag--
|| |||| |||||||| ||||||||||| || ||| | |||||||||||||||||||| |||||||||||||||||||| |||||||||||||||||||||||||   ||| |   ||    | || |  |||  |   ||   ||| |     || |   | |||     ||         || |||    
AGGCGGAGCTGCAGGCCCAGCTCAAGGACCTCAAGGCGGAGCTCTCCCTCCTCCGCGTCGCCAAGGTCACCGGCGGCGCCCCCAACAAGCTCTCCAAGATgtgcgcctccttcctccttctctctcgctcgtttgttggtgtggctggatctcgctca-cgggttcttggggtggtgaattttttttcgcag

upper sequence: GRMZM2G043279_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g30050.1 (Oryza sativa), 5'ss of exon 2
AGACGGACCTGCAGGCGCAGCTCAAGGAGCTGAAGTCTGAGCTCTCCCTCCTCCGCGTAGCCAAGGTCACCGGCGGCGCACCCAACAAGCTCTCCAAGATgtgcgtacctgcaatctctattttctcctgttattctctgctcctgaactcgactg-aatcgattcgaattgtatccggcccttcttcag
|| |||| |||||||| ||||||||||| || ||| | |||||||||||||||||||| |||||||||||||||||||| |||||||||||||||||||||| ||  | |           |  | |   || |   ||  | |||    |   ||  || ||||  |  | | |  ||   || | |||
AGGCGGAGCTGCAGGCCCAGCTCAAGGACCTCAAGGCGGAGCTCTCCCTCCTCCGCGTCGCCAAGGTCACCGGCGGCGCCCCCAACAAGCTCTCCAAGATgtacgcgcttcgcgctcgcgctcgcgctcattctctcctctttctgtgtgcccttgtgattgattgaatctctgt--gg---ttttgcag

upper sequence: GRMZM2G043279_T03 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA15G04730.1 (Glycine max), 5'ss of exon 2
AGACGGACCTGCAGGCGCAGCTCAAGGAGCTGAAGTCTGAGCTCTCCCTCCTCCGCGTAGCCAAGGTCACCGGCGGCGCACCCAACAAGCTCTCCAAGATgtgcgtacctgcaatctctattttctcctgttattctctgctcctgaactcgactgaatcga--ttcgaattgtatccggcccttcttcag---------
|  | || || | |   || || ||||| || ||  | || ||| | ||||||||||| || |||||||||||||| || || |||||||| ||||| |||| | | |||    ||| |  | ||   |       ||       || |   | ||   |||  ||  || |||||  ||      ||||          
AAGCAGAGCTTCTGAACCAACTTAAGGATCTCAAAGCAGAACTCGCTCTCCTCCGCGTCGCTAAGGTCACCGGCGGAGCCCCAAACAAGCTTTCCAAAATgtaccttccttttctctttcatatcaaatccccaattcctaattggatcgaaattgttacgaatttgaaagtgtatttggattagattcatggtgggaaa

upper sequence: GRMZM2G043279_T03 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA10G05270.1 (Glycine max), 5'ss of exon 2
AGACGGACCTGCAGGCGCAGCTCAAGGAGCTGAAGTCTGAGCTCTCCCTCCTCCGCGTAGCCAAGGTCACCGGCGGCGCACCCAACAAGCTCTCCAAGATgtgc-gtacctgcaatctctattttctcctgttattctctgctcctgaactcgactgaatcgattcgaat-tgtatccggcccttcttcag----------------------------------------------------------
|| |||| |||| |   ||||| ||||| || ||| | |||||  |||| |||||||| |||||||||||||||||||| ||||||||||||||||| ||||   |||      ||   |||       |    || | |   |   |   ||  |||||  ||    || | ||| |     |   |                                                             
AGGCGGAGCTGCTGAACCAGCTGAAGGATCTCAAGGCGGAGCTTGCCCTGCTCCGCGTCGCCAAGGTCACCGGCGGCGCCCCCAACAAGCTCTCCAAAATgtattgtagtgattattgttatgcgggaatcgcgttttgtaaacgaaatggcgtttgaatatatatatatatatatacatatatatatatatatatatatatatatatatgtatgtatgtatgtatgtatttttttattttttttgcag

upper sequence: GRMZM2G043279_T03 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA10G43770.1 (Glycine max), 5'ss of exon 2
AGACGGACCTGCAGGCGCAGCTCAAGGAGCTGAAGTCTGAGCTCTCCCTCCTCCGCGTAGCCAAGGTCACCGGCGGCGCACCCAACAAGCTCTCCAAGATgtgcgtacctgcaatctctattttctcctgttattctctgctcctgaactcgactgaatcgattcgaattgtatccggcccttcttcag
|| | || |||  |   ||||| ||||| || ||| | |||||  || | || || || || |||||||||||||| ||||| ||||||||||| |||||||   ||     |||||     |||  |  || |  | |||   |||  |          |  |    ||| |   |    ||   |||
AGGCTGATCTGTTGAATCAGCTGAAGGACCTCAAGGCCGAGCTTGCCTTGCTTCGTGTTGCTAAGGTCACCGGCGGTGCACCTAACAAGCTCTCTAAGATgta-ataatcttaatctaataattcctcgtttctcttttgcctttgaggtttgtgtttatgtgttattttgaaattgaggtttg--cag

upper sequence: GRMZM2G043279_T03 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA13G40700.1 (Glycine max), 5'ss of exon 2
AGACGGACCTGCAGGCGCAGCTCAAGGAGCTGAAGTCTGAGCTCTCCCTCCTCCGCGTAGCCAAGGTCACCGGCGGCGCACCCAACAAGCTCTCCAAGATgtgcgtacctgcaatctctattttctcctgttattctctgctcctgaactcgactgaatcgatt-cgaatt-gtatccggcccttcttcag------
|  | || || | |   || || ||||| || ||  | || ||| | ||||||||||| ||||||||||||||||| || || |||||||| ||||| |||    ||||| |  ||||| |||  |      | || ||  | |  || | || ||||  | || |||||| | || ||    || |   |      
AAGCAGAGCTTCTGAACCAACTGAAGGATCTCAAAGCAGAACTCGCTCTCCTCCGCGTCGCCAAGGTCACCGGCGGAGCCCCGAACAAGCTTTCCAAAATg----taccttccctctctctttcatatca--aatccctaattcctaattggattgaaatgcttacgaatttgaatgcgtttgttgtgtggatgtag

upper sequence: GRMZM2G043279_T03 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA13G19650.1 (Glycine max), 5'ss of exon 1
AGACGGACCTGCAGGCGCAGCTCAAGGAGCTGAAGTCTGAGCTCTCCCTCCTCCGCGTAGCCAAGGTCACCGGCGGCGCACCCAACAAGCTCTCCAAGATgtgcgtacctgcaatctctattttctcctgttattctctgctcctgaactcgactg--aatcgattcgaattgtatccggcccttcttcag----------------------------------
|| |||| || | |   ||||||||||| || ||| | |||||  |||| |||||||| |||||||| ||||||||||| || |||||||||||||| |||| |  ||   || |  | |  || ||    | ||   |  ||||||     | |   | |      |||| |  |   |          |                                  
AGGCGGAGCTACTGAACCAGCTCAAGGATCTCAAGGCGGAGCTAGCCCTGCTCCGCGTCGCCAAGGTTACCGGCGGCGCCCCAAACAAGCTCTCCAAAATgtaccaact--cacttccaacattttctcagtgtttgtttgtcctgattattattattagtatgcgggaatcgcgttttgtgaacgaaacgaaacggcgttttaattgtttttttttttttgcag

upper sequence: GRMZM2G043279_T03 (Zea mays), 5'ss of exon 2
lower sequence: AT5G02610.1 (Arabidopsis thaliana), 5'ss of exon 2
AGACGGACCTGCAGGCGCAGCTCAAGGAGCTGAAGTCTGAGCTCTCCCTCCTCCGCGTAGCCAAGGTCACCGGCGGCGCACCCAACAAGCTCTCCAAGATgtgcgtacctgcaatctctattttctcctgt-tattctctgctcctgaactcgactgaatcgattcgaattgtatccggcccttc--ttcag--------
|||| || || |||   ||| | |||||  | ||| |||| ||| | |||||||| || || || |||||||| ||||| ||||||||||||||||| ||||  ||   |   || |||| ||   | | | |||    ||    |  |     |   ||   || | |||   |    |  | |  ||  |        
AGACCGATCTTCAGAATCAGTTGAAGGAATTCAAGGCTGAACTCGCTCTCCTCCGTGTCGCTAAAGTCACCGGAGGCGCTCCCAACAAGCTCTCCAAAATgtatgtcttttatatatctacttatacgtatatatgaaatgtgtgtatatatatcctcatttgttaggatttagtgttactttccaatttggagacattt

upper sequence: GRMZM2G043279_T03 (Zea mays), 5'ss of exon 2
lower sequence: AT5G02610.2 (Arabidopsis thaliana), 5'ss of exon 2
AGACGGACCTGCAGGCGCAGCTCAAGGAGCTGAAGTCTGAGCTCTCCCTCCTCCGCGTAGCCAAGGTCACCGGCGGCGCACCCAACAAGCTCTCCAAGATgtgcgtacctgcaatctctattttctcctgt-tattctctgctcctgaactcgactgaatcgattcgaattgtatccggcccttc--ttcag---------------------------------------------------------------------------------------------------------
|||| || || |||   ||| | |||||  | ||| |||| ||| | |||||||| || || || |||||||| ||||| ||||||||||||||||| ||||  ||   |   || |||| ||   | | | |||    ||    |  |     |   ||   || | |||   |    |  | |  ||  |                                                                                                         
AGACCGATCTTCAGAATCAGTTGAAGGAATTCAAGGCTGAACTCGCTCTCCTCCGTGTCGCTAAAGTCACCGGAGGCGCTCCCAACAAGCTCTCCAAAATgtatgtcttttatatatctacttatacgtatatatgaaatgtgtgtatatatatcctcatttgttaggatttagtgttactttccaatttggagacatttcacttagatttagagtaattgaagaatttggagtaagagaacatatggtgctctgttttggaatttgcatttgtatcatcatttgggatatcatcag

upper sequence: GRMZM2G043279_T03 (Zea mays), 5'ss of exon 2
lower sequence: Vv00s0317g00130.t01 (Vitis vinifera), 5'ss of exon 2
AGACGGACCTGCAGGCGCAGCTCAAGGAGCTGAAGTCTGAGCTCTCCCTCCTCCGCGTAGCCAAGGTCACCGGCGGCGCACCCAACAAGCTCTCCAAGATgtgcgtacctgcaatct-ctattttctcctgttattctctgctcc---tgaactcgactgaatcgattcgaattgtatccggcccttcttcag---------
|| ||||| ||  || |||| | |||||| ||||| | || ||  | || ||||| || |||||||||||||| || ||||| ||||||||||||||||||| |   | |    ||| | ||||     | |   ||| || |     || | |   |    |   ||   ||| |||  ||   || | | |         
AGGCGGACTTGTTGGTGCAGTTGAAGGAGTTGAAGGCCGAACTTGCTCTTCTCCGAGTTGCCAAGGTCACCGGTGGTGCACCAAACAAGCTCTCCAAGATgtactctcttttcctcttccatttatgtatatatatctgtgttatatgtgtatttttcaagttttgttaagatt-tatt-ggtgtttatgcggtttgttagg

upper sequence: GRMZM2G043279_T03 (Zea mays), 5'ss of exon 2
lower sequence: EFJ18648 (Selaginella moellendorffii), 5'ss of exon 2
AGACGGACCTGCAGGCGCAGCTCAAGGAGCTGAAGTCTGAGCTCTCCCTCCTCCGCGTAGCCAAGGTCACCGGCGGCGCACCCAACAAGCTCTCCAAGATgtgcgtacctgcaatctctattttctcctgttattctctgctcctgaactcgactgaatcgattcgaattgtatccggcccttcttcag
||  |||  |||  |  |||||||||||||| || || |||||| |  | || ||||| ||||| ||||| || ||||| ||||||||||||||||| ||||| | |  | | |    |   |     | ||  | |   || | |   |    |    |                             
AGCAGGATTTGCTCGTCCAGCTCAAGGAGCTCAAATCCGAGCTCGCTTTGCTGCGCGTGGCCAAAGTCACTGGAGGCGCCCCCAACAAGCTCTCCAAAATgtgag-attttcgagtgttccctcgcgattttgattttcacttcggtgttttgtttctccag---------------------------

upper sequence: GRMZM2G043279_T03 (Zea mays), 5'ss of exon 2
lower sequence: EFJ36167 (Selaginella moellendorffii), 5'ss of exon 2
AGACGGACCTGCAGGCGCAGCTCAAGGAGCTGAAGTCTGAGCTCTCCCTCCTCCGCGTAGCCAAGGTCACCGGCGGCGCACCCAACAAGCTCTCCAAGATgtgcgtacctgcaatctctattttctcctgttattctctgctcctgaactcgactgaatcgattcgaattgtatccggcccttcttcag
||  |||| |||  |  |||||||||||||| || || |||||| |  | || ||||| ||||| ||||| || ||||| ||||||||||||||||| ||||| | |  | | |    |   |     | ||  | |   || | |   |    |    |                             
AGCAGGACTTGCTCGTCCAGCTCAAGGAGCTCAAATCCGAGCTCGCTTTGCTGCGCGTGGCCAAAGTCACTGGAGGCGCCCCCAACAAGCTCTCCAAAATgtgag-attttcgagtgttccctcacgattttgattttcacttcggtgtttcgtttctccag---------------------------

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|74243811|gb|DT651725.1|DT651725
EST:     CTCCGCGTAGCCAAGGTCACCGGCGGCGCACCCAACAAGCTCTCCAAGAT                         CAAGGTGGTGCGCACCTCGATCGCGCGCGTGCTCACAGTGATCTCGCAGAA
genomic: CTCCGCGTAGCCAAGGTCACCGGCGGCGCACCCAACAAGCTCTCCAAGATgtgcgtacct ... ccttcttcagCAAGGTGGTGCGCACCTCGATCGCGCGCGTGCTCACAGTGATCTCGCAGAA
EST: gi|211289869|gb|FL479952.1|FL479952
EST:     CTCCGCGTAGCCAAGGTCACCGGCGGCGCACCCAACAAGCTCTCCAAGAT                         CAAGGTGGTGCGCACCTCGATCGCGCGCGTGCTCAC-GTTATCTC
genomic: CTCCGCGTAGCCAAGGTCACCGGCGGCGCACCCAACAAGCTCTCCAAGATgtgcgtacct ... ccttcttcagCAAGGTGGTGCGCACCTCGATCGCGCGCGTGCTCACAGTGATCTC
EST: gi|211186249|gb|FL001313.1|FL001313
EST:     CTCCGCGTAGCCAAGGTCACCGGCGGCGCACCCAACAAGCTCTCCAAGAT                         CAAGGTGGTGCGCACCTCGATCGCGCGCGTGCTCACAGTGATCTCGCAGAA
genomic: CTCCGCGTAGCCAAGGTCACCGGCGGCGCACCCAACAAGCTCTCCAAGATgtgcgtacct ... ccttcttcagCAAGGTGGTGCGCACCTCGATCGCGCGCGTGCTCACAGTGATCTCGCAGAA
EST: gi|211188653|gb|FL001327.1|FL001327
EST:     CTCCGCGTAGCCAAGGTCACCGGCGGCGCACCCAACAAGCTCTCCAAGAT                         CAAGGTGGTGCGCACCTCGATCGCGCGCGTGCTCACAGTGATCTCGCAGAA
genomic: CTCCGCGTAGCCAAGGTCACCGGCGGCGCACCCAACAAGCTCTCCAAGATgtgcgtacct ... ccttcttcagCAAGGTGGTGCGCACCTCGATCGCGCGCGTGCTCACAGTGATCTCGCAGAA
EST: gi|32936499|gb|CF041318.1|CF041318
EST:     CTCCGCGTAGCCAAGGTCACCGGCGGCGCACCCAACAAGCTCTCCAAGAT                         CAAGGTGGTGCGCACCTCGATCGCGCGCGTGCTCACAGTGATCTCGC
genomic: CTCCGCGTAGCCAAGGTCACCGGCGGCGCACCCAACAAGCTCTCCAAGATgtgcgtacct ... ccttcttcagCAAGGTGGTGCGCACCTCGATCGCGCGCGTGCTCACAGTGATCTCGC
EST: gi|211186247|gb|FL001311.1|FL001311
EST:     CTCCGCGTAGCCNAGGTCACCGGCGGCGCACCCAACAAGCTCTCCAAGAT                         CAAGGTGGTGCGCACCTCGATCGCGCGCGTGCTCACAGTGATCTCGCAGAA
genomic: CTCCGCGTAGCCAAGGTCACCGGCGGCGCACCCAACAAGCTCTCCAAGATgtgcgtacct ... ccttcttcagCAAGGTGGTGCGCACCTCGATCGCGCGCGTGCTCACAGTGATCTCGCAGAA
EST: gi|29130231|gb|CB380935.1|CB380935
EST:     CTCCGCGTAGCCAAGGTCACCGGCGGCGCACCCAACAAGCTCTCCAAGAT                         CAAGGTGGTGCGCACCTCGATCGCGCGCGTGCTCACAGTGATCTCGCAGAA
genomic: CTCCGCGTAGCCAAGGTCACCGGCGGCGCACCCAACAAGCTCTCCAAGATgtgcgtacct ... ccttcttcagCAAGGTGGTGCGCACCTCGATCGCGCGCGTGCTCACAGTGATCTCGCAGAA
EST: gi|211188656|gb|FL001330.1|FL001330
EST:     CTCCGCGTAGCCAAGGTCACCGGCGGCGCACCCAACAAGCTCTCCAAGAT                         CAAGGGTGGTGCGCACCCTCGAATCGCGCGCGTGCTCACAGTGATCTCCCA
genomic: CTCCGCGTAGCCAAGGTCACCGGCGGCGCACCCAACAAGCTCTCCAAGATgtgcgtacct ... ccttcttcagCAAGG-TGGTGCGCACC-TCGA-TCGCGCGCGTGCTCACAGTGATCTCGCA
EST: gi|161582527|gb|EY955898.1|EY955898
EST:     CGGCGGCGCACCCAACAAGCTCTCCAAGAT                         CAAGGTGGTGCGCACCTCGATCGCGCGCGTGCTCACAGTGATCTCGCAGAA
genomic: CGGCGGCGCACCCAACAAGCTCTCCAAGATgtgcgtacct ... ccttcttcagCAAGGTGGTGCGCACCTCGATCGCGCGCGTGCTCACAGTGATCTCGCAGAA
EST: gi|71768079|gb|DR966016.1|DR966016
EST:     CTCCGCGTAGCCAAGGTCACCGGCGGCGCACCCAACAAGCTCTCCAAGAT                         CAAGGTGGTGCGCACCTCGATCGCGCGCGTGCTCACAGTGATCTCGCAGAA
genomic: CTCCGCGTAGCCAAGGTCACCGGCGGCGCACCCAACAAGCTCTCCAAGATgtgcgtacct ... ccttcttcagCAAGGTGGTGCGCACCTCGATCGCGCGCGTGCTCACAGTGATCTCGCAGAA

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: 1013

AGACGGACCTGCAGGCGCAGCTCAAGGAGCTGAAGTCTGAGCTCTCCCTCCTCCGCGTAGCCAAGGTCACCGGCGGCGCACCCAACAAGCTCTCCAAGATgtgcgtacct ... ccttcttcagCAAGGTGGTGCGCACCTCGATCGCGCGCGTGCTCACAGTGATCTCGCAGAAGCAGAAGTCGGCGTTGCGGGAGGCGTACAAGAAGAAGAACCTGCTCCCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 631

AGACGGACCTGCAGGCGCAGCTCAAGGAGCTGAAGTCTGAGCTCTCCCTCCTCCGCGTAGCCAAGGTCACCGGCGGCGCACCCAACAAGCTCTCCAAGATgtgcgtacct ... ccttcttcagCAAGGTGGTGCGCACCTCGATCGCGCGCGTGCTCACAGTGATCTCGCAGAAGCAGAAGTCGGCGTTGCGGGAGGCGTACAAGAAGAAGAACCTGCTCCCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 557

AGACGGACCTGCAGGCGCAGCTCAAGGAGCTGAAGTCTGAGCTCTCCCTCCTCCGCGTAGCCAAGGTCACCGGCGGCGCACCCAACAAGCTCTCCAAGATgtgcgtacct ... ccttcttcagCAAGGTGGTGCGCACCTCGATCGCGCGCGTGCTCACAGTGATCTCGCAGAAGCAGAAGTCGGCGTTGCGGGAGGCGTACAAGAAGAAGAACCTGCTCCCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 318

AGACGGACCTGCAGGCGCAGCTCAAGGAGCTGAAGTCTGAGCTCTCCCTCCTCCGCGTAGCCAAGGTCACCGGCGGCGCACCCAACAAGCTCTCCAAGATgtgcgtacct ... ccttcttcagCAAGGTGGTGCGCACCTCGATCGCGCGCGTGCTCACAGTGATCTCGCAGAAGCAGAAGTCGGCGTTGCGGGAGGCGTACAAGAAGAAGAACCTGCTCCCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGACGGACCTGCAGGCGCAGCTCAAGGAGCTGAAGTCTGAGCTCTCCCTCCTCCGCGTAGCCAAGGTCACCGGCGGCGCACCCAACAAGCTCTCCAAGATgtgcgtacctgcaatctctattttctcctgttattctctgctcctgaactcgactgaatcgattcgaattgtatccggcccttcttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT