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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGAATCCCATCGCTGTGAATAGCAAGTATTGCAATGTATTCACTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAGgtttgcatttctgctcttttccttattgttatgttcaatgctcatgtagtttataatcttttccattatttattaaatagttgagactagtctggattga...

Basic information

species Zea mays
transcript GRMZM2G133885_T01
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133885_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g72940.1 (Oryza sativa), 5'ss of exon 16
GTGAATCCCATCGCTGTGAATAGCAAGTATTGCAATGTATTCACTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAGgtttgcatttctgctcttttcctt----attgttatgttcaatgctcatgtagtttataatcttttccattatttattaaatagttgag-actagtctggattga
|| ||||| || |||||||| ||||| ||||| ||||| ||||| ||||| ||| ||||||| ||||| || |||||||||||||||||||||||||| | ||||  ||||||||      | |   | || | |   |  ||   |   |     |  |      |  ||   | ||  |  |  ||| ||      
GTCAATCCTATTGCTGTGAACAGCAAATATTGTAATGTTTTCACCGAGAACAAACGAGTTGTTTCAATAATCTCAACTTCAGAGTTTGGAAAGgtttgtacttctattcttttccccctagactaccaggtaccagcttactgctttgcgtgcctctcgcttcctctgtttcttttgtcaaacatcagtatgc-----

upper sequence: GRMZM2G133885_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA15G05680.1 (Glycine max), 5'ss of exon 19
GTGAATCCCATCGCTGTGAATAGCAAGTATTGCAATGTATTCACTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAGgtttg-catttctgctcttttcctt----attgttatgttcaatgctcatgtagt-ttataatcttttccat-tatttattaaatagttgagactagtctggattga-------------------------------------------------------------
||||||||||| ||||| ||||| ||||| || ||||| ||||| ||||| || |||||| | ||||  || ||||||  ||| |||||||||||| | |||| |   |  |||   |    ||| ||  ||||    || || |  |  |  ||| | | |||  | ||||| ||||  |      ||      ||| |                                                             
GTGAATCCCATTGCTGTAAATAGTAAGTACTGTAATGTCTTCACGGAGAACAAGAGAGTTATTTCAAGAATTTCAACTGTAGATTTTGGAAAGgttagtcattgcaattaatttgtgtctgaattcttgagttcgggact-atatcctgctgaaatttatgccacatgtttatgaaatgatatgagttacctataatttattgccattttagcttatagttgtagacatgtattaaccattatcttataatttggattcag

upper sequence: GRMZM2G133885_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA08G19310.2 (Glycine max), 5'ss of exon 17
GTGAATCCCATCGCTGTGAATAGCAAGTATTGCAATGTATTCACTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAGgtttg-catttctgctcttttcctt------attgttatgttcaatgctcatgtagt-ttataatcttttccattatttattaaatagttg---agactagtctggattga---------------------------------------------------------------------
|| |||||||| ||||| ||||||||||| |||||||| ||||| ||||| || |||||||| |||||  | ||||||  ||| |||||||||||| | |||| |   |  |||| ||      ||||||  ||||| ||   || |  |  |  ||| | | |||| | ||  | |||  ||        ||      ||  |                                                                     
GTCAATCCCATTGCTGTAAATAGCAAGTACTGCAATGTCTTCACGGAGAACAAGAGAGTTGTTTCAATAGTTTCAACTGTAGATTTTGGAAAGgttggtcattgcaattaatttctttgtctgaattgttgagttca-tgactatatcctgctgaaatttataccataagtttgtgaattattatctgagttacctataatctactgcctctactttcatttttgcttatagttgcagacctttattgaccagtatcttataattttattcag

upper sequence: GRMZM2G133885_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT4G25970.1 (Arabidopsis thaliana), 5'ss of exon 18
GTGAATCCCATCGCTGTGAATAGCAAGTATTGCAATGTATTCACTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAGgtttgcatttctgctcttttccttattgttatgttcaatgctcatgtagtttataatcttttcca-ttatttattaaatagttgagact---agtctggattga--------------------------------------------------------------------------------
|| ||||| || ||||| ||||||||||| || ||||| ||||||||||||||| |     |   ||| ||||||||  |||||||||||||||| ||   |  ||      || | |   |  | ||    | || ||  | | | ||| |||  || ||   | ||   |  ||||  ||   |      |||||                                                                                
GTTAATCCGATTGCTGTCAATAGCAAGTACTGTAATGTGTTCACTGAGAATAAACGGACCATCGTAATTATATCAACAGCAGAGTTTGGAAAGgtatgtcatcttgtataagtcataaacatcttttttctcggtc-tgctgatgaaaatatttctcagttgcctcttg--tgcttgatgctttgaactcaaattgaagcagtattttataaacgaaggtgtacaatgaaatctgatcttatcgcagaacttgatctcagcttaatatatgtaacag

upper sequence: GRMZM2G133885_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv12s0055g00710.t01 (Vitis vinifera), 5'ss of exon 15
GTGAATCCCATCGCTGTGAATAGCAAGTATTGCAATGTATTCACTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAGgtttgcatttctgctcttttccttattgttatgttcaatgctcatgtagtttataatcttttccattatttattaaatag--ttgagactagtctggattga
|| |||||||| |||||||||||||||||||||||||||||||| ||||| ||  |||| |||||  | || ||||| ||||| ||||| ||||| ||   ||    || |||  |  ||| |   ||||    || || | || ||     |||   | |   |  ||| |   |  ||  |  |||       
GTTAATCCCATTGCTGTGAATAGCAAGTATTGCAATGTATTCACAGAGAACAAGCGAGTAGTATCTGTTATTTCAACATCAGATTTTGGGAAGgtctgtgatttcaatcatttgat-gttgcttgattcacatttcttgaatttcatctgtctttatgtaacaaaaaaaacaagctccagttttttcttttcca-

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|5922429|gb|AW055718.1|AW055718
EST:     CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAG                         GTAGCATTTGTTGCGATTGGAGCAACAATGGTAGGAAGCATCACGTTCTTG
genomic: CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAGgtttgcattt ... catggttcagGTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
EST: gi|32844513|gb|CD984194.1|CD984194
EST:     CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAG                         GTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
genomic: CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAGgtttgcattt ... catggttcagGTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
EST: gi|6194556|gb|AW146660.1|AW146660
EST:     CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAG                         GGAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
genomic: CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAGgtttgcattt ... catggttcagGTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
EST: gi|6021540|gb|AW066468.1|AW066468
EST:     CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAG                         GTAGCATTTGTTGCGATTGGAGCAACAATGGTAGGAAGCATCACGTTCTTG
genomic: CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAGgtttgcattt ... catggttcagGTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
EST: gi|37361294|gb|CF602583.1|CF602583
EST:     CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAG                         GTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
genomic: CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAGgtttgcattt ... catggttcagGTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
EST: gi|32912653|gb|CF017465.1|CF017465
EST:     CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAG                         GTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
genomic: CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAGgtttgcattt ... catggttcagGTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
EST: gi|33770671|gb|CF272965.1|CF272965
EST:     CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAG                         GTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
genomic: CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAGgtttgcattt ... catggttcagGTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
EST: gi|6095730|gb|AW120397.1|AW120397
EST:     CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAG                         GTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
genomic: CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAGgtttgcattt ... catggttcagGTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
EST: gi|32913231|gb|CF018043.1|CF018043
EST:     CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAG                         GTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
genomic: CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAGgtttgcattt ... catggttcagGTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
EST: gi|211196234|gb|FL472452.1|FL472452
EST:     CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAG                         GTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
genomic: CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAGgtttgcattt ... catggttcagGTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
EST: gi|60396723|gb|DN229588.1|DN229588
EST:     CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAG                         GTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
genomic: CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAGgtttgcattt ... catggttcagGTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
EST: gi|78103985|gb|DV522403.1|DV522403
EST:     CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAG                         GTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
genomic: CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAGgtttgcattt ... catggttcagGTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
EST: gi|40302877|gb|CK347264.1|CK347264
EST:     CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAG                         GTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
genomic: CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAGgtttgcattt ... catggttcagGTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG

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), 45 (downstream exon)
Score: 95

GTGAATCCCATCGCTGTGAATAGCAAGTATTGCAATGTATTCACTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAGgtttgcattt ... catggttcagGTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTGAAAAAAGAGGGTGACTACGTCCGCAAAGGAGATGAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 89

GTGAATCCCATCGCTGTGAATAGCAAGTATTGCAATGTATTCACTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAGgtttgcattt ... catggttcagGTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTGAAAAAAGAGGGTGACTACGTCCGCAAAGGAGATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 159

GTGAATCCCATCGCTGTGAATAGCAAGTATTGCAATGTATTCACTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAGgtttgcattt ... catggttcagGTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTGAAAAAAGAGGGTGACTACGTCCGCAAAGGAGATGAG


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 62

GTGAATCCCATCGCTGTGAATAGCAAGTATTGCAATGTATTCACTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAGgtttgcattt ... catggttcagGTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTGAAAAAAGAGGGTGACTACGTCCGCAAAGGAGATGAG