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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcactggtgccttccccatgattttattttgccttgtgttggttccatcttttatttgtttccagttgatgtcttgtactacatttgctttagtt...

Basic information

species Zea mays
transcript GRMZM5G841900_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G841900_T04 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g57070.1 (Oryza sativa), 5'ss of exon 3
GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtg-gtgcactggtgccttccc---catgattttattttgccttgtgttggttccatcttttatttgtttccagttgatgtcttgtactacatttgctt-tagtt----------------------------------------------------------------------------------
|| || |||||||||||||| ||||| ||||||||||| ||||||||||||||||||||| |||  |||||||||||||||||||||||||  | |  ||| |  |||  |    ||| ||  ||||   | | | |  |     |||| |||| | |||   |||| |||   ||| | |     ||  | |                                                                                   
GTGACGAAGGTTATGGCTAGGATGGCTTCTGCAGATATAATGTGTGTTGACTCAAAGGCTGTCAAGGAAAAGTTCACTGGCATGATAAGgtacgggttctgttttctttgctgatatgcttccatttaaacctttttcagggatctcttgtatt-gcttcgctttga-gtcagttaccaaacacatttacaatccaatgctcctgcttgccatatgttccttttagactatcacaacaaagttcttcatggttcagctatgctcctctgtttgtag

upper sequence: GRMZM5G841900_T04 (Zea mays), 5'ss of exon 3
lower sequence: Vv04s0043g00400.t01 (Vitis vinifera), 5'ss of exon 3
GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtg-gtgcactggtgccttccccatgattttattttgccttgtgttggttccatcttttatttgtttccagttgatgtcttgtactacatt-tgctttagtt--
|| || || |||||||||||||||||||| || ||||| |||||||||| | | ||| || |  ||||||| || ||||| || || ||||  ||  | |  |   |  |     | |  |        ||       ||  |  |||| |||||    |||||| |  || | |  |||    ||||  |  
GTTACTAAAGTTATGGCTAGAATGGCCTCAGCTGATATAATGTGTGTTGGCCCCAAGTCTGTGCGAGAAAAATTTACTGGAATAATTAGgtatgtaaatttttatgtatctgtctaatggaaaaaaggatgca---aatctgttatttagttgttgattgttgat-ttgtgcaatgaattgcagtttaaatga
















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|211118858|gb|FL110173.1|FL110173
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
EST: gi|148935198|gb|EC879233.2|EC879233
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
EST: gi|60336704|gb|DN203677.1|DN203677
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
EST: gi|211102907|gb|FK962288.1|FK962288
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
EST: gi|148991615|gb|EE033149.2|EE033149
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
EST: gi|211118854|gb|FL110169.1|FL110169
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
EST: gi|211102910|gb|FK962291.1|FK962291
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
EST: gi|78180011|gb|DV550384.1|DV550384
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
EST: gi|211118860|gb|FL110175.1|FL110175
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGT
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGT
EST: gi|12046009|gb|BF728044.1|BF728044
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
EST: gi|211326704|gb|FL445906.1|FL445906
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
EST: gi|32796285|gb|CD948521.1|CD948521
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
EST: gi|211118861|gb|FL110176.1|FL110176
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
EST: gi|60341943|gb|DN208916.1|DN208916
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
EST: gi|211118859|gb|FL110174.1|FL110174
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATSATAAG                         GCAGCAAGATGTTCGTGCAACTGAAAT
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAAT
EST: gi|166676501|gb|EG058226.1|EG058226
EST:     AGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAAAT
genomic: AGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAA-T
EST: gi|28873659|gb|CB329617.1|CB329617
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
EST: gi|148965500|gb|EE016317.2|EE016317
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
EST: gi|18180077|gb|BM381287.1|BM381287
EST:     GTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
genomic: GTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
EST: gi|211102908|gb|FK962289.1|FK962289
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGANATTGACAAGGTGGATATGTACCAATC
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
EST: gi|211102903|gb|FK962284.1|FK962284
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
EST: gi|71439027|gb|DR820077.1|DR820077
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
EST: gi|211102902|gb|FK962283.1|FK962283
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
EST: gi|71759867|gb|DR957804.1|DR957804
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
EST: gi|148935199|gb|EC879234.2|EC879234
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC

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: 48 (upstream exon), 48 (downstream exon)
Score: 124

GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATCATATCGTCCTGGGGACATTGTTAAAGCTATGGTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 59

GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATCATATCGTCCTGGGGACATTGTTAAAGCTATGGTT


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 58

GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATCATATCGTCCTGGGGACATTGTTAAAGCTATGGTT


Block sizes: 47 (upstream exon), 39 (downstream exon)
Score: 41

GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATCATATCGTCCTGGGGACATTGTTAAAGCTATGGTT