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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATCACTTGGCTATGATAACTGTGCAATCTGAAAATCAAAGTAGAAAGAAGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactctatttctgtgctcgtattaccaatttaatgtggacctgtgttaggtcttcatctaattccttgccgcttgctcctgtcttctccatatgcag

Basic information

species Zea mays
transcript GRMZM2G114172_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G114172_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g65450.1 (Oryza sativa), 5'ss of exon 5
GGATCACTTGGCTATGATAACTGTGCAATCTGAAAATCAAAGTAGAAAGAAGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactctatttctgtgctcgtattaccaatttaatgtggacctgtgttaggtcttcatctaattccttgccgcttgctcctgtcttctccatatgcag
|||||||||||| ||||||||||||||||||||||| |       |||||| |||||||| ||||||||||||||||||||||||||||||||||| ||||||||||          |||  |||  |||        |||| |  ||||   | |  ||||  ||||  ||||   ||||| |||| |  | |||||||||
GGATCACTTGGCGATGATAACTGTGCAATCTGAAAACCTGTCAGAAAAGAAAACTTTTGATTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCCGAGgttagta----------gtgg-cgtggtac--------tgtgaatttgtgactgattctcattgaattatttgctcattgcttctgtttctttcatatgcag

upper sequence: GRMZM2G114172_T03 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA08G13320.1 (Glycine max), 5'ss of exon 5
---------GGATCACTTGGCTATGATAACTGTGCAATCTGAAAATCAAAGTAGAAAGAAGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactctatttctgtgct-cgtattaccaatttaat--gtggacctgtgttaggtcttcatctaattccttgccgcttgctcctgt-cttctccatatgcag
          || ||| |||| ||||| || || ||  ||     ||   |         |   ||||| ||||||||||||||| | || |||||| ||||||||||||| | || | |            |     |   ||||  |   ||||    |  |||   |   |     |  |||    |   || |   || | || | | |  
CGCACTTCTTGACCACATGGCAATGATCACGGTTCAGACTTCTTCTCGTGG---------GGTCTTTGATTGCAAGCCTCTTGGTTTGATCTGGGCTAAGTTCCCTGAGgt-aatattatgcaataaaataacacgccatttattttcttaatggaaagttaatagaattatgttagcatatttg---ttcaatcatacactcccccgtctac--

upper sequence: GRMZM2G114172_T03 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA05G30160.1 (Glycine max), 5'ss of exon 5
---------GGATCACTTGGCTATGATAACTGTGCAATCTGAAAATCAAAGTAGAAAGAAGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactctatttctgtgct-cgtattaccaatttaatgtggacctgtgttaggtcttcatctaattccttgccgcttgctcctgtcttctccatatgcag
          || ||| |||| ||||| || || ||  ||     ||   |         |   ||||| ||||||||||||||| | || |||||| |||||||||||||         | |  | |||     | || || |   || |       |  | |    | | |       |    || |  |  |    ||      |||  
CGCACTTCTTGACCACATGGCAATGATCACGGTTCAGACTTCTTCTCGTGG---------GGTCTTTGATTGCAAGCCTCTTGGTTTGATCTGGGCTAAGTTCCCTGAGgtataattatgaatattatgcaataaactaaca-tgccatttattttcttaatggaaagttaacaggagtatgttagcatatttgttcaatcatacattgc--

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|78106133|gb|DV524551.1|DV524551
EST:     AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAG                         TACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
genomic: AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactc ... ccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
EST: gi|37401670|gb|CF638203.1|CF638203
EST:     AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAG                         TACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
genomic: AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactc ... ccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
EST: gi|78180520|gb|DV551013.1|DV551013
EST:     AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAG                         TACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
genomic: AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactc ... ccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
EST: gi|5791422|gb|AI978214.1|AI978214
EST:     AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAG                         TACTACAACGAAAAGAACACCATAATGTTTGATGACCTAAGAAGGAATTTC
genomic: AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactc ... ccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
EST: gi|148958196|gb|EC904401.2|EC904401
EST:     AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAG                         TACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
genomic: AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactc ... ccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
EST: gi|78090560|gb|DV518934.1|DV518934
EST:     AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAG                         TACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
genomic: AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactc ... ccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
EST: gi|8551534|gb|BE128880.1|BE128880
EST:     AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAG                         TACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
genomic: AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactc ... ccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
EST: gi|78113537|gb|DV531928.1|DV531928
EST:     AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAG                         TACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
genomic: AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactc ... ccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
EST: gi|211170844|gb|FL475252.1|FL475252
EST:     AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAG                         TACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
genomic: AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactc ... ccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
EST: gi|76021043|gb|DT948213.1|DT948213
EST:     AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAG                         TACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
genomic: AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactc ... ccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
EST: gi|37383817|gb|CF628944.1|CF628944
EST:     AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAG                         TACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
genomic: AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactc ... ccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
EST: gi|78106134|gb|DV524552.1|DV524552
EST:     GACTTTTGACTGGCA-GCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAG                         TACTACAACGAAAAGA-CACCATAATGTTTGATGATCTAAGAAGGAATTTC
genomic: GACTTTTGACTG-CAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactc ... ccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
EST: gi|78543692|gb|DV621190.1|DV621190
EST:     AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAG                         TACTACAACGAAAAGAACACCATAATGTTTGATGACCTAAGAAGGAATTTC
genomic: AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactc ... ccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
EST: gi|9743097|gb|BE519245.1|BE519245
EST:     AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAG                         TACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
genomic: AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactc ... ccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
EST: gi|110957655|gb|EE177707.1|EE177707
EST:     AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAG                         TACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
genomic: AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactc ... ccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
EST: gi|20337038|gb|BQ172668.1|BQ172668
EST:     AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAG                         TACTACAACGAAAAGAACACCATAATGTTTGATGACCTAAGAAGGAATTTC
genomic: AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactc ... ccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
EST: gi|60351760|gb|DN218733.1|DN218733
EST:     AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAG                         TACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
genomic: AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactc ... ccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
EST: gi|78090561|gb|DV518935.1|DV518935
EST:     AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAG                         TACTACANCGAAAAAGA-CACCATAATGTTTGATGAT
genomic: AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactc ... ccatatgcagTACTACAACGAAAA-GAACACCATAATGTTTGATGAT
EST: gi|78103926|gb|DV522344.1|DV522344
EST:     AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAG                         TACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
genomic: AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactc ... ccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
EST: gi|37377229|gb|CF625199.1|CF625199
EST:     AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAG                         TACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
genomic: AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactc ... ccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
EST: gi|12058284|gb|BF733104.1|BF733104
EST:     AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAG                         TACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
genomic: AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactc ... ccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
EST: gi|86470825|gb|DY237195.1|DY237195
EST:     AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAG                         TACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
genomic: AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactc ... ccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
EST: gi|149088593|gb|EE177708.2|EE177708
EST:     AGACTTTTGACTGCAAGCCTCTTGGTGTCTTTTGGGCTCAGTTCCCTGAG                         TACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAGGGAATTTC
genomic: AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactc ... ccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
EST: gi|37401175|gb|CF637951.1|CF637951
EST:     AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAG                         TACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
genomic: AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactc ... ccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
EST: gi|101394401|gb|EB819135.1|EB819135
EST:     AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAG                         TACTACAACGAAAAGAACACCATAATGTTTGATGATTTAAGAAGGAATTTC
genomic: AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactc ... ccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
EST: gi|71772417|gb|DR970350.1|DR970350
EST:     AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAG                         TACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAAGAATTT
genomic: AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactc ... ccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTT

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), 48 (downstream exon)
Score: 110

GGATCACTTGGCTATGATAACTGTGCAATCTGAAAATCAAAGTAGAAAGAAGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactc ... ccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTCGTCATGAATCCACAGAACGGTCTCGTGATCAAGCCATTCAGGAAAGCGC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 79

GGATCACTTGGCTATGATAACTGTGCAATCTGAAAATCAAAGTAGAAAGAAGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactc ... ccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTCGTCATGAATCCACAGAACGGTCTCGTGATCAAGCCATTCAGGAAAGCGC


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 77

GGATCACTTGGCTATGATAACTGTGCAATCTGAAAATCAAAGTAGAAAGAAGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactc ... ccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTCGTCATGAATCCACAGAACGGTCTCGTGATCAAGCCATTCAGGAAAGCGC


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 109

GGATCACTTGGCTATGATAACTGTGCAATCTGAAAATCAAAGTAGAAAGAAGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactc ... ccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTCGTCATGAATCCACAGAACGGTCTCGTGATCAAGCCATTCAGGAAAGCGC