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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGAGATGGAAGGGGGCCTGCTTCTACGAGAACGAGGCGTGGCTGGTGTTCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAGgtacgggcctcctcccccgaccgaagctgagcacaattttgcagtaacacggtgtgcttgtgctgccgaacaaattaagatggatccagagagagagagg...

Basic information

species Zea mays
transcript GRMZM2G139374_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139374_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g58114.1 (Oryza sativa), 5'ss of exon 1
GGTGAGATGGAAGGGGGCCTGCTTCTACGAGAACGAGGCGTGGCTGGTGTTCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAGgtacgggcctcctcc-cccgaccga--agctgagcacaattttgcagtaacacggtgtgcttgtgctgccgaacaaattaagatggatccagagagagagagg
| ||   |||||||| ||||||||||||||||||||||||||||||||  ||||||||||   ||| ||||||||||| |||||||| ||||| |||||||||||| |    ||  |   | | |  | ||| |  ||||||||    |    | |  |||    |  |  | ||| | |  |  |  | ||   || |    
GCTGGAGTGGAAGGGCGCCTGCTTCTACGAGAACGAGGCGTGGCTGGTCCTCCACAACGACTCCGGCTCCAAGTACGGAGGCGGCACGCTCCACATCAAGgtacggtcagtttcggcataaactaccaactgtgtgcaattttggctcatgctgctaagctaaaacaactaatcaagtgaccaatgg-ctagttcgatacg--

upper sequence: GRMZM2G139374_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g58114.2 (Oryza sativa), 5'ss of exon 1
GGTGAGATGGAAGGGGGCCTGCTTCTACGAGAACGAGGCGTGGCTGGTGTTCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAGgtacgggcctcctcccccgaccgaagctgagcacaattttgcagtaacacggtgtgcttgtgctgccgaacaaattaagatggatccagagagagagagg----
 |     |||||||| |||||||||||||| |||  ||||||| ||| ||||||||||| ||  |           || || || || |||||| || ||||  | |||    ||     |||   |  ||      || ||  |   ||  || ||  | |  |    |   |||         | || ||| |||       
CGCCGAGTGGAAGGGCGCCTGCTTCTACGATAACCGGGCGTGGATGGAGTTCCACAACGGGACTGATGGGGGCCTTGGAGGTGGTACGCTCCATCTCGAGgtgagtgccggtcccaagccccgcgtcccagtg----ttggctctgttactctgagccggaggcggtagaaccattcttcctccccaagggagggaggcaattg
















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|211101229|gb|FL336543.1|FL336543
EST:     TCCACAACGAGACCGGGTCCAAGTACGGCGGCGGCACGCTCCATATCAAG                         ACATCCAAAGCGCACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACA
genomic: TCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAGgtacgggcct ... acttgcgcagACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACA
EST: gi|110202367|gb|EC884264.1|EC884264
EST:     TTCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAG                         ACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACA
genomic: TCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAGgtacgggcct ... acttgcgcagACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACA
EST: gi|211004794|gb|FL233604.1|FL233604
EST:     TCCACAACGAGACCGGGTCCAAGTACGGCGGCGGCACGCTCCATATCAAG                         ACATCCAAAGCGCACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACA
genomic: TCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAGgtacgggcct ... acttgcgcagACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACA
EST: gi|211231193|gb|FL349074.1|FL349074
EST:     TCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAG                         ACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCA-CA
genomic: TCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAGgtacgggcct ... acttgcgcagACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACA
EST: gi|211004797|gb|FL233607.1|FL233607
EST:     TCCACAACGAGACCGGGTCCAAGTACGGCGGCGGCACGCTCCATATCAAG                         ACATCCAAAGCGCACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACA
genomic: TCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAGgtacgggcct ... acttgcgcagACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACA
EST: gi|148931314|gb|EC874175.2|EC874175
EST:     TCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAG                         ACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACA
genomic: TCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAGgtacgggcct ... acttgcgcagACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACA
EST: gi|211004799|gb|FL233609.1|FL233609
EST:     TCCACAACGAGACCGGGTCCAAGTACGGCGGCGGCACGCTCCATATCAAG                         ACATCCAAAGCGCACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACA
genomic: TCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAGgtacgggcct ... acttgcgcagACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACA
EST: gi|93284093|gb|EB676357.1|EB676357
EST:     TCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAG                         ACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACA
genomic: TCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAGgtacgggcct ... acttgcgcagACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACA
EST: gi|148955706|gb|EC901392.2|EC901392
EST:     TCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAG                         ACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACA
genomic: TCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAGgtacgggcct ... acttgcgcagACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACA
EST: gi|101393781|gb|EB818823.1|EB818823
EST:     TCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAG                         ACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACA
genomic: TCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAGgtacgggcct ... acttgcgcagACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACA
EST: gi|76011882|gb|DT939052.1|DT939052
EST:     TCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAG                         ACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACA
genomic: TCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAGgtacgggcct ... acttgcgcagACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACA
EST: gi|149110172|gb|EE293987.2|EE293987
EST:     TCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAG                         ACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACA
genomic: TCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAGgtacgggcct ... acttgcgcagACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACA
EST: gi|74235211|gb|DT643125.1|DT643125
EST:     TCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAG                         ACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACA
genomic: TCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAGgtacgggcct ... acttgcgcagACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACA
EST: gi|148965948|gb|EE016864.2|EE016864
EST:     TCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAG                         ACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACA
genomic: TCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAGgtacgggcct ... acttgcgcagACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACA
EST: gi|211364274|gb|FL199171.1|FL199171
EST:     C-ACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATNCA-G                         ACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAAC
genomic: CCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATAT-CAAGgtacgggcct ... acttgcgcagACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAAC
EST: gi|149079827|gb|EE168827.2|EE168827
EST:     TCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAG                         ACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACA
genomic: TCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAGgtacgggcct ... acttgcgcagACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACA
EST: gi|211004795|gb|FL233605.1|FL233605
EST:     TCCACAACGAGACCGGGTCCAAGTACGGCGGCGGCACGCTCCATATCAAG                         ACATCCAAAGCGCACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACA
genomic: TCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAGgtacgggcct ... acttgcgcagACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACA
EST: gi|148946744|gb|EC892010.2|EC892010
EST:     TCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAG                         ACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACA
genomic: TCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAGgtacgggcct ... acttgcgcagACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACA
EST: gi|148967020|gb|EE018178.2|EE018178
EST:     TCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAG                         ACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACA
genomic: TCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAGgtacgggcct ... acttgcgcagACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACA
EST: gi|71311670|gb|DR792243.1|DR792243
EST:     TCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAG                         ACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACA
genomic: TCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAGgtacgggcct ... acttgcgcagACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACA

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: 46 (upstream exon), 47 (downstream exon)
Score: 68

GGTGAGATGGAAGGGGGCCTGCTTCTACGAGAACGAGGCGTGGCTGGTGTTCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAGgtacgggcct ... acttgcgcagACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACACCATACAGAGTTACATGGGATTACTACTTTCTGGGGCGAGAGCACACTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 190

GGTGAGATGGAAGGGGGCCTGCTTCTACGAGAACGAGGCGTGGCTGGTGTTCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAGgtacgggcct ... acttgcgcagACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACACCATACAGAGTTACATGGGATTACTACTTTCTGGGGCGAGAGCACACTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 203

GGTGAGATGGAAGGGGGCCTGCTTCTACGAGAACGAGGCGTGGCTGGTGTTCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAGgtacgggcct ... acttgcgcagACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACACCATACAGAGTTACATGGGATTACTACTTTCTGGGGCGAGAGCACACTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 177

GGTGAGATGGAAGGGGGCCTGCTTCTACGAGAACGAGGCGTGGCTGGTGTTCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAGgtacgggcct ... acttgcgcagACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACACCATACAGAGTTACATGGGATTACTACTTTCTGGGGCGAGAGCACACTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGAGATGGAAGGGGGCCTGCTTCTACGAGAACGAGGCGTGGCTGGTGTTCCACAACGAGAGCGGGTCCAAGTACGGCGGCGGCACACTCCATATCAAGgtacgggcctcctcccccgaccgaagctgagcacaattttgcagtaacacggtgtgcttgtgctgccgaacaaattaagatggatccagagagagagagg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcccc