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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcttgtaatgatagtattcttgtcctccagaaccgtagcctatcttctagcgttattacttgaaaatggtcttgatggatatgtatatttcagGCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCGCAGTCCAAGCTATAGCAGGAGCAGGAGCCGGAGCCGGAGCCGGAGCTAT

Basic information

species Zea mays
transcript GRMZM2G099317_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G099317_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g02880.1 (Oryza sativa), 3'ss of exon 5
--------------gtgcttgtaatgatagtattcttgtcctccagaaccgtagc-ctatcttctagcgttattacttgaaaatggtcttgatggata----tgtatatttcagGCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCGCAGTCCAAGCTATAGCAGGAGCAGGAGCCGGAGCCGGAGCCGGAGCTAT
              ||   | | || |       |   | |    |  |||  |  || | ||  |    | | ||||  | ||       ||| |||    | | | |||||||||||| |||||||| ||| |||| ||||| |||||||||||| | ||||||||||  ||||||||| ||||| ||||||||||||| ||    ||    
gtattgattgataagttgatctgataaagagcagcacttgcaattgttccgaggtactgtatttgaataatttaactt--agatttctccaatgcatacttctttttttttcagGCGTGAGAGAAGTTATTCATGCTCTCCATCGCCACGCCGTGGACGTGGTCGCAGTCGGAGCTATAGCCGGAGCCGGAGCCGGAGCCGCAGTTACAG----

upper sequence: GRMZM2G099317_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g17710.1 (Oryza sativa), 3'ss of exon 5
---gtgcttgtaatgatagtattcttgtcctccagaaccgtagcctatcttctagcgtt---attacttgaaaatggtcttgatggatatgta-tatttcagGCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCGCAGTCCAAGCTATAGCAGGAGCAGGAGCCGGAGCCGGAGCCGGAGCTAT
    || |||  |   | |      |   ||  || ||  |   |||   |     |||   ||||||  | | |  ||   ||   ||  |  | || |||||| || |||||||| || ||||||||||| |||||||||||| | ||||   |||  ||   ||||   ||| ||||||||||| ||||    ||    
gtattgattgataccgttggtcagatacactgtagcactctgttctaaggtactatgtttgaattactcaagacttctcc-aatacgtacttggttttccagGCGAGAGAGAAGTTATTCGCGCTCCCCATCGCCACGCCGTGGACGTGGTCATGGTCGTAGTCGTAGCTATAGCCGGAGCCGGAGCAGGAGTTACAG----
















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|87155664|gb|DY400453.1|DY400453
EST:     GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAG                         GCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
genomic: GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAGgtgcttgtaa ... tatatttcagGCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
EST: gi|86472004|gb|DY238374.1|DY238374
EST:     GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCGG                         GTGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
genomic: GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAGgtgcttgtaa ... tatatttcagGCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
EST: gi|71298910|gb|DR785450.1|DR785450
EST:     CCTAGGAGCGTCAG                         GCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
genomic: CCTAGGAGCGTCAGgtgcttgtaa ... tatatttcagGCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
EST: gi|71310802|gb|DR791706.1|DR791706
EST:     GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAG                         GCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
genomic: GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAGgtgcttgtaa ... tatatttcagGCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
EST: gi|50336824|gb|CO531950.1|CO531950
EST:     GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAG                         GCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
genomic: GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAGgtgcttgtaa ... tatatttcagGCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
EST: gi|76280523|gb|DV020091.1|DV020091
EST:     GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAG                         GCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
genomic: GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAGgtgcttgtaa ... tatatttcagGCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
EST: gi|148941832|gb|EC886805.2|EC886805
EST:     GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAG                         GCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
genomic: GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAGgtgcttgtaa ... tatatttcagGCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
EST: gi|71438958|gb|DR820008.1|DR820008
EST:     GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAG                         GCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
genomic: GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAGgtgcttgtaa ... tatatttcagGCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
EST: gi|22491590|gb|BU051513.1|BU051513
EST:     GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAG                         GCGTGAAAGAAGTTACT
genomic: GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAGgtgcttgtaa ... tatatttcagGCGTGAAAGAAGTTACT
EST: gi|71298912|gb|DR785451.1|DR785451
EST:     GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAG                         GCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
genomic: GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAGgtgcttgtaa ... tatatttcagGCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
EST: gi|148934490|gb|EC878531.2|EC878531
EST:     GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAG                         GCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
genomic: GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAGgtgcttgtaa ... tatatttcagGCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
EST: gi|71771421|gb|DR969358.1|DR969358
EST:     GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAG                         GCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
genomic: GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAGgtgcttgtaa ... tatatttcagGCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
EST: gi|19436214|gb|BM952624.1|BM952624
EST:     GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAG                         GCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
genomic: GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAGgtgcttgtaa ... tatatttcagGCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
EST: gi|31406034|gb|CD484766.1|CD484766
EST:     GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAG                         GCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
genomic: GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAGgtgcttgtaa ... tatatttcagGCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
EST: gi|26558569|gb|CA830804.1|CA830804
EST:     GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAG                         GCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCC
genomic: GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAGgtgcttgtaa ... tatatttcagGCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCC
EST: gi|211248809|gb|FL007474.1|FL007474
EST:     GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAG                         GCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
genomic: GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAGgtgcttgtaa ... tatatttcagGCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
EST: gi|76282712|gb|DV022280.1|DV022280
EST:     GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAG                         GCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
genomic: GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAGgtgcttgtaa ... tatatttcagGCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
EST: gi|74232122|gb|DT640036.1|DT640036
EST:     GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAG                         GCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
genomic: GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAGgtgcttgtaa ... tatatttcagGCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
EST: gi|19351122|gb|BM895654.1|BM895654
EST:     GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAG                         GCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCC
genomic: GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAGgtgcttgtaa ... tatatttcagGCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCC
EST: gi|113816600|gb|DW936623.1|DW936623
EST:     GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAG                         GCGTGAAAGAAGTTACTCACGNTCCCCA
genomic: GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAGgtgcttgtaa ... tatatttcagGCGTGAAAGAAGTTACTCACGCTCCCCA
EST: gi|87153453|gb|DY398242.1|DY398242
EST:     GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAG                         GCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
genomic: GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAGgtgcttgtaa ... tatatttcagGCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
EST: gi|149070621|gb|EE159032.2|EE159032
EST:     GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAG                         GCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
genomic: GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAGgtgcttgtaa ... tatatttcagGCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
EST: gi|89251320|gb|DY623106.1|DY623106
EST:     GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAG                         GCGTGAAAGAAGTTACT
genomic: GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAGgtgcttgtaa ... tatatttcagGCGTGAAAGAAGTTACT
EST: gi|76014888|gb|DT942058.1|DT942058
EST:     GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAG                         GCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
genomic: GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAGgtgcttgtaa ... tatatttcagGCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
EST: gi|50333687|gb|CO528813.1|CO528813
EST:     GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAG                         GCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
genomic: GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAGgtgcttgtaa ... tatatttcagGCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
EST: gi|76289551|gb|DV029119.1|DV029119
EST:     GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAG                         GCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
genomic: GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAGgtgcttgtaa ... tatatttcagGCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
EST: gi|211251031|gb|FL007480.1|FL007480
EST:     GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAG                         GCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
genomic: GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAGgtgcttgtaa ... tatatttcagGCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
EST: gi|23357517|gb|BU645166.1|BU645166
EST:     GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAG                         GCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
genomic: GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAGgtgcttgtaa ... tatatttcagGCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
EST: gi|148934137|gb|EC878155.2|EC878155
EST:     GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAG                         GCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
genomic: GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAGgtgcttgtaa ... tatatttcagGCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCG
EST: gi|148959184|gb|EE010639.2|EE010639
EST:     GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAG                         GCGTGAAAAGAAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGT
genomic: GAAAGAGGGCATATAGAAAGAAATTGCCAGAACAGTCCTAGGAGCGTCAGgtgcttgtaa ... tatatttcagGCGTGAAA-GAA-GTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctatcttctagcgttattacttgaaaatggtcttgatggatatgtatatttcagGCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCGCAGTCCAAGCTATAGCAGGAGCAGGAGCCGGAGCCGGAGCCGGAGCTAT
                               tcttgat  putative branch site (score: 4)
              ttattacttgaaaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcttgtaatgatagtattcttgtcctccagaaccgtagcctatcttctagcgttattacttgaaaatggtcttgatggatatgtatatttcagGCGTGAAAGAAGTTACTCACGCTCCCCATCTCCACGCCGTGGAAGAGGTCGCAGTCCAAGCTATAGCAGGAGCAGGAGCCGGAGCCGGAGCCGGAGCTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT