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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccttttggcttgttcagatgtatagccagagtgacattattttggggacaggttgtatatttttatatataatggtacttaatttaatctttattcccagGTCACGGAGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGATTCTGAGAAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACA

Basic information

species Zea mays
transcript GRMZM2G075485_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075485_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g10220.1 (Oryza sativa), 3'ss of exon 4
ccttttggcttgttcagatgtatagccagagtgacattattttggggacaggttgtatatttttatatataatggtacttaatttaatctttattcccagGTCACGGAGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGATTCTGAGAAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACA
      |  |  ||  | |  ||| | | |   | | |  |          | | | | ||    |||| |||| |   | ||    |     |   ||||| || |||||||| |||||||||||||||||||| || ||||||||||||||||| |||| |||||||||||| || || ||||||| ||| |||||||
------gtatctttttggtccatatcaacaaaaaaacttgt----------gctatctgttcacctatacaatgatcggtgatgacctacacttctgcagGTTACTGAGGCTGATATTGAAGAATTTGAAGCTAAGTACAGAGGGTCAGATTCTGAAAAAAAGGACTTGAAGGATCTATATACAAAATTTAAAGGCAACA
















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|211337601|gb|FL103353.1|FL103353
EST:     GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAA                         GTCACGGAGGCTGACATTGAAGAATTTGA
genomic: GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAAgtatggttgc ... ttattcccagGTCACGGAGGCTGACATTGAAGAATTTGA
EST: gi|78117499|gb|DV535886.1|DV535886
EST:     GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAA                         GTCACGGAGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGAT
genomic: GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAAgtatggttgc ... ttattcccagGTCACGGAGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGAT
EST: gi|78116316|gb|DV534703.1|DV534703
EST:     GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAA                         GTCACGGAGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGAT
genomic: GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAAgtatggttgc ... ttattcccagGTCACGGAGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGAT
EST: gi|211337600|gb|FL103352.1|FL103352
EST:     GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAA                         GTCACGGAGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGAT
genomic: GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAAgtatggttgc ... ttattcccagGTCACGGAGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGAT
EST: gi|211339984|gb|FL103354.1|FL103354
EST:     GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAA                         GTCACGGAGGCTGAC
genomic: GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAAgtatggttgc ... ttattcccagGTCACGGAGGCTGAC
EST: gi|211342376|gb|FL103369.1|FL103369
EST:     GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAA                         GTCACGGAGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGAT
genomic: GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAAgtatggttgc ... ttattcccagGTCACGGAGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGAT
EST: gi|211339995|gb|FL103365.1|FL103365
EST:     GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAA                         GTCACGGAGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGAT
genomic: GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAAgtatggttgc ... ttattcccagGTCACGGAGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGAT
EST: gi|91870824|gb|EB401103.1|EB401103
EST:     GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAA                         GTCACGGAGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGAT
genomic: GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAAgtatggttgc ... ttattcccagGTCACGGAGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGAT
EST: gi|211339988|gb|FL103358.1|FL103358
EST:     GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAA                         GTCACGGAGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGAT
genomic: GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAAgtatggttgc ... ttattcccagGTCACGGAGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGAT
EST: gi|211339990|gb|FL103360.1|FL103360
EST:     GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAA                         GTCACGGAGGCTGACATTGAAGAATTTGAAGCTAAATATAG
genomic: GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAAgtatggttgc ... ttattcccagGTCACGGAGGCTGACATTGAAGAATTTGAAGCTAAATATAG
EST: gi|211342377|gb|FL103370.1|FL103370
EST:     GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAA                         GTCACGGAGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGAT
genomic: GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAAgtatggttgc ... ttattcccagGTCACGGAGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGAT
EST: gi|211339987|gb|FL103357.1|FL103357
EST:     GAGAAGCTGCNAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAA                         GTCTCSGAGGCTGACATTGAAGAATTTGAAGC
genomic: GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAAgtatggttgc ... ttattcccagGTCACGGAGGCTGACATTGAAGAATTTGAAGC
EST: gi|211337598|gb|FL103350.1|FL103350
EST:     GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAA                         GTCACGGAGGCTGACATTGAAGAATTTGAAGC
genomic: GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAAgtatggttgc ... ttattcccagGTCACGGAGGCTGACATTGAAGAATTTGAAGC
EST: gi|211339993|gb|FL103363.1|FL103363
EST:     GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAA                         GTCACGGAGGCTGACATTGAAGAATTTGAAGCTCAATATAGAGGGTCAGA
genomic: GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAAgtatggttgc ... ttattcccagGTCACGGAGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGA
EST: gi|32909541|gb|CF014353.1|CF014353
EST:     GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAA                         GTCACGGAGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGAT
genomic: GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAAgtatggttgc ... ttattcccagGTCACGGAGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGAT
EST: gi|71443604|gb|DR824654.1|DR824654
EST:     GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAA                         GTCACGGAGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGAT
genomic: GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAAgtatggttgc ... ttattcccagGTCACGGAGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGAT
EST: gi|211337592|gb|FL103344.1|FL103344
EST:     GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAA                         GTCACGGAGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGAT
genomic: GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAAgtatggttgc ... ttattcccagGTCACGGAGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGAT
EST: gi|60341956|gb|DN208929.1|DN208929
EST:     GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAA                         GTCACGGAGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGAT
genomic: GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAAgtatggttgc ... ttattcccagGTCACGGAGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGAT
EST: gi|211342378|gb|FL103371.1|FL103371
EST:     GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAA                         GTCACGGAGGCTGACATTGAAGAATTTGAAGCT
genomic: GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAAgtatggttgc ... ttattcccagGTCACGGAGGCTGACATTGAAGAATTTGAAGCT
EST: gi|211339992|gb|FL103362.1|FL103362
EST:     GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAA                         GTCACGGAGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGAT
genomic: GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAAgtatggttgc ... ttattcccagGTCACGGAGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGAT
EST: gi|211337591|gb|FL103343.1|FL103343
EST:     GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAA                         GTCACGGAGGCTGACATTGAAGAATTTGAAGCT
genomic: GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAAgtatggttgc ... ttattcccagGTCACGGAGGCTGACATTGAAGAATTTGAAGCT
EST: gi|211339989|gb|FL103359.1|FL103359
EST:     GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTWCAAGAAA                         GTCMCGGAGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGG
genomic: GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAAgtatggttgc ... ttattcccagGTCACGGAGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGG
EST: gi|211025378|gb|FL421223.1|FL421223
EST:     GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAA                         GTCACGGAGGCTGACATTGAAGAATTTGAAGCT
genomic: GAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAAgtatggttgc ... ttattcccagGTCACGGAGGCTGACATTGAAGAATTTGAAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggacaggttgtatatttttatatataatggtacttaatttaatctttattcccagGTCACGGAGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGATTCTGAGAAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACA
                                    atttaat  putative branch site (score: 4)
                                          tctttattccc  CT-rich tract
          tatatttttatatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccttttggcttgttcagatgtatagccagagtgacattattttggggacaggttgtatatttttatatataatggtacttaatttaatctttattcccagGTCACGGAGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGATTCTGAGAAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA