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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattctttcagccttggatcattgcagtatccacattgaatgtctcaagaaaaatgtatttgagcatatatcacgttagcagtgctttaaaagtttgcacatgagagagatagaaagcatcacttcctattgatcatctatgattaccatttttacagGATGAACACCTCAGATGTTCCTTGTCACCTGAATCTCAAATTGAAGATAGTGGTACTGAAGCATCAACTGATGATGGTAATTTGGAAGCCAAGGGCAATG

Basic information

species Zea mays
transcript GRMZM2G115975_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G115975_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os03g24180.1 (Oryza sativa), 3'ss of exon 12
gtaagattctttcagccttggatcattgcagtatccacattgaatgtctcaagaaaaatgtatttgagcatatatcacgttagcagtgctttaaaagtttgcacatgagagagatagaaagcatcacttcctattgatcatctatgattaccatttttacagGATGAACAC---CTCAGATGTTCCTTGTCACCTGAATCTCAAATTGAAGATAGTGGTACTGAAGCATCAACTGATGATGGTAATTTGGAAGCCAAGGGCAATG
                                                          | |   |     | |     ||      |  ||| |||   ||   |  ||| | | ||| | ||  | |  |||||||||||  ||  |||    | ||||||| |||||||   || ||||| ||| |||| || || ||||||||||||||||| ||||  || |||||||| |||||||  |||||||| | |||||| |   
---------------------------------------------------------ctatgcctttttcttttctgtgtagaacatattttgaaa---tgtgaactagaaataaagacaacactaat--ctattgatcattcatatttatatatcttacagGGTGAACACAACCTTAGATGCTCCCTGTCGCCAGAGTCTCAAATTGAAGATAGCGGTAGCGAGGCATCAACAGATGATGTAAATTTGGATGTCAAGGGTA---
















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|33094425|gb|CF054419.1|CF054419
EST:     CTCAAGGAATTGTCGCAACTCTCTTGGAGGAATATGAGGGCATTTTTCAT                         GATGAACACCTCAGATGTTCCTTGTCACCTGAACCTCAAATTGAAGATAGT
genomic: CTCAAGGAATTGTCGCAACTCTCTTGGAGGAATATGAGGGCATTTTTCATgtaagattct ... atttttacagGATGAACACCTCAGATGTTCCTTGTCACCTGAATCTCAAATTGAAGATAGT
EST: gi|31363590|gb|CD447947.1|CD447947
EST:     CTCAAGGAATTGTCACAACTCTCTTGGAGGAATATGAGGGCATTTTTCAT                         GATGAACACCTCAGATGTTCCTTGTCACCTGAATCTCAAATTGAAGATAGT
genomic: CTCAAGGAATTGTCGCAACTCTCTTGGAGGAATATGAGGGCATTTTTCATgtaagattct ... atttttacagGATGAACACCTCAGATGTTCCTTGTCACCTGAATCTCAAATTGAAGATAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagagatagaaagcatcacttcctattgatcatctatgattaccatttttacagGATGAACACCTCAGATGTTCCTTGTCACCTGAATCTCAAATTGAAGATAGTGGTACTGAAGCATCAACTGATGATGGTAATTTGGAAGCCAAGGGCAATG
                        tattgat  putative branch site (score: 3)
                                           ccattttt  putative PPT
                                             atttttaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagattctttcagccttggatcattgcagtatccacattgaatgtctcaagaaaaatgtatttgagcatatatcacgttagcagtgctttaaaagtttgcacatgagagagatagaaagcatcacttcctattgatcatctatgattaccatttttacagGATGAACACCTCAGATGTTCCTTGTCACCTGAATCTCAAATTGAAGATAGTGGTACTGAAGCATCAACTGATGATGGTAATTTGGAAGCCAAGGGCAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG