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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtctctgttatgttgctctcaattgtgtttcactctggcgttttaaaagtttctatattatggaggcagctatgcttactatgttttgctgtcttttcagATATACCAAATACAGGATAACTTCATTGGAGAAAAACTATATTCCTAAAATGATTGTCCCTGAGGATATTGGGATACCTCTTGACCTACTTGACATGAGT

Basic information

species Zea mays
transcript GRMZM2G055520_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G055520_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g06070.1 (Oryza sativa), 3'ss of exon 2
gtctctgttatgttgctctcaattgtgtttcactct----ggcgttttaaaagtttctatattatggaggcagcta-tgcttactatgtt--ttgctg--tcttttcagATATACCAAATACAGGATAACTTCATTGGAGAAAAACTATATTCCTAAAATGATTGTCCCTGAGGATATTGGGATACCTCTTGACCTACTTGACATGAGT
          |||| ||||| | |||  ||| |  |    || | | | ||  ||  | ||  |||   |     | |  ||  | || |    |||   ||||| |||||||||||||||||| || |||||||||||||| ||||| || || |||||||||||||| |||||| | || |||||||||||||||||||| ||||| 
---------ctgtttctctctactgttcttcgccgtgcatggtgctcttaatattattttaggatgtctgtgttcactctttgttttgctatccgctacctctttgcagATATACCAAATACAGAATCACTTCATTGGAGAAGAACTACATACCCAAAATGATTGTCCCCGAGGATCTCGGAATACCTCTTGACCTACTTGATATGAGC
















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|32801570|gb|CD953806.1|CD953806
EST:     GATCCCAGTGCTCAGCTGAAATGGCTGCCCCTGAATAAGGATAAGGACCG                         ATATACCAAATACAGGATAACTTCATTGGAGAAAAACTATATTCCTAAAAT
genomic: GATCCAAGTGCTCAGCTGAAATGGCTGCCCCTGAATAAGGATAAGGACCGgtatgcatca ... gtcttttcagATATACCAAATACAGGATAACTTCATTGGAGAAAAACTATATTCCTAAAAT
EST: gi|32824006|gb|CD963728.1|CD963728
EST:     GATCTAAGTGCTCAGCTGAAATGGCTGCCCCTGAATAAGGATAAGGACCG                         ATATACCAAATACAGGATAACTTCATTGGAGAAAAACTATATTCCTAAAAT
genomic: GATCCAAGTGCTCAGCTGAAATGGCTGCCCCTGAATAAGGATAAGGACCGgtatgcatca ... gtcttttcagATATACCAAATACAGGATAACTTCATTGGAGAAAAACTATATTCCTAAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagtttctatattatggaggcagctatgcttactatgttttgctgtcttttcagATATACCAAATACAGGATAACTTCATTGGAGAAAAACTATATTCCTAAAATGATTGTCCCTGAGGATATTGGGATACCTCTTGACCTACTTGACATGAGT
                           tgcttac  putative branch site (score: 2)
                                      ttttgctgtcttttc  putative PPT
     ttctatattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctctgttatgttgctctcaattgtgtttcactctggcgttttaaaagtttctatattatggaggcagctatgcttactatgttttgctgtcttttcagATATACCAAATACAGGATAACTTCATTGGAGAAAAACTATATTCCTAAAATGATTGTCCCTGAGGATATTGGGATACCTCTTGACCTACTTGACATGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - tgttgct
- - - - - - - - - - - -tgtgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcagcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttttgct