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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcatgtctgctgcattgtttattgtaaacagtatacgttcaaggttgtaggcagttcttgatttctaaattatcttaacactttggcagAATGCAGCTGATGCAAAAGAGCGCACACTTATTGGAACATTGCAGAAGTTCATTAAGGAACAGAAGCTAGAAGAACTGCCCATTTTTGAAGAAGCTAACA

Basic information

species Zea mays
transcript GRMZM2G032423_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G032423_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g09310.1 (Oryza sativa), 3'ss of exon 2
gtgcatgtctgctgca-ttgtttattgtaaacagtatacgttcaaggttgtaggcagttcttgatttctaaattatcttaacactttggcagAATGCAGCTGATGCAAAAGAGCGCACACTTATTGGAACATTGCAGAAGTTCATTAAGGAACAGAAGCTAGAAGAACTGCCCATTTTTGAAGAAGCTAACA
|| ||| | ||||||| ||    |||    ||  ||  | || ||    |||     |  || | |  ||||        ||      ||||| || ||| ||||||||||||||||  ||  | |||  ||||||||||||||| || || ||||||||||||||||| || ||||| |||  || |||  
gtacatttatgctgcagtttcacattaggtactttaggcattaaaaaccgtataagctagttaaatcttaaa--------acggaactgcagACTGAAGCCGATGCAAAAGAGCGCATGCTGCTCGGAGTATTGCAGAAGTTCATCAAAGACCAGAAGCTAGAAGAACTACCTATTTTGGAAATAGTTAAAC
















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|91054339|gb|EB164757.1|EB164757
EST:     TTGCTGGTAAGATGATCCGCATCAGGGGAGATGATCTTGCTACTCAG                         AATGCAGCTGATGCAAAAGAGCGCACACTTATTG
genomic: TTGCTGGTAAGATGATCCGCATCAGGGGAGATGATCTTGCTACTCAGgtgcatgtct ... actttggcagAATGCAGCTGATGCAAAAGAGCGCACACTTATTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgttcaaggttgtaggcagttcttgatttctaaattatcttaacactttggcagAATGCAGCTGATGCAAAAGAGCGCACACTTATTGGAACATTGCAGAAGTTCATTAAGGAACAGAAGCTAGAAGAACTGCCCATTTTTGAAGAAGCTAACA
                                      tcttaac  putative branch site (score: 2)
                       ttgatttctaaattat  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcatgtctgctgcattgtttattgtaaacagtatacgttcaaggttgtaggcagttcttgatttctaaattatcttaacactttggcagAATGCAGCTGATGCAAAAGAGCGCACACTTATTGGAACATTGCAGAAGTTCATTAAGGAACAGAAGCTAGAAGAACTGCCCATTTTTGAAGAAGCTAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC