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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggatccgcgtgccccatggcttagttagtcgcgcgttttgcgcgtgttgatgtgcggtggctaaatttctgtttctgtttttttttatacagCGCGGACGATTGGAAGTTCGCGGCAGAGCAGTTTGTGAGGCGGATGCCGGACAAGGTGATCGTGCACC

Basic information

species Zea mays
transcript GRMZM5G820727_T06
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G845339_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os08g34750.1 (Oryza sativa), 3'ss of exon 1
---gtggatccgcgt--------------gccccatggcttagttagtcg-------cgcgttttgcgcgtgtt-gatgtgcggtggctaaatt---tctgtttctgtttttttttatacagCGCGGACGATTGGAAGTTCGCGGCAGAGCAGTTTGTGAGGCGGATGCCGGACAAGGTGATCGTGCACC
   ||||||||| ||              |   ||| |||| | | |||         ||    |||  |  || |   ||| || |  |||||      |||  | ||||||||| | ||||||||| || ||||| |||||||| |||||||| ||||||||||||||||| || |||||||||||||
gtggtggatccgtgttactgtttgtttttggttcatcgctttgcttgtcagctctgatgcaacctgctggcatttggcttgcagtcgtaaaattagcctggttgttttttttttttttgcagCGCGGATGACTGGAAATTCGCGGCGGAGCAGTTCGTGAGGCGGATGCCGGAAAAAGTGATCGTGCACC
















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|71772904|gb|DR970827.1|DR970827
EST:     GGGGCGTTCCCCGAGCACCTCGTCATCATGGTCAATGGCCTCGTCGGGAG                         CGCGGACGATTGGAAGTTCGCGGCAGAGCAGTTTGTGAGGCGGATGCCGGA
genomic: GGGGCGTTCCCCGAGCACCTCGTCATCATGGTCAATGGCCTCGTCGGGAGgtggatccgc ... ttttatacagCGCGGACGATTGGAAGTTCGCGGCAGAGCAGTTTGTGAGGCGGATGCCGGA
EST: gi|78113514|gb|DV531905.1|DV531905
EST:     GGGGCGTTCCCCGAGCACCTCGTCATCATGGTCAATGGCCTCGTCGGGAG                         CGCGGACGATTGGAAGTTCGCGGCAGAGCAGTTTGTGAGGCGGATGCCGGA
genomic: GGGGCGTTCCCCGAGCACCTCGTCATCATGGTCAATGGCCTCGTCGGGAGgtggatccgc ... ttttatacagCGCGGACGATTGGAAGTTCGCGGCAGAGCAGTTTGTGAGGCGGATGCCGGA
EST: gi|148942263|gb|EC887279.2|EC887279
EST:     GGGGCGTTCCCCGAGCACCTCGTCATCATGGTCAATGGCCTCGTCGGGAG                         CGCGGACGATTGGAAGTTCGCGGCAGAGCAGTTTGTGAGGCGGATGCCGGA
genomic: GGGGCGTTCCCCGAGCACCTCGTCATCATGGTCAATGGCCTCGTCGGGAGgtggatccgc ... ttttatacagCGCGGACGATTGGAAGTTCGCGGCAGAGCAGTTTGTGAGGCGGATGCCGGA
EST: gi|76020655|gb|DT947825.1|DT947825
EST:     GGGGCGTTCCCCGAGCACCTCGTCATCATGGTCAATGGCCTCGTCGGGAG                         CGCGGACGATTGGAAGTTCGCGGCAGAGCAGTTTGTGAGGCGGATGCCGGA
genomic: GGGGCGTTCCCCGAGCACCTCGTCATCATGGTCAATGGCCTCGTCGGGAGgtggatccgc ... ttttatacagCGCGGACGATTGGAAGTTCGCGGCAGAGCAGTTTGTGAGGCGGATGCCGGA
EST: gi|78090975|gb|DV519349.1|DV519349
EST:     GGGGCGTTCCCCGAGCACCTCGTCATCATGGTCAATGGCCTCGTCGGGAG                         CGCGGACGATTGGAAGTTCGCGGCAGAGCAGTTTGTGAGGCGGATGCCGGA
genomic: GGGGCGTTCCCCGAGCACCTCGTCATCATGGTCAATGGCCTCGTCGGGAGgtggatccgc ... ttttatacagCGCGGACGATTGGAAGTTCGCGGCAGAGCAGTTTGTGAGGCGGATGCCGGA
EST: gi|78082075|gb|DV510487.1|DV510487
EST:     GGGGCGTTCCCCGAGCACCTCGTCATCATGGTCAATGGCCTCGTCGGGAG                         CGCGGACGATTGGAAGTTCGCGGCAGAGCAGTTTGTGAGGCGGATGCCGGA
genomic: GGGGCGTTCCCCGAGCACCTCGTCATCATGGTCAATGGCCTCGTCGGGAGgtggatccgc ... ttttatacagCGCGGACGATTGGAAGTTCGCGGCAGAGCAGTTTGTGAGGCGGATGCCGGA
EST: gi|78106692|gb|DV525110.1|DV525110
EST:     GGGGCGTTCCCCGAGCACCTCGTCATCATGGTCAATGGCCTCGTCGGGAG                         CGCGGACGATTGGAAGTTCGCGGCAGAGCAGTTTGTGAGGCGGATGCCGGA
genomic: GGGGCGTTCCCCGAGCACCTCGTCATCATGGTCAATGGCCTCGTCGGGAGgtggatccgc ... ttttatacagCGCGGACGATTGGAAGTTCGCGGCAGAGCAGTTTGTGAGGCGGATGCCGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcgcgtgttgatgtgcggtggctaaatttctgtttctgtttttttttatacagCGCGGACGATTGGAAGTTCGCGGCAGAGCAGTTTGTGAGGCGGATGCCGGACAAGGTGATCGTGCACC
                     ggctaaa  putative branch site (score: 3)
                            tttctgtttctgtttt  CT-rich tract
                        taaatttctgtttctg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggatccgcgtgccccatggcttagttagtcgcgcgttttgcgcgtgttgatgtgcggtggctaaatttctgtttctgtttttttttatacagCGCGGACGATTGGAAGTTCGCGGCAGAGCAGTTTGTGAGGCGGATGCCGGACAAGGTGATCGTGCACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG