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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacgatgagcaacctgttgcagtgtgcaccaaactgtttatattatggctctgtaagttttgggttttgttttgttatctgagtctcctattcatttcagGTAAATCTGAGGTTTCTGCCATTCTTTATAAAGCCGGAGAGTGCATGCAGGAGCTTCTGAAATCATGGAAAGATTTTGAAGCAACTCAGGAGGCTACAAA

Basic information

species Zea mays
transcript GRMZM2G464000_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G464000_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g29450.1 (Oryza sativa), 3'ss of exon 3
aacgatgagcaacctgttgcagtgtgcaccaaactgtttatattatg--gctctgtaagttttgggttttgt--tttgttatctgagtctcctattcatttcagGTAAATCTGAGGTTTCTGCCATTCTTTATAAAGCCGGAGAGTGCATGCAGGAGCTTCTGAAATCATGGAAAGATTTTGAAGCAACTCAGGAGGCTACAAA
  | |    |||  ||  |||   ||    ||  | | ||   || |  | |  | |||||   | ||||||  |||| ||||| ||| || | | |||| |||||||||||||||  || |||||| | |||||||| || ||||||||||| ||||||||||||||||||||||| ||||||||||| |  || |||| || 
tgcaactttcaaattga-gcataatga--taatttatctaaggtaggctggtaaggaagttgctgtttttgtattttgctatcttagtttcat-tccattgcagGTAAATCTGAGGCATCAGCCATTGTCTATAAAGCTGGTGAGTGCATGCAAGAGCTTCTGAAATCATGGAAAGAGTTTGAAGCAACCCCAGAAGCTAAAAG
















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|211146179|gb|FK958443.1|FK958443
EST:     GCGTGATGGCGAAGGGGCTCAAG
genomic: GCGTGATGGCGAAGGGGCTCAAG
EST: gi|116822827|gb|EC866276.1|EC866276
EST:     GCGTGATGGCGAAGGGGCTCAAG
genomic: GCGTGATGGCGAAGGGGCTCAAG
EST: gi|26558158|gb|CA830393.1|CA830393
EST:     GCGTGATGGCGAAGGGGCTCAAG
genomic: GCGTGATGGCGAAGGGGCTCAAG
EST: gi|67024103|gb|CO452852.1|CO452852
EST:     GCGTGATGGCGAAGGGGCTCAAG
genomic: GCGTGATGGCGAAGGGGCTCAAG
EST: gi|21987866|gb|BQ779394.1|BQ779394
EST:     GCGTGATGGCGAAGGGGCTCAAG
genomic: GCGTGATGGCGAAGGGGCTCAAG
EST: gi|32931653|gb|CF036465.1|CF036465
EST:     GCGTGATGGCGAAGGGGCTCAAG
genomic: GCGTGATGGCGAAGGGGCTCAAG
EST: gi|32934961|gb|CF039773.1|CF039773
EST:     GCGTGATGGCGAAGGGGCTCAAG
genomic: GCGTGATGGCGAAGGGGCTCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggctctgtaagttttgggttttgttttgttatctgagtctcctattcatttcagGTAAATCTGAGGTTTCTGCCATTCTTTATAAAGCCGGAGAGTGCATGCAGGAGCTTCTGAAATCATGGAAAGATTTTGAAGCAACTCAGGAGGCTACAAA
                                      tctcctattcatttc  CT-rich tract
                   ttttgttttgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacgatgagcaacctgttgcagtgtgcaccaaactgtttatattatggctctgtaagttttgggttttgttttgttatctgagtctcctattcatttcagGTAAATCTGAGGTTTCTGCCATTCTTTATAAAGCCGGAGAGTGCATGCAGGAGCTTCTGAAATCATGGAAAGATTTTGAAGCAACTCAGGAGGCTACAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA