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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGTTCAATGGTAGTGGATGGCTCATTTGTATCATCTATGTCCTCTGATAACTCAGTCGAAGAAAGCAGCTTTCAACAACTGCAGGATGCTGTTAGTCAGgtatcatgggttactagttttctttttgatttcttttaatttcccatatagcataaactctagcctacagcagtacagccccttcattttgttattgcaa...

Basic information

species Zea mays
transcript GRMZM2G093096_T02
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G093096_T04 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g27019.5 (Oryza sativa), 5'ss of exon 7
TAGTTCAATGGTAGTGGATGGCTCATTTGTATCATCTATGTCCTCTGATAACTCAGTCGAAGAAAGCAGCTTTCAACAACTGCAGGATGCTGTTAGTCAGgtatcatgggttactagttttctttttgatttcttttaatttcccatatagcataaac-tctagcctacagcagtacagccccttcattttgttattgcaa
 |  ||||||||||| ||||| || || ||||| ||||| || |||||||||||||| ||||| | ||||||||  || || |||||||| |||||||||||||    | ||| |  | | |  | || |   |||||   |     ||    || |  | |    ||        |   | | | ||||  || | || |
CACCTCAATGGTAGTTGATGGGTCCTTCGTATCGTCTATTTCTTCTGATAACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAGgtatagcagtttattt-tctgcaatgtggtccattttatggttgtgcatgaactacatatttgatatatctttcctccagctcgtaatttaattctagcga
















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|67026168|gb|CO454917.1|CO454917
EST:     TGGCCCTCTGATAACTCACGTCGAAGAAAGCAGCTTTTCA-CAACTGGCAG-ATGCTGTTAGTCAG          
genomic: CA-GTCGAAGAAAGCAGCTTT-CAACAACTG-CAGGATGCTGTTAGTCAGgtatcatggg ... tctacttcagC
EST: gi|67041729|gb|CO467984.1|CO467984
EST:     TCTATGTCCTCTGATAACTCAGTCGAAGAAAGCAGCTTTCAACAACTGCAGGATGCTGTTAGTCAG          
genomic: ACTCAGTCGAAGAAAGCAGCTTTCAACAACTGCAGGATGCTGTTAGTCAGgtatcatggg ... tctacttcagC
EST: gi|32849606|gb|CD989287.1|CD989287
EST:     TGCTGTTAGTCAG                         CTGGATGTGCAACCCAAATTGTGCATCAGGGATGGTTTATACCGATTGGCA
genomic: TGCTGTTAGTCAGgtatcatggg ... tctacttcagCTGGATGTGCAAACCAAATTGTGCATCAGGGATGGTTTATACCGATTGGCA
EST: gi|166654720|gb|EG090357.1|EG090357
EST:     AAGAAAGCAGCTTTCAACAACTGCAGGATGCTGTTAGTCAG                         CTGGATGTGCAAACCAAATTGTGCATCAGGGATGGTTTATACCGATTGGCA
genomic: AAGAAAGCAGCTTTCAACAACTGCAGGATGCTGTTAGTCAGgtatcatggg ... tctacttcagCTGGATGTGCAAACCAAATTGTGCATCAGGGATGGTTTATACCGATTGGCA
EST: gi|6021401|gb|AW066329.1|AW066329
EST:     ACTCAGTCGAAGAAAGCAGCTTTCAACAACTGCAGGATGCTGTTAGTCAG                         CTGGATGTGCAAACCAAATTGTGCATCAGGGATGGTTTATACCGATTGGCA
genomic: ACTCAGTCGAAGAAAGCAGCTTTCAACAACTGCAGGATGCTGTTAGTCAGgtatcatggg ... tctacttcagCTGGATGTGCAAACCAAATTGTGCATCAGGGATGGTTTATACCGATTGGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAGTTCAATGGTAGTGGATGGCTCATTTGTATCATCTATGTCCTCTGATAACTCAGTCGAAGAAAGCAGCTTTCAACAACTGCAGGATGCTGTTAGTCAGgtatcatgggttactagttttctttttgatttcttttaatttcccatatagcataaactctagcctacagcagtacagccccttcattttgttattgcaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cagcccc