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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGCAATATTGAAGATGCATTGCAGAAAATACAGgtatgcttcttcaattcagtttcattttctagggctagaccacttacattactccacaatttgccctgaacag

Basic information

species Zea mays
transcript GRMZM2G170532_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G170532_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g14510.2 (Oryza sativa), 5'ss of exon 5
GGGCAATATTGAAGATGCATTGCAGAAAATACAGgtatgcttcttcaattcagtttcattttctagggctagaccactta--cattactccacaatttgccctgaacag----------------------------
||| || ||||||||||| |||||||||||||||||||||||     |||    ||| || ||  |   ||     |  |  | | |    |   |   |||  | |                              
GGGAAACATTGAAGATGCTTTGCAGAAAATACAGgtatgctttactcatttcagttctttgtcaggaagtaatttgcagaggcttcatgttattgtgctcccctagctttttaactaaacaagtatctccttaacag
















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|18164644|gb|BM334483.1|BM334483
EST:     GGGCAATATT-AAGATGCATTGCAGAAAA-ACAG                         GCAATCATTGATGCTGCATCATATGTTCCTCCACCCCCAACAGAAGACC
genomic: GGGCAATATTGAAGATGCATTGCAGAAAATACAGgtatgcttct ... ccctgaacagGCAATCATTGATGCTGCATCATATGTTCCTCCACCCCCAACAGAAGACC
EST: gi|18168069|gb|BM337909.1|BM337909
EST:     GGGCAATATTGAAGATGCATTGCAGAAAATACAG                         GCAATCATTGATGCTGCATCATATGTTCCTCCACCCCCAACAGAAGACC
genomic: GGGCAATATTGAAGATGCATTGCAGAAAATACAGgtatgcttct ... ccctgaacagGCAATCATTGATGCTGCATCATATGTTCCTCCACCCCCAACAGAAGACC
EST: gi|18166092|gb|BM335931.1|BM335931
EST:     GGGCAATATTGAAGATGCATTGCAGAAAATACAG                         GCAATCATTGATGCTGCATCATATGTTCCTCCACCCCCAACAGAAGACC
genomic: GGGCAATATTGAAGATGCATTGCAGAAAATACAGgtatgcttct ... ccctgaacagGCAATCATTGATGCTGCATCATATGTTCCTCCACCCCCAACAGAAGACC
EST: gi|18173601|gb|BM348989.1|BM348989
EST:     GGGCAATATTGAAGATGCATTGCAGAAAATACAG                         GCAATCATTGATGCTGCATCATATGTTCCTCCACCCCCAACAGAAG
genomic: GGGCAATATTGAAGATGCATTGCAGAAAATACAGgtatgcttct ... ccctgaacagGCAATCATTGATGCTGCATCATATGTTCCTCCACCCCCAACAGAAG
EST: gi|18175793|gb|BM350979.1|BM350979
EST:     GGGCAATATTGAAGATGCATTGCAGAAAATACAG                         GCAATCATTGATGCTGCATCATATGTTCCTCCACCCCCAACAGAAGACC
genomic: GGGCAATATTGAAGATGCATTGCAGAAAATACAGgtatgcttct ... ccctgaacagGCAATCATTGATGCTGCATCATATGTTCCTCCACCCCCAACAGAAGACC
EST: gi|18175280|gb|BM350651.1|BM350651
EST:     GGGCAATATTGAAGATGCATTGCAGAAAATACAG                         GCAATCATTGATGCTGCATCATATGTTCCTCCACCCCCAACAGAAG
genomic: GGGCAATATTGAAGATGCATTGCAGAAAATACAGgtatgcttct ... ccctgaacagGCAATCATTGATGCTGCATCATATGTTCCTCCACCCCCAACAGAAG
EST: gi|17931962|gb|BM268922.1|BM268922
EST:     GGGCAATATTGAAGATGCATTGCAGAAAATACAG                         GCAATCATTGATGCTGCATCATATGTTCCTCCACCCCCAACAGAAGACC
genomic: GGGCAATATTGAAGATGCATTGCAGAAAATACAGgtatgcttct ... ccctgaacagGCAATCATTGATGCTGCATCATATGTTCCTCCACCCCCAACAGAAGACC
EST: gi|17931672|gb|BM268632.1|BM268632
EST:     GGGCAATATTGAAGATGCATTGCAGAAAATACAG                         GCAATCATTGATGCTGCATCATATGTTCCTCCACCCCCAACAGAAGACC
genomic: GGGCAATATTGAAGATGCATTGCAGAAAATACAGgtatgcttct ... ccctgaacagGCAATCATTGATGCTGCATCATATGTTCCTCCACCCCCAACAGAAGACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGCAATATTGAAGATGCATTGCAGAAAATACAGgtatgcttcttcaattcagtttcattttctagggctagaccacttacattactccacaatttgccctgaacag

- - - - TTGAAG
- - - -  TGAAGA
- - - - -  AAGATG