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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAAGAATAGCAGAAAAGGTCGGTTTTGTCCATCCAAGCTAAAAGGAAAGAGAGTGATTGAATTAGGAGCTGGCTGTGGCCTGGCTGGGTTCGgtaagctcaatttaactgcccgtcagatgtatttcaggatcttagtcctattggcttcctcttttaaaattgtttgcttatctcctttag

Basic information

species Zea mays
transcript GRMZM2G471805_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G471805_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g57330.1 (Oryza sativa), 5'ss of exon 4
GAAAAGAATAGCAGAAAAGGTCGGTTTTGTCCATCCAAGCTAAAAGGAAAGAGAGTGATTGAATTAGGAGCTGGCTGTGGCCTGGCTGGGTTCGgtaagctcaatttaactgcccgtcagatgtatt-tcaggatcttagtcctattggcttcctcttttaaaattgtttgcttatctcctttag
||||||||||||||||||||| | |||| |||||| || || |||||||| || ||||||||  |||||||||| ||||| || |||||| | |||||| |   |  || | ||  |||||  || | || | |||||  |  |  | ||  ||  |   |||||||   |||| || ||     
GAAAAGAATAGCAGAAAAGGTAGATTTTCTCCATCTAAACTGAAAGGAAAAAGGGTGATTGAGCTAGGAGCTGGTTGTGGTCTAGCTGGGCTTGgtaagatgggtcgaattacct-tcagagatactatctgaatcttgatggtgctcgc--ccaataacaaaattgc--gcttctccccag---

upper sequence: GRMZM2G471805_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g57330.2 (Oryza sativa), 5'ss of exon 3
------GAAAAGAATAGCAGAAAAGGTCGGTTTTGTCCATCCAAGCTAAAAGGAAAGAGAGTGATTGAATTAGGAGCTGGCTGTGGCCTGGCTGGGTTCGgtaagctcaatttaactgcccgtcagatgtatt-tcaggatcttagtcctattggcttcctcttttaaaattgtttgcttatctcctttag
      ||||||||||||||||||||| | |||| |||||| || || |||||||| || ||||||||  |||||||||| ||||| || |||||| | |||||| |   |  || | ||  |||||  || | || | |||||  |  |  | ||  ||  |   |||||||   |||| || ||     
GTCCAGGAAAAGAATAGCAGAAAAGGTAGATTTTCTCCATCTAAACTGAAAGGAAAAAGGGTGATTGAGCTAGGAGCTGGTTGTGGTCTAGCTGGGCTTGgtaagatgggtcgaattacct-tcagagatactatctgaatcttgatggtgctcgc--ccaataacaaaattgc--gcttctccccag---
















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|211397545|gb|FL373943.1|FL373943
EST:     GATTGAATTAGGAGCTGGCTGTGGCCTGGCTGGGTTCG                         GAATGACCTTGTTGGGTTGTGATGTTACAACAACTGACCAAGTCGAGGTGC
genomic: GATTGAATTAGGAGCTGGCTGTGGCCTGGCTGGGTTCGgtaagctcaa ... tctcctttagGAATGACCTTGTTGGGTTGTGATGTTACAACAACTGACCAAGTCGAGGTGC
EST: gi|60395803|gb|DN228673.1|DN228673
EST:     AGGAAAGAGAGTGATTGAATTAGGAGCTGGCTGTGGCCTGGCTGGGTTCG                         GAATGACCTTGTTGGGTTGTGATGTTACAACAACTGACCAAGTCGAGGTGC
genomic: AGGAAAGAGAGTGATTGAATTAGGAGCTGGCTGTGGCCTGGCTGGGTTCGgtaagctcaa ... tctcctttagGAATGACCTTGTTGGGTTGTGATGTTACAACAACTGACCAAGTCGAGGTGC
EST: gi|211167619|gb|FL375013.1|FL375013
EST:     AGGAAAGAGAGTGATTGAATTAGGAGCTGGCTGTGGCCTGGCTGGGTTCG                         GAATGACCTTGTTGGGTTGTGATGTTACAACAACTGACCAAGTCGAGGTGC
genomic: AGGAAAGAGAGTGATTGAATTAGGAGCTGGCTGTGGCCTGGCTGGGTTCGgtaagctcaa ... tctcctttagGAATGACCTTGTTGGGTTGTGATGTTACAACAACTGACCAAGTCGAGGTGC
EST: gi|211178303|gb|FL423187.1|FL423187
EST:     AGGAAAGAGAGTGATTGAATTAGGAGCTGGCTGTGGCCTGGCTGGGTTCG                         GAATGACCTTGTTGGGTTGTGATGTTACAACAACTGACCAAGTCGAGGTGC
genomic: AGGAAAGAGAGTGATTGAATTAGGAGCTGGCTGTGGCCTGGCTGGGTTCGgtaagctcaa ... tctcctttagGAATGACCTTGTTGGGTTGTGATGTTACAACAACTGACCAAGTCGAGGTGC
EST: gi|211209107|gb|FL370009.1|FL370009
EST:     AGGAAAGAGAGTGATTGAATTAGGAGCTGGCTGTGGCCTGGCTGGGTTCG                         GAATGACCTTGTTGGGTTGTGATGTTACAACAACTGACCAAGTCGAGGTGC
genomic: AGGAAAGAGAGTGATTGAATTAGGAGCTGGCTGTGGCCTGGCTGGGTTCGgtaagctcaa ... tctcctttagGAATGACCTTGTTGGGTTGTGATGTTACAACAACTGACCAAGTCGAGGTGC
EST: gi|211341427|gb|FL403611.1|FL403611
EST:     GATTGAATTAGGAGCTGGCTGTGGCCTGGCTGGGTTCG                         GAATGACCTTGTTGGGTTGTGATGTTACAACAACTGACCAAGTCGAGGTGC
genomic: GATTGAATTAGGAGCTGGCTGTGGCCTGGCTGGGTTCGgtaagctcaa ... tctcctttagGAATGACCTTGTTGGGTTGTGATGTTACAACAACTGACCAAGTCGAGGTGC
EST: gi|211219619|gb|FL402178.1|FL402178
EST:     AGGAAAGAGAGTGATTGAATTAGGAGCTGGCTGTGGCCTGGCTGGGTTCG                         GAATGACCTTGTTGGGTTGTGATGTTACAACAACTGACCAAGTCGAGGTGC
genomic: AGGAAAGAGAGTGATTGAATTAGGAGCTGGCTGTGGCCTGGCTGGGTTCGgtaagctcaa ... tctcctttagGAATGACCTTGTTGGGTTGTGATGTTACAACAACTGACCAAGTCGAGGTGC
EST: gi|211442064|gb|FL421101.1|FL421101
EST:     AGGAAAGAGAGTGATTGAATTAGGAGCTGGCTGTGGCCTGGCTGGGTTCG                         GAATGACCTTGTTGGGTTGTGATGTTACAACAACTGACCAAGTCGAGGTGC
genomic: AGGAAAGAGAGTGATTGAATTAGGAGCTGGCTGTGGCCTGGCTGGGTTCGgtaagctcaa ... tctcctttagGAATGACCTTGTTGGGTTGTGATGTTACAACAACTGACCAAGTCGAGGTGC
EST: gi|20301099|gb|BQ164042.1|BQ164042
EST:     AGGAAAGAGAGTGATTGAATTAGGAGCTGGCTGTGGCCTGGCTGGGTTCG                         GAATGACCTTGTTGGGTTGTGATGTTACAACAACTGACCAAGTCGAGGTGC
genomic: AGGAAAGAGAGTGATTGAATTAGGAGCTGGCTGTGGCCTGGCTGGGTTCGgtaagctcaa ... tctcctttagGAATGACCTTGTTGGGTTGTGATGTTACAACAACTGACCAAGTCGAGGTGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAAAGAATAGCAGAAAAGGTCGGTTTTGTCCATCCAAGCTAAAAGGAAAGAGAGTGATTGAATTAGGAGCTGGCTGTGGCCTGGCTGGGTTCGgtaagctcaatttaactgcccgtcagatgtatttcaggatcttagtcctattggcttcctcttttaaaattgtttgcttatctcctttag

- - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT