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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatgttcctttgagattccataccatccacccgttgggtggtttagccgccctcttgtcgctgactctgaaaagctcgttgtgctag

Basic information

species Zea mays
transcript GRMZM2G023528_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023528_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g03740.1 (Oryza sativa), 5'ss of exon 6
AGGAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatgttcctttgagattccataccatccacccgt-tgggtggtttagccgccctcttgtcgctgactctgaaaagctcgttgtgctag
  ||||||| ||| || |||||||||||||||||||| ||  ||||||||||||||||||| |||||||| ||||||||||||||||||||||| ||||||| ||     || | |  | || ||||| |||     | |     | ||||||  || ||  ||    ||  ||||       |    || |||
--GAAGAAGTGTACTCGAAAGATCGGGTAATTGTTGCTGTAAGGCAAGGGAACATCCTCGCTACTGCTTTTCACCCAGAATTGACATCAGACTCTAGATGgttagtgccttttcct--acataccatatcatgttttcatgcatcttgtttag--gctctgatgctcatggatctgtctgctcctgcttgatag
















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|60355990|gb|DN222963.1|DN222963
EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
EST: gi|15079808|gb|BI388841.1|BI388841
EST:     TGCTTTCCCCCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: TGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
EST: gi|78021114|gb|DV489501.1|DV489501
EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
EST: gi|71303445|gb|DR787832.1|DR787832
EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
EST: gi|5714344|gb|AI944329.1|AI944329
EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
EST: gi|60396175|gb|DN229044.1|DN229044
EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
EST: gi|6020378|gb|AW065306.1|AW065306
EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
EST: gi|15215333|gb|BI431244.1|BI431244
EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
EST: gi|6194740|gb|AW146844.1|AW146844
EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
EST: gi|5804744|gb|AI979714.1|AI979714
EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTN
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
EST: gi|5597195|gb|AI891188.1|AI891188
EST:     CCTCGC-ACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: CCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
EST: gi|18166881|gb|BM336720.1|BM336720
EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
EST: gi|6095634|gb|AW120301.1|AW120301
EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatgttcctttgagattccataccatccacccgttgggtggtttagccgccctcttgtcgctgactctgaaaagctcgttgtgctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG