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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATAGTCCAGAAAGCCTCTAGTGTCATGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAGgtatgtgttaaattaatatctgcaacaacaccaaagccttttagtcccaaacaagttggggtaggctagagttgaaacctaatggaaaaccacaagtcaa...

Basic information

species Zea mays
transcript GRMZM5G834205_T03
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G834205_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os08g01740.2 (Oryza sativa), 5'ss of exon 7
TATAGTCCAGAAAGCCTCTAGTGTCATGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAGgtat---------gtgttaaattaatatctgcaacaacaccaaagcctttt--agtcccaaacaagttggggtaggctagagttgaaaccta-atggaaaaccacaagtcaa-----------------------------------------------------------------------------
|||| | | |||||| |||||||||||||||||  | | ||| |||||| |||| ||||||||||| |||||||||||||         |  ||  ||    || |||   | ||  |    |||||  | | |   |    |     |||  |    ||    | |   |      || |  |  ||                                                                             
TATAATTCGGAAAGCTTCTAGTGTCATGGAAGTTCTAAAGGACGTGCTTGATTCGATGGATCCTAGACACCCTGAGgtatagatatggtggattgtatcctcatttgcgtgatcaatagtttctttttcatttcttgattgttgtttatagatttacctttttgctttcgtatgcctcctccggggaaaataacttaagaggcaatttatttttctcaagcaccgtgaactcttacatggttatatctgcaactgtattttgtag
















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|101391432|gb|EB817651.1|EB817651
EST:     TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAG                         GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
genomic: TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAGgtatgtgtta ... gttcttgtagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
EST: gi|78077690|gb|DV506124.1|DV506124
EST:     TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAG                         GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
genomic: TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAGgtatgtgtta ... gttcttgtagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
EST: gi|149050347|gb|EE155591.2|EE155591
EST:     TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAG                         GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
genomic: TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAGgtatgtgtta ... gttcttgtagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
EST: gi|84970062|gb|DW468434.1|DW468434
EST:     TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAG                         GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
genomic: TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAGgtatgtgtta ... gttcttgtagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
EST: gi|37375076|gb|CF623952.1|CF623952
EST:     TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAG                         GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
genomic: TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAGgtatgtgtta ... gttcttgtagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
EST: gi|71302875|gb|DR787549.1|DR787549
EST:     AGGGATGTGCTTATTTCTATGGATCCTAGGCACCCTGAG                         GGAGCAACGGATGATTTTGTGTTGGATCTTGTCGAGCAATGTACG-TTCAG
genomic: AGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAGgtatgtgtta ... gttcttgtagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
EST: gi|71761883|gb|DR959820.1|DR959820
EST:     TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAG                         GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
genomic: TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAGgtatgtgtta ... gttcttgtagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
EST: gi|86472430|gb|DY238800.1|DY238800
EST:     TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAG                         GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
genomic: TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAGgtatgtgtta ... gttcttgtagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
EST: gi|48690727|gb|CO049262.1|CO049262
EST:     TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAG                         GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
genomic: TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAGgtatgtgtta ... gttcttgtagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
EST: gi|50325059|gb|CO520185.1|CO520185
EST:     TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAG                         GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
genomic: TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAGgtatgtgtta ... gttcttgtagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
EST: gi|211390578|gb|FL303487.1|FL303487
EST:     CTATGGATCCTAGGCACCCTGAG                         GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
genomic: CTATGGATCCTAGGCACCCTGAGgtatgtgtta ... gttcttgtagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
EST: gi|37394180|gb|CF634361.1|CF634361
EST:     TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAG                         GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
genomic: TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAGgtatgtgtta ... gttcttgtagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
EST: gi|76291817|gb|DV031385.1|DV031385
EST:     TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAG                         GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
genomic: TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAGgtatgtgtta ... gttcttgtagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
EST: gi|32837204|gb|CD976882.1|CD976882
EST:     TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAG                         GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGT
genomic: TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAGgtatgtgtta ... gttcttgtagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATAGTCCAGAAAGCCTCTAGTGTCATGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAGgtatgtgttaaattaatatctgcaacaacaccaaagccttttagtcccaaacaagttggggtaggctagagttgaaacctaatggaaaaccacaagtcaa

- - - - - - - - - - - - - TGGAAG