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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCACTGTGAAAGTGAGGAGGAGGGAGTTCGGAATGTTGTTGCAGAGTGTTTAGGAAAAATTTCTCTAATTGAACCAAAAAAACTAGTCCCTGCTTTGGAGgtgtgacatggctaaccagcaaatttattctccacattgcagctatattgctttgtcatcctaatgaaatctctctctag

Basic information

species Zea mays
transcript GRMZM2G168629_T05
intron # 23
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168629_T01 (Zea mays), 5'ss of exon 23
lower sequence: LOC_Os02g07120.1 (Oryza sativa), 5'ss of exon 23
TCACTGTGAAAGTGAGGAGGAGGGAGTTCGGAATGTTGTTGCAGAGTGTTTAGGAAAAATTTCTCTAATTGAACCAAAAAAACTAGTCCCTGCTTTGGAGgtgtgacatggctaaccagcaaatttattctccacattgcagctatattgctttgtcatcctaatgaaatctctctctag-----------------------
||||||||||||||||||||| |||||||||||||| |||||||| || ||||| |||||| |||| |||||||| |  ||| || |||||||| |  |||||  |   |  || | | | ||  |||| ||  ||||   | | || ||   | | ||  | | ||  ||| |   |                         
TCACTGTGAAAGTGAGGAGGAAGGAGTTCGGAATGTAGTTGCAGAATGCTTAGGCAAAATTGCTCTGATTGAACCTAGGAAATTAATCCCTGCTCTAAAGgtgaaatgggatta-ctatctaaactattttcttcatttt-gttctactgtcatttaatgatta-gaggtcttttggttcattccttgcgtttttttttgtag

upper sequence: GRMZM2G168629_T01 (Zea mays), 5'ss of exon 23
lower sequence: GLYMA17G00570.1 (Glycine max), 5'ss of exon 23
TCACTGTGAAAGTGAGGAGGAGGGAGTTCGGAATGTTGTTGCAGAGTGTTTAGGAAAAATTTCTCTAATTGAACCAAAAAAACTAGTCCCTGCTTTGGAGgtgtgacatggctaaccagcaaatttattctccacattgcagctatattgctttgtcatcctaatgaaatctctctctag---------------------------
 ||||||||||||||||| |||||||| || ||||| || || |||||||| || |||||| |||| ||||| ||   ||||||  |||||||  |  |||| |   |    ||    |  |   | | ||      ||   ||    ||  ||||  |  | ||||    | | | | |                           
CCACTGTGAAAGTGAGGAAGAGGGAGTGCGCAATGTAGTGGCGGAGTGTTTGGGCAAAATTGCTCTTATTGAGCCTGTAAAACTCATCCCTGCACTCAAGgtatctgaattttattttggtatcctgtacttgtgcctgagacttgcatgtgttgtatt--tgatgattgtttttttttgttttgttttgttttgaaacttctatag

upper sequence: GRMZM2G168629_T01 (Zea mays), 5'ss of exon 23
lower sequence: GLYMA07G40230.2 (Glycine max), 5'ss of exon 24
TCACTGTGAAAGTGAGGAGGAGGGAGTTCGGAATGTTGTTGCAGAGTGTTTAGGAAAAATTTCTCTAATTGAACCAAAAAAACTAGTCCCTGCTTTGGAGgtgtgaca--------tggctaaccagcaaatttattctccacattgcagctatattgctttgtcatcctaatgaaatctctctctag--------
 ||||||||||||||||| |||||||| || ||||| || || |||||||| || |||||| |||| ||||| ||    |||||  |||||||  |  |||| |   |        | | || || | |  | |       || |||||  | |  |  ||  | ||  |  | | || | |    |         
CCACTGTGAAAGTGAGGAAGAGGGAGTGCGCAATGTAGTGGCGGAGTGTTTGGGCAAAATTGCTCTTATTGAGCCTGTTAAACTCATCCCTGCACTCAAGgtatctgaattttcttttggtatcctgtacttgtgcctgtgac-ttgcaagtgttgtatttgatgattgtttttatatgttttgaaacttctatag

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|91877710|gb|EB407667.1|EB407667
EST:     TAGGAAAAATTTCTCTAATTGAACCNNNNNNNCTAGTCCCTGCTTTGGAG                         GTACGCACGTCTAGCCCAGCAGCAAATACAAGAGCTACGGTTGCTATTGCT
genomic: TAGGAAAAATTTCTCTAATTGAACCAAAAAAACTAGTCCCTGCTTTGGAGgtgtgacatg ... ctctctctagGTACGCACGTCTAGCCCAGCAGCAAATACAAGAGCTACGGTTGCTATTGCT
EST: gi|16746077|gb|BM032507.1|BM032507
EST:     TAGGAAAAATTTCTCTAATTGAACCAAAAAACCTAGTCCCTGCTTTGGAG                         GTACGCACGTCTAGCCCAGCAGCAAATACAAGAGCTACGGTTGCTATTGCT
genomic: TAGGAAAAATTTCTCTAATTGAACCAAAAAAACTAGTCCCTGCTTTGGAGgtgtgacatg ... ctctctctagGTACGCACGTCTAGCCCAGCAGCAAATACAAGAGCTACGGTTGCTATTGCT
EST: gi|67019143|gb|CO447892.1|CO447892
EST:     TAGGAAAAATT-CTCTAATTGAACCNNNNNNNCTAGTCCCTGCTTTGGAG                         -TACGCACGTCTAGCCCAGCAGCANATACAA
genomic: TAGGAAAAATTTCTCTAATTGAACCAAAAAAACTAGTCCCTGCTTTGGAGgtgtgacatg ... ctctctctagGTACGCACGTCTAGCCCAGCAGCAAATACAA
EST: gi|31354241|gb|CD438598.1|CD438598
EST:     TAGGAAAAATTTCTCTAATTGAACCNNNNNNNCTAGTCCCTGCTTTGGAG                         GTACGCACGTCTAGCCCAGCAGCAAATACAAGAGCTACGGTTGCT
genomic: TAGGAAAAATTTCTCTAATTGAACCAAAAAAACTAGTCCCTGCTTTGGAGgtgtgacatg ... ctctctctagGTACGCACGTCTAGCCCAGCAGCAAATACAAGAGCTACGGTTGCT
EST: gi|89761370|gb|DY689409.1|DY689409
EST:     TAGGAAAAATTTCTCTAATTGAACCNNNNNNNCTAGTCCCTGCTTTGGAG                         GTACGCACGTCTAGCCCAGCAGCAAATACAAGAGCTACGGTTGCTATTGCT
genomic: TAGGAAAAATTTCTCTAATTGAACCAAAAAAACTAGTCCCTGCTTTGGAGgtgtgacatg ... ctctctctagGTACGCACGTCTAGCCCAGCAGCAAATACAAGAGCTACGGTTGCTATTGCT
EST: gi|78119497|gb|DV537881.1|DV537881
EST:     TAGGAAAAATTTCTCTAATTGAACCNNNNNNNCTAGTCCCTGCTTTGGAG                         GTACGCACGTCTAGCCCAGCAGCAAATACAAGAGCTACGGTTGCTATTGCT
genomic: TAGGAAAAATTTCTCTAATTGAACCAAAAAAACTAGTCCCTGCTTTGGAGgtgtgacatg ... ctctctctagGTACGCACGTCTAGCCCAGCAGCAAATACAAGAGCTACGGTTGCTATTGCT

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCACTGTGAAAGTGAGGAGGAGGGAGTTCGGAATGTTGTTGCAGAGTGTTTAGGAAAAATTTCTCTAATTGAACCAAAAAAACTAGTCCCTGCTTTGGAGgtgtgacatggctaaccagcaaatttattctccacattgcagctatattgctttgtcatcctaatgaaatctctctctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG