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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGGCCGTACCCAAATTTTCAAGATCCATACACGTACCATGAACTGTGAGCGAGATATTCGTTTCGAGCTTCTGGCACGGCTCTGCCCCAACTCTACTGgtgtggtttcatctgagtggtttctgctttattcgatgacagacgatcaggttctcacattgccttgcttgttgctccag

Basic information

species Zea mays
transcript GRMZM2G110185_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110185_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os06g09290.1 (Oryza sativa), 5'ss of exon 6
GAGGGCCGTACCCAAATTTTCAAGATCCATACACGTACCATGAACTGTGAGCGAGATATTCGTTTCGAGCTTCTGGCACGGCTCTGCCCCAACTCTACTGgt-------gtggtttcat------ctgagt--ggtttctg-ctttattcgatgacagacgatcaggttctcacattgccttgcttgttgctccag---------------------------
|||||||| ||||| || ||||||||||| || || ||||||||||| ||||| || || || || ||||| || || || |||||||||||||| ||||||       | |  ||| |      | || |   || |||| ||   |||  |  ||    ||     | | || |  ||||  || || |||  |                           
GAGGGCCGGACCCAGATCTTCAAGATCCACACTCGCACCATGAACTGCGAGCGGGACATCCGGTTTGAGCTGCTCGCTCGCCTCTGCCCCAACTCCACTGgtaagtgccgggaattcttgcatgacagaatccagtctctggctagtttctgttccatgtcatttatctttaacct--ccttttttttttctcacgtttggctatttgtgtttgttggaacag

upper sequence: GRMZM2G110185_T01 (Zea mays), 5'ss of exon 8
lower sequence: EDP03835 (Chlamydomonas reinhardtii), 5'ss of exon 11
GAGGGCCGTACCCAAATTTTCAAGATCCATACACGTACCATGAACTGTGAGCGAGATATTCGTTTCGAGCTTCTGGCACGGCTCTGCCCCAACTCTACTGgtgt-ggtttcatctgagtggtttctgctttattcgatgacagacgatcaggttctcacattgccttgcttgttgctccag--------------------------------------------------------------------------------------------------------------------------
             | || ||| ||||||| |||||||||||||||   ||||| || || || |||||||| || || ||||| ||||||||||| || || |  |   |||  || |  |     |         |   |   | | |   | | | |||  ||||| | |   ||   |                                                                                                                          
-------------AGATCTTCCAGATCCACACACGTACCATGAACGTGGAGCGGGACATCCGCTTCGAGCTGCTAGCGCGGCTGTGCCCCAACTCCACCGGCGCCGACATCAGgtgcggcgaccgcgtgcggccgcaccccgccccaccgcatcc-ctcatc-ccttgttggaatctgtggtgacgcgctaggaccttgctcctgccccgccggtatcatgccaccatcacagatgccactcaaaactgtttgtatgtcattaaacattatgaacggtattgctgttgtgcgaccactcgcag

upper sequence: GRMZM2G110185_T01 (Zea mays), 5'ss of exon 8
lower sequence: PP1S49_256V6.1 (Physcomitrella patens), 5'ss of exon 9
GAGGGCCGTACCCAAATTTTCAAGATCCATACACGTACCATGAACTGTGAGCGAGATATTCGTTTCGAGCTTCTGGCACGGCTCTGCCCCAACTCTACTGgtgtggtttcat--ctgagtggtttctgcttt--attcgatgacagacga--tcaggttctcacattgccttgcttgttgctccag--------------
||  | || ||||||||||||||||| ||||| || |||||||||   || ||||| |||||||||||||||||||| || || ||||| || || || |||   | ||| |  ||   |  ||| ||  ||    ||| |   |  ||   | ||  | | | |||  ||||  ||| |||   |              
GAAAGTCGAACCCAAATTTTCAAGATTCATACTCGGACCATGAACACAGAACGAGACATTCGTTTCGAGCTTCTGGCTCGCCTTTGCCCTAATTCAACAGgttctgattcttttcttgctaatttttgtattcagatcggttgtatccgtgtttagaatatgatattttcttgaatgtagctgtcggataagattggaat

upper sequence: GRMZM2G110185_T01 (Zea mays), 5'ss of exon 8
lower sequence: PP1S152_13V6.2 (Physcomitrella patens), 5'ss of exon 9
GAGGGCCGTACCCAAATTTTCAAGATCCATACACGTACCATGAACTGTGAGCGAGATATTCGTTTCGAGCTTCTGGCACGGCTCTGCCCCAACTCTACTGgtgtggtttcatctgagtggttt----ctgctttattcgatgacagacgatcaggttctcacattgccttgcttgttgctccag----------------
||  |||| ||||| ||||||||||||||||| || ||||||||    |||||||| |||||||||||||||||  | || || |||||||| || || |||     |  |  | | ||| ||    |||  |   || |||        |  | || ||||      |  | |     | ||                 
GAAAGCCGAACCCAGATTTTCAAGATCCATACGCGAACCATGAATACCGAGCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAGgttctaatctacgtcattgggttaggtctggatgcatctatgtgttgaagttggcttttcacggaatttgacgttggctttcaattttatgttcgtttaa

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|211174291|gb|FL481216.1|FL481216
EST:     GCGAGATATTCGTTTCGAGCTTCTGGCACGGCTCTGCCCCAACTCTACTG                         GAGCTGATATAAGGAGCGTTTGCACAGAAGCCGGGATGTACGCCATTCGTG
genomic: GCGAGATATTCGTTTCGAGCTTCTGGCACGGCTCTGCCCCAACTCTACTGgtgtggtttc ... gttgctccagGAGCTGATATAAGGAGCGTTTGCACAGAAGCCGGGATGTACGCCATTCGCG
EST: gi|5030783|gb|AI714977.1|AI714977
EST:     GCGAGATATTCGTTTCGAGCTTCTGGCACGGCTCTGCCCCAACTATACTG                         GAGCTGATATAAGGAGCGTTTGCACAGAAGCCGGGATGTACGCCATTCGTG
genomic: GCGAGATATTCGTTTCGAGCTTCTGGCACGGCTCTGCCCCAACTCTACTGgtgtggtttc ... gttgctccagGAGCTGATATAAGGAGCGTTTGCACAGAAGCCGGGATGTACGCCATTCGCG
EST: gi|19436439|gb|BM952849.1|BM952849
EST:     GCGAGATATTCGTTTCGAGCTTCTGGCACGGCTCTGCCCCAACTCTACTG                         GAGCTGATATAAGGAGCGTTTGCACAGAAGCCGGGATGTACGCCATTCGTG
genomic: GCGAGATATTCGTTTCGAGCTTCTGGCACGGCTCTGCCCCAACTCTACTGgtgtggtttc ... gttgctccagGAGCTGATATAAGGAGCGTTTGCACAGAAGCCGGGATGTACGCCATTCGCG
EST: gi|5740404|gb|AI948094.1|AI948094
EST:     GCGAGATATTCGTTTCGAGCTTCTGGCACGGCTCTGCCCCAACTCTACTG                         GAGCTGATATAAGGAGCGTTTGCACAGAAGCCGGGATGTACGCCATTCGCG
genomic: GCGAGATATTCGTTTCGAGCTTCTGGCACGGCTCTGCCCCAACTCTACTGgtgtggtttc ... gttgctccagGAGCTGATATAAGGAGCGTTTGCACAGAAGCCGGGATGTACGCCATTCGCG
EST: gi|12973054|gb|BG268289.1|BG268289
EST:     GCGAGATATTCGTTTCGAGCTTCTGGCACGGCTCTGCCCCAACTCTACTG                         GAGCTGATATAAGGAGCGTTTGCACAGAAGCCGGGATGTACGCCATTCGCG
genomic: GCGAGATATTCGTTTCGAGCTTCTGGCACGGCTCTGCCCCAACTCTACTGgtgtggtttc ... gttgctccagGAGCTGATATAAGGAGCGTTTGCACAGAAGCCGGGATGTACGCCATTCGCG
EST: gi|5804712|gb|AI979682.1|AI979682
EST:     GCGAGATATTCGTTTCGAGCTTCTGGCTCGGCTCTGCCCCAACTCTACTG                         GAGCTGATATAAGGAGCGTTTGC
genomic: GCGAGATATTCGTTTCGAGCTTCTGGCACGGCTCTGCCCCAACTCTACTGgtgtggtttc ... gttgctccagGAGCTGATATAAGGAGCGTTTGC
EST: gi|6563830|gb|AW231362.1|AW231362
EST:     TTCGTTTCGAGCTTCTGGCACGGCTCTGCCCCAACTCTACTG                         GAGCTGATATAAGGAGCGTTTGCCCAGAAGCCGGGATGTACGCCATTCGCG
genomic: TTCGTTTCGAGCTTCTGGCACGGCTCTGCCCCAACTCTACTGgtgtggtttc ... gttgctccagGAGCTGATATAAGGAGCGTTTGCACAGAAGCCGGGATGTACGCCATTCGCG
EST: gi|61119189|gb|DN560150.1|DN560150
EST:     GCGAGATATTCGTTTCGAGCTTCTGGCACGGCTCTGCCCCAACTCTACTG                         GAGCTGATATAAGGAGCGTTTGCACAGAAGCCGGGATGTACGCCATTCGCG
genomic: GCGAGATATTCGTTTCGAGCTTCTGGCACGGCTCTGCCCCAACTCTACTGgtgtggtttc ... gttgctccagGAGCTGATATAAGGAGCGTTTGCACAGAAGCCGGGATGTACGCCATTCGCG
EST: gi|1298504|gb|W21754.1|W21754
EST:     GCGAGATATTCGTTTCGAGCTTCTGGCACGGCTCTGCCC-AACTCTACTG                         GAGCTGATATAAGGAGCGTTTGCACAGAAGCCGGGATGTAC
genomic: GCGAGATATTCGTTTCGAGCTTCTGGCACGGCTCTGCCCCAACTCTACTGgtgtggtttc ... gttgctccagGAGCTGATATAAGGAGCGTTTGCACAGAAGCCGGGATGTAC
EST: gi|4753546|gb|AI657456.1|AI657456
EST:     GCGAGATATTCGTTTCGAGCTTCTGGCACGGCTCTGCCCCAACTCTACTG                         GAGCTGATATAAGGAGCGTTTGCACAGAAGCCGGGATGTACGCCATTCGTG
genomic: GCGAGATATTCGTTTCGAGCTTCTGGCACGGCTCTGCCCCAACTCTACTGgtgtggtttc ... gttgctccagGAGCTGATATAAGGAGCGTTTGCACAGAAGCCGGGATGTACGCCATTCGCG

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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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGGCCGTACCCAAATTTTCAAGATCCATACACGTACCATGAACTGTGAGCGAGATATTCGTTTCGAGCTTCTGGCACGGCTCTGCCCCAACTCTACTGgtgtggtttcatctgagtggtttctgctttattcgatgacagacgatcaggttctcacattgccttgcttgttgctccag

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