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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggagttcttcgcttccaatctaatatcttttgtctgacctgcaaagtttgggtcatgtactagatcttctcaatttatttatgttttggtttgttgtgactacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCG

Basic information

species Zea mays
transcript GRMZM5G876621_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G876621_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 9
gtaggagttcttcgcttccaatctaatatcttttgtctgacctgcaaagtttgggtcatgtactagatcttctcaatttatttatgttttggtttgttgtgactacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCG
          | |  ||| ||||| | || |||| |     ||  |   |||   | || || ||     |     || |||| || |  | || |   ||  |||||||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||| ||||||||||| ||||||||||||||||||
---------gtacagttctaatctgagatattttcttaatactttattattt---ttatttaata-----ttgtggttaatttgtgct--gcttcgcactggttacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCG

upper sequence: GRMZM5G876621_T02 (Zea mays), 3'ss of exon 9
lower sequence: AT1G65430.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaggagttcttcgcttccaatctaatatcttttgtctgacctgcaaagtttgggtcatgtactagatcttctcaatttatttatgttttggtttgttgtgactacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCG
||| |||||||   |     ||    ||| ||    |||||   |||    |  ||| | |  ||  | |   ||  || ||| | |||     | || |   | |||||||||||  ||||||   |  |||| |||||||||||||| ||||||||||| || || || |||||  |||||||| ||||||| |||
gtatgagttctgtac-----attgtttatgttc---ctgactaacaactaatatgtc-tat-ttatctttgaacatattttttgtctttcataatctt-tctgtgcagTATGATGAGACTGAAAAACGCCGAGAGATGGCAAAGAACTCTCTTGAGAGATATACCCACTACTATGAGAGATGGGCAACCAATCAATCG

upper sequence: GRMZM5G876621_T02 (Zea mays), 3'ss of exon 9
lower sequence: Vv00s0207g00090.t01 (Vitis vinifera), 3'ss of exon 9
gtaggagttcttcgcttccaatctaatatcttttgtctgacctgca-aagtttgggtcatgtactagatcttctcaatttatttatgttttggtttgttgtgactacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCG
      | || ||||  ||  |   | || | ||| | |  || || |||| |     |||      ||          | |   || |||  |||| ||    | |||||||||||  |||| |   |||| || ||||| ||||||||  | |||||||| || ||||||||||||||||||||  |||| || || 
-----tggtcctcgccccc--ttagaaatgtattgacggtgctacagaagtatcttctatggcactaatgggaaggtgctgtacttgatttattttgctgc--ttgcagTATGATGAGGCTGAGAAACGAAGGGATATGGCTAAGAACTCTTTGGAGAGATATACTCATTATTATGAACGATGGGCGACCAACCAATCT

upper sequence: GRMZM5G876621_T02 (Zea mays), 3'ss of exon 9
lower sequence: PP1S156_28V6.1 (Physcomitrella patens), 3'ss of exon 9
gtaggagttcttcgcttccaatctaatatcttttgtctgacctgcaaagtttgggtcatgtactagatcttctcaatttattta--tgttttggtttgttgtgactacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCG
    ||| |  || |   |||   || ||| |  || |   ||     | | | ||| ||| ||   |||   ||  | |  ||  || |   | |  ||     | |||||||||||| | ||  |||| || || ||||| ||||||||||||||  | |||||||||||||||||||| |||||| | ||| | || 
---cgagctggtcacactcaacagaagatcctaggtttttgcta-ggtgatggagtcctgt-ctgagtctctgcagatgagctaactgctacagataatt-----tgcagTATGATGAAGCAGAGCGGAGGAGGGAGATGGCTAAGAACTCCCTTGAACGTTACACACATTATTATGAACGCTGGGCAACGAATGAATCT

upper sequence: GRMZM5G876621_T02 (Zea mays), 3'ss of exon 9
lower sequence: PP1S114_2V6.1 (Physcomitrella patens), 3'ss of exon 9
gtaggagttcttcgcttccaatctaatatcttttgtctgacctgcaaagtttgggtcatgtactagatcttctcaatttatttatgttttggtttgttgtgactacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCG
 |||  | |   | |||  | || |    |    |  | | ||     || ||  |    | |||| |    || |   | | | ||||   |   ||| |  | |||||||||||| | ||  ||||||| |||||||| |||||||| |||||  | || |||||||| |||||||| |||||  | ||  | || 
-tagaggctgg-cacttgaattcaagcgacg--agatttatcttttgggtctgttt----tcctagttacaatccagagagtgacgtttacttagtttgagtttgcagTATGATGAAGCAGAGCGGAGAAGGGAAATGGCTAAGAACTCGCTTGAACGCTATACACATTACTATGAACGTTGGGCTACAAACGAATCT

upper sequence: GRMZM5G876621_T02 (Zea mays), 3'ss of exon 9
lower sequence: PP1S178_72V6.2 (Physcomitrella patens), 3'ss of exon 10
-----gtaggagttcttcgcttccaatctaatatcttttgtctgacctgcaaagtttgggtcatgtactagatcttctcaatttatttatgttttggtttgttgtgactacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCG
       | ||| |  | ||||        ||       ||   |  | || || |||   | | ||  |       | | || ||    ||||| |||||||    || ||||| |||||| | ||  |||| || |||||||| |||||||| |||||  | ||||||||||| |||||||| |||||  | ||| |||| 
tcaagcaaagagattgttgcttttggctctatcgtccccgttatatat-cagaggttgacgcttatataaa------taagttgata---gttttagtttgttt---ctgcagTACGATGAAGCAGAGCGGAGGAGGGAAATGGCTAAGAACTCTCTTGAACGCTACACACATTACTATGAACGTTGGGCTACAAATGAGTCT

upper sequence: GRMZM5G876621_T02 (Zea mays), 3'ss of exon 9
lower sequence: PP1S9_199V6.1 (Physcomitrella patens), 3'ss of exon 10
--gtaggagttcttcgcttccaatctaatatcttttgtctgacctgcaaagtttgggtcatgtactagatcttctcaatttatttatgttttggtttgttgtgactacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCG
   | |   | ||| ||  |   ||   || |  |  |||      || | ||      | || || ||  ||    |  ||  |  | |   |||  || |   | |||||||||||| | ||  ||||||| |||||||| ||||||||||||||  | |||||||| |||||||| || |||||  | ||  | || 
agctggtcatactttgcaacaggtcc--tagccatattctaggtgacagaattctttcaaagtccttgaattt---gagctaact--gctacagttcattct---tccagTATGATGAAGCAGAGCGGAGAAGGGAAATGGCGAAGAACTCCCTTGAACGTTACACACACTATTATGAGCGTTGGGCTACAAACGAATCT

upper sequence: GRMZM5G876621_T02 (Zea mays), 3'ss of exon 9
lower sequence: EFJ15174 (Selaginella moellendorffii), 3'ss of exon 9
gtaggagttcttcgcttccaatctaatatcttttgtctgacctgcaaagtttgggtcatgtactagatcttctcaatttatttatgttttggtttgttgtgactacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCG
                                                       | || |    | |   ||  |   | | ||  |   ||||||       |||||| |||||| |||| ||||| ||||||||||| ||||||||  | |||||||| |||||||| || || ||||||||  | ||  | || 
-----------------------------------------------gtaccaattgatatttacgtttcccttcacggactcatcct---gtttgt----gtaacagTACGATGAAGCTGAGAGGAGGAGAGAAATGGCTAAGAACTCGTTAGAGAGATATACACATTACTACGAGCGATGGGCCACGAACGAATCA

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|87155958|gb|DY400747.1|DY400747
EST:     GTGGATTTTATGCTTGTAACCGCTATGAGTCAGCAAGGCAAGAAGGAGCG                         TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGA
genomic: GTGGATTTTATGCTTGTAACCGCTATGAGTCAGCAAGGCAAGAAGGAGCGgtaggagttc ... gtgactacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtcatgtactagatcttctcaatttatttatgttttggtttgttgtgactacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCG
                ttctcaatttatttat  TA-rich tract