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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagcaattctgagcttccaatctgatatcttttgtccggcctgcaaaatttgggtcatgtactagattttctgaatttatttatgttttgttgtggctacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCG

Basic information

species Zea mays
transcript GRMZM2G006428_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006428_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 9
gtagcaattctgagcttccaatctgatatcttttgtccggcctgcaaaatttgggtcatgtactagattttctgaatttatttatgttttgttgtggctacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCG
          |    ||| ||||||| || |||| |     ||  |  ||||   |    || |    ||    ||||| |   || || |   ||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||||||||||||||||
---------gtacagttctaatctgagatattttcttaatactttattatttttatttaatattgtggtt----aatttgtgc-tgcttcgcactggttacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCG

upper sequence: GRMZM2G006428_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT1G65430.1 (Arabidopsis thaliana), 3'ss of exon 9
gtagcaattctgagcttccaatctgatatcttttgtccggcctgcaaaatt-tgggtcatgtactagattttctgaatttatttatgttttgttgtggctacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCG
|||  | |||||  | |    | || |      |  |   |    |    | |   || |  |  | ||||| ||  |||  | || |||   ||||    |||||||||||  ||||||   |  |||| |||||||||||||| |||||||||||||| || || |||||  |||||||| ||||||| |||
gtatgagttctgtacattgtttatgttcctgactaac-aactaatatgtctatttatctttgaacatattttttgtctttcataatctttc--tgtg----cagTATGATGAGACTGAAAAACGCCGAGAGATGGCAAAGAACTCTCTTGAGAGATATACCCACTACTATGAGAGATGGGCAACCAATCAATCG

upper sequence: GRMZM2G006428_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv00s0207g00090.t01 (Vitis vinifera), 3'ss of exon 9
gtagcaattctgagcttccaatctgatatcttttgtccggcctgcaaaa------tttgggtcatgtactagatttt-ctgaatttatttatgttttgttgtggctacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCG
       | ||   |  ||  |  || || | ||| | |  || || ||      | |  | ||   |   ||   | ||| | ||  || | ||||| ||    | |||||||||||  |||| |   |||| || ||||| ||||||||  | ||||||||||| ||||||||||||||||||||  |||| || || 
----tggtcct---cgcccccttagaaatgtattgacggtgctacagaagtatcttctatggcactaatgggaaggtgctgtacttgatt-tattttgctgc--ttgcagTATGATGAGGCTGAGAAACGAAGGGATATGGCTAAGAACTCTTTGGAGAGATATACTCATTATTATGAACGATGGGCGACCAACCAATCT

upper sequence: GRMZM2G006428_T01 (Zea mays), 3'ss of exon 9
lower sequence: PP1S156_28V6.1 (Physcomitrella patens), 3'ss of exon 9
gtagcaattctgagcttccaatctgatatcttttgtccggcctgcaaaatttgggtcatgtactagattttctgaatttattta-tgttttgttgtggctacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCG
     |  |     |   |||    | ||| |  ||     ||     ||  | ||| |||   ||  | |    ||    | | || |          | |||||||||||| | ||  |||| || || ||||| |||||||| |||||  | || ||||||||||||||||| |||||| | ||| | || 
---cgagctggtcacactcaacagaagatcctaggtttttgctaggtgatg-gagtcctgtctgagtctctgcagatgagctaactgctacagataatttgcagTATGATGAAGCAGAGCGGAGGAGGGAGATGGCTAAGAACTCCCTTGAACGTTACACACATTATTATGAACGCTGGGCAACGAATGAATCT

upper sequence: GRMZM2G006428_T01 (Zea mays), 3'ss of exon 9
lower sequence: PP1S114_2V6.1 (Physcomitrella patens), 3'ss of exon 9
gtagcaattctgagcttccaatctgatatcttttgtccggcctgcaaaatttgggtcatgtactagattttctgaatttatttatgttttgtt-gtggctacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCG
 |||    |    ||     |  | |        |      ||      | ||  |       || | |      | | |  | |  || ||| | |  | |||||||||||| | ||  ||||||| |||||||| ||||||||||||||  | ||||||||||| |||||||| |||||  | ||  | || 
-tagaggct---ggcacttgaattcaagcgacgagatttatcttttgggtctgttttcctagttacaatccagagagtgacgtttacttagtttgagtttgcagTATGATGAAGCAGAGCGGAGAAGGGAAATGGCTAAGAACTCGCTTGAACGCTATACACATTACTATGAACGTTGGGCTACAAACGAATCT

upper sequence: GRMZM2G006428_T01 (Zea mays), 3'ss of exon 9
lower sequence: EFJ08409 (Selaginella moellendorffii), 3'ss of exon 9
gtagcaattctgagcttccaatctgatatcttttgtccggcctgcaaaatttgggtcatgtactagattttctgaatttatttatgttttgttgtggctacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCG
                                           | |  | |||    || |||  | ||  ||  |   | | ||    ||||   |  |||||| |||||| |||| ||||| || |||||||| ||||||||| | ||||||||||||||||| || || ||||||||  | ||  | || 
-------------------------------------------gtaccaattga--tatttac--gtttcccttcacggactcat--cctgtttgtgtaacagTACGATGAAGCTGAGAGGAGGAGGGAAATGGCTAAGAACTCGTTAGAGAGATATACACATTACTACGAGCGATGGGCCACGAACGAATCA

upper sequence: GRMZM2G006428_T01 (Zea mays), 3'ss of exon 9
lower sequence: EFJ15174 (Selaginella moellendorffii), 3'ss of exon 9
gtagcaattctgagcttccaatctgatatcttttgtccggcctgcaaaatttgggtcatgtactagattttctgaatttatttatgttttgttgtggctacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCG
                                           | |  | |||    || |||  | ||  ||  |   | | ||    ||||   |  |||||| |||||| |||| ||||| ||||||||||| ||||||||| | ||||||||||||||||| || || ||||||||  | ||  | || 
-------------------------------------------gtaccaattga--tatttac--gtttcccttcacggactcat--cctgtttgtgtaacagTACGATGAAGCTGAGAGGAGGAGAGAAATGGCTAAGAACTCGTTAGAGAGATATACACATTACTACGAGCGATGGGCCACGAACGAATCA

upper sequence: GRMZM2G006428_T01 (Zea mays), 3'ss of exon 9
lower sequence: EFJ16231 (Selaginella moellendorffii), 3'ss of exon 9
gtagcaattctgagcttccaatctgatatcttttgtccggcctgcaaaatttgggtcatgtactagattttctgaatttatttatgttttgttgtggctacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCG----------
                                          | |  | | | |||   || ||   |      ||||||   | ||||| ||      ||||||||||||| |||||||| | ||||| ||||| ||||||  ||||||  | |||||||| || || ||| |||||||  | ||  ||||           
-----------------------------------------gtacgta-tctaggta--gttctcactgcctcaaatttac--aagttttctt------acagTATGATGAAGCTGAAAGGCGTAGAGAGATGGCTAAGAACATGCTTGAACGTTATACACACTACTACGAAAGATGGGCCACAAACGAGTCATCCAGGCAAA

upper sequence: GRMZM2G006428_T01 (Zea mays), 3'ss of exon 9
lower sequence: EFJ17699 (Selaginella moellendorffii), 3'ss of exon 9
gtagcaattctgagcttccaatctgatatcttttgtccggcctgcaaaatttgggtcatgtactagattttctgaatttatttatgttttgt-tgtggctacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCG----------
                                                     |  | | |    |   |||| | |   |  |  ||     | |   |||||||||||||| |||||||| | ||||| ||||| ||||||  ||||||  | |||||||| || || ||| |||||||  | ||  ||||           
-----------------------------------------------------gtacgtatctaggtacttctcactgcctcaactttacaaattttcttacagTATGATGAAGCTGAAAGGCGTAGAGAGATGGCTAAGAACATGCTTGAACGTTATACACACTACTACGAAAGATGGGCCACAAACGAGTCATCCAGGCAAA

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|76281609|gb|DV021177.1|DV021177
EST:     GTGGATTTTATGCTTGTAACCGCTATGAGTCAGCAAGGCAAGAAGGAGTG                         TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGA
genomic: GTGGATTTTATGCTTGTAACCGCTATGAGTCAGCAAGGCAAGAAGGAGTGgtagcaattc ... gtggctacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGA
EST: gi|211292139|gb|FL375498.1|FL375498
EST:     GTGGATTTTATGCTTGTAACCGCTATGAGTCAGCAAGGCAAGAAGGAGTG                         TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGA
genomic: GTGGATTTTATGCTTGTAACCGCTATGAGTCAGCAAGGCAAGAAGGAGTGgtagcaattc ... gtggctacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGA
EST: gi|22521335|gb|BU080146.1|BU080146
EST:     GTGGATTTTATGCTTGTAACCGCTATGAGTCAGCAAGGCAAGAAGGAGCG                         TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGA
genomic: GTGGATTTTATGCTTGTAACCGCTATGAGTCAGCAAGGCAAGAAGGAGTGgtagcaattc ... gtggctacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgggtcatgtactagattttctgaatttatttatgttttgttgtggctacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCG
               tagattttctgaattt  TA-rich tract