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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttttcttttgatttcctttatatctctctcacagttttattcccaactggatcaatgtttcttttagtctgttttaggtgccgtgacaaataaacttttcgccactctaaactaagaattttccaacacggtttgttacagAATGCATTGCGGCAACAAAGATTTGTCCGTGAAGTGACTATACAGTACAATCTGTGCAATGAGCCATG

Basic information

species Zea mays
transcript GRMZM2G146118_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G146118_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os07g29450.1 (Oryza sativa), 3'ss of exon 8
gtatttttcttttgatttcctttatatctctctcacagttttattcccaactggatcaatgtttcttt-tagtctgttttaggtgccgtgacaaataaacttt-tcgccactctaaactaagaattttc-caacacggtttgttacagAATGCATTGCGGCAACAAAGATTTGTCCGTGAAGTGACTATACAGTACAATCTGTGCAATGAGCCATG
||| ||||||    |  |||| | | | |     |   ||| ||| | ||     |  |  |  ||||  |   | |  |   ||   | |  |  || |||| ||   | |||  ||||||  ||||  ||| |   | | |  |||||||| || || |||||||||||||| || ||||| || |||||||||||||| ||||| ||||||||
gtaattttct----acctcctctttctgttatcaatgttttcatttcaaagacattttacttcactttgcaacatttagtttttgttatcatgagcaatctttgtctatattctgtactaaggtttttttcaatataatctat-gcagAATGCGTTACGTCAACAAAGATTTGTTCGGGAAGTCACAATACAGTACAATCTCTGCAACGAGCCATG

upper sequence: GRMZM2G146118_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA20G35720.1 (Glycine max), 3'ss of exon 7
gtatttttcttttgatttcctttatatctctctcacagttttattcccaactggatcaatgtttcttttagtctgttttaggtgccgtgacaaa---taaacttttcgccactctaaactaagaattttccaacacggtttgttacagAATGCATTGCGGCAACAAAGATTTGTCCGTGAAGTGACTATACAGTACAATCTGTGCAATGAGCCATG
                                                ||    |  | ||| |     | | |  |||      | ||   ||   |    |||  |   || ||  |||  ||||  |   |   |||  || ||||||||||||||||||||||||||||| || ||||| || |||||||||||||| ||||||||||| ||
-----------------------------------------------aaaaaaaactattgtattcgagaattttatttttcacacatgctgaactctgggatttgtgttgctatat-ctataaattaccatgctgtgttattttcagAATGCATTGCGGCAACAAAGATTTGTTCGAGAAGTCACAATACAGTACAATCTCTGCAATGAGCCTTG

upper sequence: GRMZM2G146118_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA09G28530.1 (Glycine max), 3'ss of exon 6
gtatttttcttttgatttcctttatatctctctcacagttttattcccaactggatcaatgtttcttttagtctgttttaggtgccgtgacaaataaacttttcgccactctaaactaagaattttccaacacgg--tttgtta--cagAATGCATTGCGGCAACAAAGATTTGTCCGTGAAGTGACTATACAGTACAATCTGTGCAATGAGCCATG
                          | | ||  | | ||||||     | | ||  ||  |   ||| |  |||         || |  ||||| ||   ||   || ||||  || |   || |    || ||  ||||||   ||||||||||||||||| ||||||||||| || ||||| || ||||||||||| || |||||||| |||||
-------------------------gtttgtccaatatttttatcttataattgacaaacct---tttcatactg--------accat--caaattaataatttcacattctatgctcatc-ttatttggcatggcctttgttcttcagAATGCATTGCGGCAGCAAAGATTTGTACGCGAAGTTACAATACAGTACAACCTCTGCAATGAACCATG

upper sequence: GRMZM2G146118_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA16G33300.1 (Glycine max), 3'ss of exon 7
gtatttttcttttgatttcctttatatctctctcacagttttattcccaactggatcaatgtttcttttagtctgttttaggtgccgtgacaaataaacttttcgccactctaaactaagaattttccaacacgg--tttgtta--cagAATGCATTGCGGCAACAAAGATTTGTCCGTGAAGTGACTATACAGTACAATCTGTGCAATGAGCCATG
                          | | ||  | |  ||||   |  |  | |||||     |||||      | ||      || ||  |||||   |||| | | ||||  || |   || |       ||  || |||   ||||||||||||||||| ||||||||||| |||||||| || ||||||||||| || |||||||| || ||
-------------------------gtttgtccaatatctttaa--ctga--gaatcaacaaacctttt----catattgaccatcg-gattaataa---tttcac-attctatgctcatc-ttatttggtgtggccttcgttcttcagAATGCATTGCGGCAGCAAAGATTTGTACGTGAAGTTACAATACAGTACAACCTCTGCAATGAACCTTG

upper sequence: GRMZM2G146118_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA10G31960.1 (Glycine max), 3'ss of exon 8
gtatttttcttttgatttcctttatatctctctcacagttttattcccaactggatcaatgtttcttttagtctgttttaggtgccgtgacaaataaacttttcgccactctaaactaagaattttccaacacg---gtttgttacagAATGCATTGCGGCAACAAAGATTTGTCCGTGAAGTGACTATACAGTACAATCTGTGCAATGAGCCATG
                                                |     |  | ||| |     | | | ||||     |      || |      || |     ||| |   |||| || |||  | |   |||  ||  |||||||||||||||||||||||||||| || ||||| || |||||||||||||| ||||||||||||||
------------------------------------------------agaaaaactattgtattcaagaatttattttccacacatgttgaactctgggatttgtgttgctatatctagaaattaccatgatgtctgttatttttagAATGCATTGCGGCAACAAAGATTTGTTCGAGAAGTCACAATACAGTACAATCTCTGCAATGAGCCATG

upper sequence: GRMZM2G146118_T02 (Zea mays), 3'ss of exon 8
lower sequence: AT5G08450.3 (Arabidopsis thaliana), 3'ss of exon 8
gtatttttcttttgatttcctttatatct-ctctcacagttttattcccaactggatcaatgtttcttttagtctgttttaggtgccgtgacaaataaacttttcgccactctaa-actaagaattttccaacacggtttgttacagAATGCATTGCGGCAACAAAGATTTGTCCGTGAAGTGACTATACAGTACAATCTGTGCAATGAGCCATG
||||||| |||   | ||     |||||| |||||  | | || || | ||||     | | || |   | | | | ||     |   |  || ||    ||     |  || || ||| |  | ||    ||    | |  |  |||||||  ||||||||||||| ||||| || ||||| || ||||| |||||||| |||||||| || ||
gtattttccttcc-actttggaaatatctgctctcttaatcttcttac-aactcttggattattacacatgg-cggcttgcatagttttctcatat----ttcatatctttcgaacactgacgacttatttac----tgttctgtagAATGCTCTGCGGCAACAAAGGTTTGTACGAGAAGTCACAATACAATACAATCTCTGCAATGAACCTTG

upper sequence: GRMZM2G146118_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv07s0130g00270.t01 (Vitis vinifera), 3'ss of exon 7
gtatttttcttttgatttcctttatatctctctcacagttttattcccaactggatcaatgtttcttttagtctgttttaggtgccgtgacaaataaacttttcgccactctaaactaagaattttccaacacggtttgttacagAATGCATTGCGGCAACAAAGATTTGTCCGTGAAGTGACTATACAGTACAATCTGTGCAATGAGCCATG
                                |||||    | ||   ||     | | | ||  |||   ||| ||| |  ||   | | |||| |  |  ||  |    |  |    |  ||||        |||   | |||||||| |||||||||||||||||||| || ||||| || |||||||||||  | || ||||| || ||
----------------------------gtaatcacatggattttattaatcatgttagtattgtttt--atctattt-atttgttattataaatga--taatcatcttctttgat--ggtgtttt--------gtt--cttcagAATGCGTTGCGGCAACAAAGATTTGTACGAGAAGTCACAATACAGTACAACTTATGTAATGAACCTTG

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|60397960|gb|DN230776.1|DN230776
EST:     TCGCCCCAGTTGCAGTTGAGCGTACAATGACGACAAGAGCTGCAGCTTCT                         AATGCATTGCGGCAACAAAGATTTGTCCGTGAAGTGACTATACAGTACAAT
genomic: TCGCCCCAGTTGCAGTTGAGCGTACAATGACGACAAGAGCTGCAGCTTCTgtatttttct ... tttgttacagAATGCATTGCGGCAACAAAGATTTGTCCGTGAAGTGACTATACAGTACAAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaataaacttttcgccactctaaactaagaattttccaacacggtttgttacagAATGCATTGCGGCAACAAAGATTTGTCCGTGAAGTGACTATACAGTACAATCTGTGCAATGAGCCATG
                  ctctaaa  putative branch site (score: 3)
                     taaactaagaatttt  TA-rich tract