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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgacatttgacatttgttgccttataatttcaaacctggttttgcatttccaatgtgaaggtaatggcatttgacatttgaaatgttgtgccactgaagacatgtttctttgtgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT

Basic information

species Zea mays
transcript GRMZM2G141587_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 13
gtaatgacatttgacatttgttgccttataatttcaaacctggttttgcatttccaatgtgaaggtaatggcatttgacatttgaaatgttgtgccactgaa---gacatgtttctttgt--gtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT
                                        |  |||||  |     || | ||  |  |      || |||||| ||| || ||   || ||   ||  || ||  || |  ||||||||| || ||||| || |||||||||||||| |||||||||||||| || ||||||||||||||||| || |||
-----------------------------------gtgagtaattttgt-tcctggatttaaatttttttttgcgtgtcatttggaatattatgatgctaaataggatctgctttcttatttgtagAATCTCTATTGGGCCGATAGTGGTGATTTAGTGACAATTGCAAGTGACACCTCATTCTACATTTTGAAGTACAAT

upper sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 4
gtaatgacatttgacatttgttgccttataatttcaaacctggttttgcatttccaatgtgaaggtaatggcatttgacatttgaaatgttgtgccactgaa---gacatgtttctttg--tgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT
                                        |  |||||  ||       | ||  | ||      || |||||| ||| || ||   || ||   ||   | ||  ||   |||||||||| || ||||| || |||||||||||||| |||||||||||||| || ||||||||||||||||| || |||
-----------------------------------gtgagtaattttg--ttcatggattcaaatttattttgcgtgtcatttggaatattatgatgctaaataggatccgctttcttatttgtagAATCTCTATTGGGCCGATAGTGGTGATTTAGTGACAATTGCAAGTGACACCTCATTCTACATTTTGAAGTACAAT

upper sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 13
gtaatgacatttgacatttgttgccttataatttcaaacctggttttgcatttccaatgtgaaggtaatggcatttgacatttgaaatgttgtgccactgaagacatgtttctttgtgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT
||||  || ||||  ||| | || | | || ||    | ||| | ||    |||  ||       | || |  ||| | ||    ||| ||||   | | |        |  | |||  |||| || ||||||||||||||||||||| ||||||||||||| || ||||| |||||||||||| |||| || |||
gtaagtac-tttg--attaggtgacatttagtt----atctgctcttttccttcttat-------tcattg--tttaatat----aattttgt--tattaa--------tcttgtgt-cagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT

upper sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 2
gtaatgacatttgacatttgttgccttataatttcaaacctggttttgcatttccaatgtgaaggtaatggcatttgacatttgaaatgttgtgccactgaagacatgtttctttgtgt-agAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT
                            ||| | |   | ||   |  |||   |  | ||    || |     ||    |||    ||||       | || |    |||  |||||| |||| || ||||||||||| ||||||||| |||| || ||||| |||||||| |||||||| ||  |||| || |||
---------------------------gtaagtgcttgcatgaggtgacatcagctttctgcttttatttcttcttactgtttct--tgttaattttgttaaaa----ttttcttgtgtcagAACCTCTACTGGGCTGATAGTGGTGATCTAGTGACGATTGCTAGTGATACATCATTCTATATCCTGAAGTACAAT

upper sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 13
gtaatgacatttgacatttgttgccttataatttcaaacctggttttgcatttccaatgtgaaggtaatggcatttgacatttgaaatgttgtgccactgaagacatgtttctttgtgt-agAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT
                            ||| | |   | ||   | ||||   |  | ||    || |     ||    |||   || ||       | ||      |||  |||||| |||| || ||||||||||| || ||||||||||| || ||||| |||||||| |||||||| ||  | || || |||
---------------------------gtaagtgcttgcatgaggtggcatcagctttctgcttttatttcttcttactgtttcttatttt----tgttaaat-----ttttcttgtgtcagAACCTGTACTGGGCTGATAGCGGTGATTTAGTGACGATTGCTAGTGATACATCATTCTATATCCTTAAGTACAAT

upper sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 13
gtaatgacatttgacatttgttgccttataatttcaaacctggttttgcatttccaatgtgaaggtaatggcatttgacatttgaaatgttgtgccactgaagacatgtttctttgtgt-agAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT
||||  || ||||  ||| | || | | || ||    | ||| | ||    |||  ||  |  | | |    |||| |  ||      ||| |               ||   |||||| |||| || ||||||||||||||||||||| ||||||||||||| |||||||| |||||||||||| |||| || |||
gtaagtac-tttg--attaggtgacatctagtt----atctgctcttttccttcttattcgttgttta----atttaatttt------gttat---------------ttatcttgtgtcagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGTGATACATCATTCTACATTCTGAAGTACAAT

upper sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 13
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 17
----------------------------------------------------------gtaatgacatttgacat-ttgttgccttataatttcaaacctggttttgcatttccaatgtgaaggtaatggcat-ttgacatttgaaatgttgtgccactgaagacatgtttctttgtgta--------gAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT
                                                          || | |   |  |  || || ||     | || | ||||    |||    || |  ||| | || | ||  |||  |||  | |      | |    ||||    || | ||| ||| |  |        ||||||||| ||||| |||||||||||| ||||  ||||||| |||||||| |||||||||||  | || |  |||
gtaagtgcttatataccagaagtagatccattagtttctacaagaaaatagtttataggttacgttttcagtaatatttttattggagaaatacaaaag-agttccttatctgaaatttaaacgcaaaagcagattggtact--gctcgcttattcacttttaacgtttttgtttattcaatgtttcagAATCTTTATTGGGCGGACAGTGGTGATCTAGTTGCAATTGCCAGTGATACATCATTCTACATCCTTAAGTTCAAT

upper sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 13
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 13
-----------------------------gtaatgacatttgacatttgttgccttataatt--tcaaacctggttttgc-atttccaatgtgaaggtaatggcatttgacatttgaaatgttgtgccactgaagacatgtttctttgtgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT
                             |||| ||  |||       |     ||   | |  |  || ||  | |       | || | ||| | |     | ||||    ||      || ||  | ||  |  |  |  | || || ||||||| || |||||||||||||||||||||||| | ||||| ||||| || ||||||||||| |||||||  || 
gtatcccagttaacttggctcagtttattgtaa-gaagtttacttcaagacatatttggaatagtggaaactaatatcattgccttcagtttgaggttttcctcgtttgtttcttctctaatt-tgt-agtgttgctacataacgtt-tgcagAATCTATATTGGGCTGACAGTGGTGATTTAGTAGCCATTGCTAGTGACACATCATTCTACATCTTGAAATTCAAC

upper sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 13
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
---------------------gtaatgacat-ttgacatttgttgccttata--atttcaaacctggttttgcatttccaatgtgaaggtaatggcatttgacatttgaaatgttgtgccactgaagacatgtttctttgtgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT
                     ||  ||| |  ||  ||||  |  | || |   | |||   | |    ||  |||| || | |||| ||  |  || ||    | |  | |        |||     ||||     || || |||||||||| |||||||| ||||||||||||||| | ||||| |||||||||||||||||||| ||||| || |||
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagt-tgaaagttgtcccaattagtgtctttactaactctttactcc---catgaaaaatt-tgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT

upper sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 13
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 13
gtaatgacatttgacatttgttgccttataatttcaaacctggttttgcatttccaatgtgaaggtaatggcatttgacatttgaaatgttgtgccactgaagacatgtttctttgtgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT
                           ||  | |||||       || | ||  ||||    ||||  ||||    || |    ||  |||      ||   |     ||   |  |  |||||||||| |||||||| ||||||||||||||  |||||||||||||| | ||||| ||||| || || || |||
-------------------------gcatgttctcaaa---aagcttac-ttcacaattaccaggttttggccacagagaaactaatagtt-catttctttgggtggtttcaatatttcagAATCTTTATTGGGCTGATAGTGGTGATTTAGTGGCAATTGCAAGTGATTCATCATTTTACATCTTAAAGTACAAT

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|211344820|gb|FK991758.1|FK991758
EST:     ATGATTGGGCAGAATGCAGATTGATACGTCGAATCGATGTCAATGTGAAG                         AATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACG
genomic: ATGATTGGGCAGAATGCAGATTGATACGTCGAATCGATGTCAATGTGAAGgtaatgacat ... ctttgtgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACG
EST: gi|211344819|gb|FK991757.1|FK991757
EST:     ATGATTGGGCAGAATGCAGATTGATACGTCGAATCGATGTCAATGTGAAG                         AATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACG
genomic: ATGATTGGGCAGAATGCAGATTGATACGTCGAATCGATGTCAATGTGAAGgtaatgacat ... ctttgtgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatggcatttgacatttgaaatgttgtgccactgaagacatgtttctttgtgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT
      atttgac  putative branch site (score: 4)
                                        tgtttcttt  putative PPT
             atttgaaat  TA-rich tract