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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttctttggtcccatgccgtgctatctttcctaagcggctaagcaaatcttaactttagcagctgcttagtattttgtaaagatgtaacctttttccttttccatctaattgaagTTGGGGGGCTACTGAATGCTACATTTGGAAATGCAACGGAAATGATTATATCAATATACGCACTGAAAAATGGGATGATTCGGGTCGTCCAGCAGTCACT

Basic information

species Zea mays
transcript GRMZM2G053004_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G053004_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g27960.1 (Oryza sativa), 3'ss of exon 3
gtatgttctttggtcccatgcc-gtgctatctttcctaagcggctaagcaaatcttaactttagcagctgcttagtattttgtaaagatgtaacctttttccttttccatctaattgaagTTGGGGGGCTACTGAATGCTACATTTGGAAATGCAACGGAAATGATTATATCAATATACGCACTGAAAAATGGGATGATTCGGGTCGTCCAGCAGTCACT
|||||| ||||  |    | || || |||||||| |         |  ||||||||  |||   | | ||           ||||||||  || |||||             || || ||||||||||||  |||||||||| ||||| ||||| || || |||||||| ||  | |||||| ||||||| |||||||| || ||||||||||| || ||
gtatgtgctttcattttgtacctgtcctatcttttc---------attcaaatcttggcttcgtcggatg-----------gtaaagattcaaacttttctg----------aactgcagTTGGGGGGCTGTTGAATGCTACCTTTGGCAATGCGACTGAGATGATTATCTCGTTGTACGCATTGAAAAACGGGATGATCCGTGTCGTCCAGCAATCGCT

upper sequence: GRMZM2G053004_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA15G00380.2 (Glycine max), 3'ss of exon 3
gtatgttctttggtcccatgccgtgctatctttcctaagcggctaagcaaatcttaactttagcagctgcttagtattttgtaaagatgtaacctttttccttttccatctaattgaagTTGGGGGGCTACTGAATGCTACATTTGGAAATGCAACGGAAATGATTATATCAATATACGCACTGAAAAATGGGATGATTCGGGTCGTCCAGCAGTCACT
                          ||||  || |       ||      | ||    |||    | |  |  | ||||          |||    |    || |  |||    | ||||||||| || || ||||| || ||||| |||||||| ||||||||||||||||| || ||| ||||||     |||||  |||| || ||||| || ||
-------------------------gtatccctctt------ttatttccctttttctcttaaggcccgtatcctctttt---------caactcactcgtgttgctttct----gcagTTGGGGGTCTGCTTAATGCCACCTTTGGCAATGCAACTGAAATGATTATATCAATTTATGCATTGAAAAGCAATATGATAAGGGTTGTTCAGCAATCCCT

upper sequence: GRMZM2G053004_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA13G44960.1 (Glycine max), 3'ss of exon 3
gtatgttctttggtcccatgccgtgctatctttcctaagcggctaagcaaatcttaactttagcagctgcttagtattttgtaaagatgtaacctttttccttttccatctaattgaagTTGGGGGGCTACTGAATGCTACATTTGGAAATGCAACGGAAATGATTATATCAATATACGCACTGAAAAATGGGATGATTCGGGTCGTCCAGCAGTCACT
          |   | |||    |  | | |||| |   |   | | ||     |  ||||  | |||          | || |  ||  |||    |||  ||   ||    ||| ||||||||| || || ||||| ||||| || |||||||| ||||||||||||||||| || ||| || |||     |||||  |||| || ||||| ||  |
---------gtatcctcat-ttattttctttttcttttcctatttatcattctctccctttgtctgct----------tcgtca--attcaactcacttctgttcatat----ttgcagTTGGGGGTCTGCTTAATGCCACATTCGGCAATGCAACTGAAATGATTATATCAATTTATGCATTGGAAAGCAATATGATAAGGGTTGTTCAGCAATCTTT

upper sequence: GRMZM2G053004_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S21_141V6.2 (Physcomitrella patens), 3'ss of exon 4
gtatgttctttggtcccatgccg-tgctatctttcctaagcggctaagcaaatcttaactttagcagctgcttagtattttgtaaagatgtaacctttttccttttccatctaattgaagTTGGGGGGCTACTGAATGCTACATTTGGAAATGCAACGGAAATGATTATATCAATATACGCACTGAAAAATGGGATGATTCGGGTCGTCCAGCAGTCACT
               | |||    |  ||     | | | | | ||| || ||   ||   |      | |||| |||| | ||  || |        ||  |||| |||    ||  |||||| || || |||||||| || ||||||||||| ||||||||||| ||||  |||   ||  |    ||    ||||| || || || |||   || ||
--------------tcaatgtgaattgtaagcacctttaacagataa-cagattcgaatgatctgttatacttattattat-tatcgaggatgttgactttatttttcat----ttccagTTGGAGGTCTCCTGAATGCGACTTTTGGAAATGCGACGGAAATGATCATATGCATAATGGCGTTACGGAAGAAAATGATACGAGTTGTACAGTTATCTCT

upper sequence: GRMZM2G053004_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S245_10V6.1 (Physcomitrella patens), 3'ss of exon 5
---------------------------------gtatgttctttggtcccatgccgtgctatctttcctaagcggcta-agcaaatcttaac--tttagcagctgcttagtattttgtaaagatgtaacctttttccttttccatctaattgaagTTGGGGGGCTACTGAATGCTACATTTGGAAATGCAACGGAAATGATTATATCAATATACGCACTGAAAAATGGGATGATTCGGGTCGTCCAGCAGTCACT
                                 | |   | || | ||  || || ||| ||||   ||       |  || ||| |  |||  |||          |  | | |||  || | ||||||||| |        | ||   || |||||| || || |||||||| || |||||||||||||| ||||||||||| |  ||    || |||   ||    ||||| || || || |||   |||||
gtatttgctgacgctaaaccctcgcagcattgtgaagcatgttcgatcgaataccttgcaatctgagcttcattcttgtaggaaaacaaaacattttgctgatctagttctctcttgctaaaaagtaacctttgtg-------acctttgtgcagTTGGAGGTCTCCTGAATGCAACTTTTGGAAATGCAACTGAAATGATTATTTGTATCATGGCCCTGCGGAAGAATATGATACGAGTTGTACAGTTATCACT

upper sequence: GRMZM2G053004_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S336_18V6.2 (Physcomitrella patens), 3'ss of exon 5
gtatgttctttggtcccatgccgtgctatctttcctaagcggctaagcaaatcttaactttagcagctgcttagtattttgtaaagatgtaacctttttccttttccatctaattgaagTTGGGGGGCTACTGAATGCTACATTTGGAAATGCAACGGAAATGATTATATCAATATACGCACTGAAAAATGGGATGATTCGGGTCGTCCAGCAGTCACT
     |  |||       |  || |  ||         | || | |   |     | ||       ||   |     |  |  ||    |    ||||||           | ||| |||||| || || |||||||| || ||||| ||||||||||||||||||||||  ||    ||  |    ||    ||||| || || || |||   |||||
-----taatttaagttgttaacgggtaatggga---gggtggttgattgatctaaagctcctatctctctctctctctcggctaaagaatggtttttttc-----------acttgcagTTGGAGGTCTTCTGAATGCGACTTTTGGCAATGCAACGGAAATGATTATATGCATCATTGCTTTACGGAAGAAAATGATACGAGTTGTACAGTTATCACT

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|76937004|gb|DV174997.1|DV174997
EST:     GCAACTTGCTTGCTACACTGGCCCAACAG                         TTGGGGGGCTACTGAATGCTACATTTGGAAATGCAACGGAAATGATTATAT
genomic: GCAACTTGCTTGCTACACTGGCCCAACAGgtatgttctt ... ctaattgaagTTGGGGGGCTACTGAATGCTACATTTGGAAATGCAACGGAAATGATTATAT
EST: gi|76011413|gb|DT938583.1|DT938583
EST:     GCAACTTGCTTGCTACACTGGCCCAACAG                         TTGGGGGGCTACTGAATGCTACATTTGGAAATGCAACGGAAATGATTATAT
genomic: GCAACTTGCTTGCTACACTGGCCCAACAGgtatgttctt ... ctaattgaagTTGGGGGGCTACTGAATGCTACATTTGGAAATGCAACGGAAATGATTATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctgcttagtattttgtaaagatgtaacctttttccttttccatctaattgaagTTGGGGGGCTACTGAATGCTACATTTGGAAATGCAACGGAAATGATTATATCAATATACGCACTGAAAAATGGGATGATTCGGGTCGTCCAGCAGTCACT
                                           atctaat  putative branch site (score: 3)
                            cctttttccttttcca  CT-rich tract
      ttagtattttgtaaa  TA-rich tract