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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtcgctaccttcattgcacgtcctaataacaagccttgatgagccattgaatcaaagagtcctgatgtgctacctaccgtatacttacaatgcagGGGCGCCCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCAACGGACCACCCACCCACGTACTACGAGGACATGCAGCGTGCC

Basic information

species Zea mays
transcript GRMZM2G056702_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G056702_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g70190.1 (Oryza sativa), 3'ss of exon 3
-------gtacgtcgctaccttcattgcacg--tcctaataacaagccttgatgagccattg-aatcaaagagtcctgatgtgctacctaccgtatacttacaatgcagGGGCGCCCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCAACGGACCACCCACCCACGTACTACGAGGACATGCAGCGTGCC
         | |    | |  ||| |  | |  |||| ||||  |   |||||||   |||| || | || |||| |||||    |||| |  ||| |    ||||||| || ||||||||||| || |||||||||||||||||||| || || || |||||||| || ||||||||||| || ||||||||||||||||||||| ||
gtgagcaccaagaacatgcaatcactcgatgcttcctcataagcattgttgatgaattattgtaacccaaaagtcttgatga---acctgctttatgc----aatgcagAGGTGCCCGTGCATCGGTGTGGGAGAACTTCAAGAACAATCCTCTTTTTGACATCTCCACAGACCACCCACCAACCTACTACGAGGACATGCAGCGTTCC

upper sequence: GRMZM2G056702_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA05G33420.1 (Glycine max), 3'ss of exon 3
--gtacgtcgctaccttcattgcacgtcctaataacaagccttgatgagccattgaatcaaagagtcctgat--gtgctacctaccgtatacttacaat---gcagGGGCGCCCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCAACGGACCACCCACCCACGTACTACGAGGACATGCAGCGTGCC
  | |  | | | | | || || | |   | |||||||  |    |  |  ||  |  |||| | ||||| |   ||  ||  ||||| |  || ||||   |||| |||||  | ||| |||| ||||||||||| ||| |||| | ||| || |||||||| || || || ||| |||| |||||||||||||||||  | |||
atgaagtttggtgcatgcaatg-atgctttcataacaaaacacacttgg--atcaa--caaataatcctggttgatgaaactgaccgtgt-tttgcaatcttgcagAGGCGCAAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCTGCTGTTTGACATCTCCACTGAGCATCCAACCACTTACTACGAGGACATGCAAAGAGCC

upper sequence: GRMZM2G056702_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G27440.1 (Arabidopsis thaliana), 3'ss of exon 3
-gtacgtcgctaccttcattgcacgtcctaataacaagccttgatgagccattgaatcaaagagtcctg--atgtgctacctaccgtata-cttacaatgcagGGGCGCCCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCAACGGACCACCCACCCACGTACTACGAGGACATGCAGCGTGCC
   |    ||   | |||||           | | |      | | ||| |    ||||||  ||  |   || ||||  ||      |  ||     |  || || ||  | ||| | || |||||||||||||||||||||||  | || ||||||||||| || |||||  | || |||||||| ||||||||| | |||
acaattaagcattcctcattaggaagttaggttatatataa-ggttagcta--agatcaaattgttttagaatctgctgactggaacttctctctttgtatagAGGTGCAAGAGCAGCGGTGTGGGAGAACTTCAAGAACAACCCTTTGTTTGACATCTCAACAGATCACCCGACAACATACTACGAAGACATGCAGAGAGCC

upper sequence: GRMZM2G056702_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv01s0150g00180.t01 (Vitis vinifera), 3'ss of exon 3
-gtacgtcgctaccttcattgcacgtcctaataacaagccttgatgagccattgaatcaaagagtcctgatgtgctaccta--ccgtatacttacaatgcagGGGCGCCCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCAACGGACCACCCACCCACGTACTACGAGGACATGCAGCGTGCC
 | | |   |  | |  ||   || |     |  |     |    |  || |||  |  ||     |  |  | ||| |||   | | || ||      ||| || ||  | ||| |||| ||||||||||| ||| ||||||||||||| |||||||| || || |||||| | || || || || |||||||| ||||| 
aggaagcaacatcttgtatgatacatggctttgtcttttatattaggtcctttgggttgaatgaatc--aactcctatctaactcttttaattgattgacagAGGTGCAAGGGCAGCAGTTTGGGAGAACTTTAAGGACAACCCGCTCTTTGACATCTCCACTGAGCACCCAACGACATATTATGAAGACATGCAACGTGCT

upper sequence: GRMZM2G056702_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ25836 (Selaginella moellendorffii), 3'ss of exon 3
gtacgtcgctaccttcattgcacgtcctaataacaagccttgatgagccattgaatcaaagagtcctgatgtgctacctaccgtatacttacaatgcagGGGCGCCCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCAACGGACCACCCACCCACGTACTACGAGGACATGCAGCGTGCC
                     | || ||   || |  | | ||  |||  |||  | |||   || |  |  | |  ||  | | | ||    ||||||||| || |||||  | || |||||||| |||||| | || || ||||| |||||||| || || |||||    ||||||||||||||||||||||| || 
------------------gtaaagttctctcaata--catagaaaagct-ttgtttgaaaagatcttattcggtt--ctgacatttgctgctcatgcagGGGTGCTCGTGCTGCTGTTTGGGAGAATTTCAAGGATAATCCTCTCTTTGACATCTCTACCGAGCACCCGATTACGTACTACGAGGACATGCAGCGAGCT

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|50322792|gb|CO517918.1|CO517918
EST:     GGTTTATTCTATGACACTGCAAATGATCCTGAGGGTGGTTACTATGCAAG                         GGGCGCCCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGA
genomic: GGTTTATTCTATGACACTGCAAATGATCCTGAGGGTGGTTACTATGCAAGgtacgtcgct ... tacaatgcagGGGCGCCCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGA
EST: gi|67029426|gb|CO458175.1|CO458175
EST:     GGTTTATTCTATGACACTGCAAATGATCCTGAGGGTGGTTACTATGCAAG                         GGGCGCCCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGA
genomic: GGTTTATTCTATGACACTGCAAATGATCCTGAGGGTGGTTACTATGCAAGgtacgtcgct ... tacaatgcagGGGCGCCCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGA
EST: gi|93281665|gb|EB673929.1|EB673929
EST:     GGTTTATTCTATGACACTGCAAATGATCCTGAGGGTGGTTACTATGCAAG                         GGGCGCTCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGA
genomic: GGTTTATTCTATGACACTGCAAATGATCCTGAGGGTGGTTACTATGCAAGgtacgtcgct ... tacaatgcagGGGCGCCCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGA
EST: gi|71444106|gb|DR825156.1|DR825156
EST:     GGTTTATTCTACGACACTGCAAATGATCCCGAGGGTGGTTACTATGCAAG                         GGGCGCCCGCGCATCAGTCTGGGAAAACTTCAAGAACAACCCGCTCTTCGA
genomic: GGTTTATTCTATGACACTGCAAATGATCCTGAGGGTGGTTACTATGCAAGgtacgtcgct ... tacaatgcagGGGCGCCCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGA
EST: gi|21330372|gb|BQ485753.1|BQ485753
EST:     GGTGGTTACTATGCAAG                         GGGCGCCCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGA
genomic: GGTGGTTACTATGCAAGgtacgtcgct ... tacaatgcagGGGCGCCCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGA
EST: gi|71764094|gb|DR962031.1|DR962031
EST:     GGTTTATTCTATGACACTGCAAATGATCCTGAGGGTGGTTACTATGCAAG                         GGGCGCCCGTGCATCAGTCTGGGAGAACTT
genomic: GGTTTATTCTATGACACTGCAAATGATCCTGAGGGTGGTTACTATGCAAGgtacgtcgct ... tacaatgcagGGGCGCCCGTGCATCAGTCTGGGAGAACTT
EST: gi|87154132|gb|DY398921.1|DY398921
EST:     GGTGGTTACTATGCAAG                         GGGCGCCCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGA
genomic: GGTGGTTACTATGCAAGgtacgtcgct ... tacaatgcagGGGCGCCCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGA
EST: gi|26455191|gb|CA826774.1|CA826774
EST:     GGTGGTTACTATGCAAG                         GGGCGCCCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGA
genomic: GGTGGTTACTATGCAAGgtacgtcgct ... tacaatgcagGGGCGCCCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGA
EST: gi|148947060|gb|EC892362.2|EC892362
EST:     GGTGGTTACTATGCAAG                         GGGCGCCCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGA
genomic: GGTGGTTACTATGCAAGgtacgtcgct ... tacaatgcagGGGCGCCCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagccattgaatcaaagagtcctgatgtgctacctaccgtatacttacaatgcagGGGCGCCCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCAACGGACCACCCACCCACGTACTACGAGGACATGCAGCGTGCC
                                         tacttac  putative branch site (score: 1)
                                       tatactta  TA-rich tract