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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgattgccttccaatgtctggttgatttgtttttatcatcccttgtgttacctttatgatgttcagcttgcagATAACAGATGCTGTTGTAGTTGCCTGGATTTTGAATGCCACACTTGTTGTACCTGAGTTAGACCACCACTCGTTCTGGAAAGACGACAG

Basic information

species Zea mays
transcript GRMZM2G101181_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101181_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g46570.1 (Oryza sativa), 3'ss of exon 3
gtatgattgccttccaatgtctggttgatttgtttt-tatcatcccttgtgttacctttatgatgttcagcttgcagATAACAGATGCTGTTGTAGTTGCCTGGATTTTGAATGCCACACTTGTTGTACCTGAGTTAGACCACCACTCGTTCTGGAAAGACGACAG
|||  | ||  || |||  | |  |||  ||| ||| ||| |||| |||| ||||| ||| ||| ||||| || |||||||||||||||||||| || ||| | || |||||||||||||||||||||||||||||||| |||||||| |||||||| || || ||
gtacaactgtatttcaactttttattgcgttgctttgtattatccattgtattaccattacgatcttcagtttccagATAACAGATGCTGTTGTTGTCGCCCGAATATTGAATGCCACACTTGTTGTACCTGAGTTAGATCACCACTCATTCTGGAAGGATGATAG

upper sequence: GRMZM2G101181_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA05G04720.1 (Glycine max), 3'ss of exon 3
----gtatgattgccttccaatgtctggttgatttg-tttttatcatccctt----------gtgttaccttt----atgatgttcag---cttg--cagATAACAGATGCTGTTGTAGTTGCCTGGATTTTGAATGCCACACTTGTTGTACCTGAGTTAGACCACCACTCGTTCTGGAAAGACGACAG
    |      | | |||    ||||  |  || |  ||||| |||     |          ||  | ||| |    ||||   |||    ||||  |||||||||||||| ||||| |||||  | ||| | ||||| ||||| |||||||||||||| || || || || || |||||||| |||||
ggaggctcagattctttctgtagtctaatgaatataatttttctcaattaattaataaacaagttcttcctgtggaaatgacaatcatattcttgtccagATAACAGATGCAGTTGTTGTTGCAAGAATTCTTAATGCTACACTAGTTGTACCTGAGTTGGATCATCAATCTTTTTGGAAAGATGACAG

upper sequence: GRMZM2G101181_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA11G03640.1 (Glycine max), 3'ss of exon 4
------------------------gtatgat-tgccttccaatgtctggttgatttgtttttatcatcccttgtgttacctttatgatgttca-gcttgcagATAACAGATGCTGTTGTAGTTGCCTGGATTTTGAATGCCACACTTGTTGTACCTGAGTTAGACCACCACTCGTTCTGGAAAGACGACAG
                         | | || |   ||  ||  |     |||     || | ||        ||  ||  | || ||||||  || | |||||||||||||||||||| |||||| | ||| | ||||||||||| || ||||| ||||| || || || || |  ||||| || |||||
gttagtttcctagtcaggctcataattttatatatttttaaaaataaaaatgaacaagttctttctatggaaatgacac--tcatcatgttcctgcatccagATAACAGATGCTGTTGTTGTTGCCCGAATTCTTAATGCCACACTAGTAGTACCGGAGTTGGATCATCATTCTTATTGGAAGGATGACAG

upper sequence: GRMZM2G101181_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA01G41740.1 (Glycine max), 3'ss of exon 3
-------------------------gtatgattgccttccaatgtctggttgatttgtttttatcatcccttgtgttacctttatgatgttca-gcttgcagATAACAGATGCTGTTGTAGTTGCCTGGATTTTGAATGCCACACTTGTTGTACCTGAGTTAGACCACCACTCGTTCTGGAAAGACGACAG
                          | |  ||   ||  ||  |     ||| |  ||| |  |        ||  ||  | || ||||||  ||   |||||||||||||||||||| |||||  | ||| | ||||||||||| || ||||||||||| || || || || |  |||||||| |||||
gttctctttcctagtcaggcagatgatttatttatttttaaaaataataatgaataatttcttcctgtggaaatg--acaatcatcatgttcctgcacccagATAACAGATGCTGTTGTTGTTGCACGAATTCTTAATGCCACACTAGTAGTACCTGAGTTGGATCATCATTCTTATTGGAAAGATGACAG

upper sequence: GRMZM2G101181_T03 (Zea mays), 3'ss of exon 3
lower sequence: Vv00s0229g00100.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------------------------------------------------------------gtatgattgccttccaa---tgtctggttgatttgtttttatcatcccttgtg--ttacctttatgatg----ttcagcttgcagATAACAGATGCTGTTGTAGTTGCCTGGATTTTGAATGCCACACTTGTTGTACCTGAGTTAGACCACCACTCGTTCTGGAAAGACGACAG
                                                                                    || |     ||  ||   ||| |   | ||||  || | | |||| || ||  |    ||||  ||     | | ||   |||||||| |||||||| ||||||||  ||||| | ||||| ||| | |||||||| ||||| || || || || ||||||||||| || ||
gtaagtataaagattcttctgtagctgctacatgttcattaaaacatatatagtggaaggatatgctgttgccgtgtcaacttcataaacatattataaacttgtttcagttatttacttgt-ttatcctttttgcatggaatttacaatccatttcctgcactcagATAACCGATGCTGTAGTAGTTGCTCGGATTCTTAATGCTACATTAGTTGTACCAGAGTTGGATCATCATTCCTTCTGGAAAGATGATAG

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|211413345|gb|FL280504.1|FL280504
EST:     GTTACTTGTTGATTGCTACTAGTGGGGGCCTGAATCAGCAGCGCATAGGG                         ATAACAGATGCTGTTGTAGTTGCCTGGATTTTGAATGCCACACTTGTTTGT
genomic: GTTACTTGTTGATTGCTACTAGTGGGGGCCTGAATCAGCAGCGCATAGGGgtatgattgc ... cagcttgcagATAACAGATGCTGTTGTAGTTGCCTGGATTTTGAATGCCACACTTGTT-GT
EST: gi|67022216|gb|CO450965.1|CO450965
EST:     GTTACTTGTTGATTGCTACTAGTGGGGGCCTGAATCANCAGCGCATAGGG                         ATAACAGATGCTGTTGTAGTTGCCTGGATTTTGAATGCCACACTTGTTGTA
genomic: GTTACTTGTTGATTGCTACTAGTGGGGGCCTGAATCAGCAGCGCATAGGGgtatgattgc ... cagcttgcagATAACAGATGCTGTTGTAGTTGCCTGGATTTTGAATGCCACACTTGTTGTA
EST: gi|76282456|gb|DV022024.1|DV022024
EST:     GTTACTTGTTGATTGCTACTAGTGGGGGCCTGAATCAGCAGCGCATAGGG                         C
genomic: GTTACTTGTTGATTGCTACTAGTGGGGGCCTGAATCAGCAGCGCATAGGGgtatgattgc ... cagcttgcag-
EST: gi|76282456|gb|DV022024.1|DV022024
EST:     GTTACTTGTTGATTGCTACTAGTGGGGGCCTGAATCAGCAGCGCATAGGG                         C
genomic: GTTACTTGTTGATTGCTACTAGTGGGGGCCTGAATCAGCAGCGCATAGGGgtatgattgc ... cagcttgcag-
EST: gi|76282456|gb|DV022024.1|DV022024
EST:     GTTACTTGTTGATTGCTACTAGTGGGGGCCTGAATCAGCAGCGCATAGGG                         C
genomic: GTTACTTGTTGATTGCTACTAGTGGGGGCCTGAATCAGCAGCGCATAGGGgtatgattgc ... cagcttgcag-
EST: gi|76282456|gb|DV022024.1|DV022024
EST:     GTTACTTGTTGATTGCTACTAGTGGGGGCCTGAATCAGCAGCGCATAGGG                         C
genomic: GTTACTTGTTGATTGCTACTAGTGGGGGCCTGAATCAGCAGCGCATAGGGgtatgattgc ... cagcttgcag-
EST: gi|76282456|gb|DV022024.1|DV022024
EST:     GTTACTTGTTGATTGCTACTAGTGGGGGCCTGAATCAGCAGCGCATAGGG                         C
genomic: GTTACTTGTTGATTGCTACTAGTGGGGGCCTGAATCAGCAGCGCATAGGGgtatgattgc ... cagcttgcag-
EST: gi|76282456|gb|DV022024.1|DV022024
EST:     GTTACTTGTTGATTGCTACTAGTGGGGGCCTGAATCAGCAGCGCATAGGG                         C
genomic: GTTACTTGTTGATTGCTACTAGTGGGGGCCTGAATCAGCAGCGCATAGGGgtatgattgc ... cagcttgcag-
EST: gi|148935747|gb|EC879791.2|EC879791
EST:     GTTACTTGTTGATTGCTACTAGTGGGGGCCTGAATCAGCAGCGCATAGGG                         ATAACAGATGCTGTTGTAGTTGCCTGGATTTTGAATGCCACACTTGTTGTA
genomic: GTTACTTGTTGATTGCTACTAGTGGGGGCCTGAATCAGCAGCGCATAGGGgtatgattgc ... cagcttgcagATAACAGATGCTGTTGTAGTTGCCTGGATTTTGAATGCCACACTTGTTGTA
EST: gi|211415883|gb|FL280506.1|FL280506
EST:     GTTACTTGTTGATTGCTACTAGTGGGGGCCTGAATCAGCAGCGCATAGGG                         ATNAACAGATGCTGTTGTAGTTGCCTGGAT
genomic: GTTACTTGTTGATTGCTACTAGTGGGGGCCTGAATCAGCAGCGCATAGGGgtatgattgc ... cagcttgcagAT-AACAGATGCTGTTGTAGTTGCCTGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggttgatttgtttttatcatcccttgtgttacctttatgatgttcagcttgcagATAACAGATGCTGTTGTAGTTGCCTGGATTTTGAATGCCACACTTGTTGTACCTGAGTTAGACCACCACTCGTTCTGGAAAGACGACAG
 ggttgat  putative branch site (score: 5)
      atttgtttttatcat  TA-rich tract