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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttattcttattgctgtgagtttgctgatctatttttttttcctttttagaacaccatgtttcttgatacatagtgagtgttcttttgcagGTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATG

Basic information

species Zea mays
transcript GRMZM2G107867_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107867_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g17980.2 (Oryza sativa), 3'ss of exon 4
gtattttattcttattgctgtgagtttgctgatctatttttttttcctttttagaacaccatgtttcttgatac-atagtg--agtgttcttttgcagGTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATG
|| |||| || || ||  |||     ||  |  |||| | || || ||  || | |  | || ||| ||  ||  |||||   |  |||| ||||||||| || ||||||||| ||||||||||||||||||| ||||||||||| ||||| ||||| ||||||||||| |||||||| |||||||||||||||||||
gttttttttttttttt-ttgtatcactgtgggactatatcttcttgctcctttgcatgcaatattttttcttattatagtattatggttcctttgcagGTGATCTCTGGTAAATTATATGCTGGACCTGAGGTTGATGTATGGAGCTGTGGAGTGATCCTTTATGCTCTCCTTTGTGGTACTCTTCCATTTGATGATG

upper sequence: GRMZM2G107867_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g37800.1 (Oryza sativa), 3'ss of exon 4
gtattttattcttattgctgtgagtttgctgatctatttttttttcctttttagaacaccatgtttcttgatacatagtgagtgttcttttgcagGTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATG
||||||| ||  |||  |||||||  |    ||||   | ||  ||||||  |    |   | ||||||  || |   | |  || | ||||||||| || ||||||||| ||||||||||||| ||||| ||||||||||| ||||| ||||| ||||||||||| |||||||| ||||||||||||||||| |
gtattttttttgtatcactgtgagactat--atct---tcttgctcctttacatgcaatattttttcttattatagtattatggtccctttgcagGTGATCTCTGGTAAATTATATGCTGGACCCGAGGTTGATGTATGGAGCTGTGGAGTGATCCTTTATGCTCTCCTTTGTGGTACTCTTCCATTTGATGACG

upper sequence: GRMZM2G107867_T04 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 4
------------------------------gtattttattcttattgctgtgagt-ttgctgatctatttttttttcct---ttttaga---acaccatgtttcttgatacatagtgagtgt-------tcttttgcagGTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATG
                              | || ||||| ||| || | | | | ||  |  | |||   |  |||      |||| |   ||  | |  |  || ||| ||   |  |         | |||  ||||| || ||||| ||| | ||||||||||| || || ||||| ||||| ||||| || ||| | ||||||||||| ||||| |||||||| ||||||||||
gtttgtaaataattaaattgtaacggaataggatattattattaatgttattattattattattatatcactacttctgagactttacatttacctccttgtgattaataaatcaaggataaactgttgtttttcacagGTTATCTCTGGAAAATTGTATGCTGGACCAGAAGTAGATGTCTGGAGCTGTGGTGTAATTTTATATGCTCTTCTCTGTGGCACTCTTCCTTTTGATGATG

upper sequence: GRMZM2G107867_T04 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G49770.1 (Glycine max), 3'ss of exon 5
gtattttattcttattgctgtgagtttgctgatctatttttttttcctttttagaacac-catgtttcttgatacatagtgagtgttcttttgcagGTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATG
        ||  || ||   |          |  |||| ||       | |  |        ||| ||||| |  | | |   |  | |||  ||||| || ||||| ||| | |||||||||||||| || ||||| ||||| ||||| || ||| | ||||| ||||||||||| || ||||| ||||||||||
-------gtttgtaatggaatacacggcaacaattattgttgaggatatatatgtgtgtgtgtgtgtcttggt-tacactttttcatttttcacagGTTATCTCTGGGAAATTGTATGCTGGACCTGAAGTGGATGTCTGGAGCTGTGGTGTAATTTTATATGCCCTTCTTTGTGGCACCCTTCCTTTTGATGATG

upper sequence: GRMZM2G107867_T04 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G26180.1 (Glycine max), 3'ss of exon 4
----gtattttattcttattgctgtgagt-ttgctgatc-tatttttttttcctttttagaacaccatgtttcttgatacatagtgagtgttcttttgcagGTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATG
    ||| |  | |   || ||    | | ||| |||   ||| | | | |  | | | |     ||| ||||||| |  | | |   |  | |||  ||||| || ||||| ||||| |||||||||||||| || ||||| ||||| ||||| || ||| | ||||| ||||||||||| |||||||| ||||||||||
gtttgtaatggaatac-atggcgaaaattattgttgaggatatatatatattgtctcttgtgattcatatttcttggt-tacactttttcatttttcacagGTTATCTCTGGGAAACTGTATGCTGGACCTGAAGTGGATGTCTGGAGCTGTGGTGTAATTTTATATGCGCTTCTTTGTGGCACTCTTCCTTTTGATGATG

upper sequence: GRMZM2G107867_T04 (Zea mays), 3'ss of exon 3
lower sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 4
gtattttattcttattgctgtgagtttgctgatctatttttttttcctttttagaacaccatgtttc--ttgatacatagtgagtgttcttttgcagGTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATG
|||  |  |||      | |  |  |     ||    |  ||   | | |||  ||    | |||    | || |  ||   | ||||      |||||||| || || ||  |||||||||| ||||| || ||||| ||||| ||||| ||||| || || |||||||| ||||| || ||||||||||||||||
gtaagtgcttcagccctcaggtatctgaggaatactataattaggcttgtttcaaatgataggttatagtcgagatctataaattgttt-----cagGTAATTTCGGGCAAGTTATATGCTGGCCCTGAAGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATG

upper sequence: GRMZM2G107867_T04 (Zea mays), 3'ss of exon 3
lower sequence: AT3G29160.2 (Arabidopsis thaliana), 3'ss of exon 4
----gtattttattcttattgctgtgagtttgctgatctattt--ttttttcctttttagaacaccatgtttcttgatacatagtgagtgttcttttgcagGTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATG
     || |||| |    || |||     ||  | | |||| |   | | ||   |||     |  | || ||||    | || |     |  | ||| |||| ||||| |||||| |||||||||||||||| || |||||||||||||| || || ||  | || |||||  | || || |||||||| ||||||||||
gtatatagtttagtaaagttactgaattgtttttcacctatgtgactatgtctcgtttctcttatga-gtgtcttatctcttact-----tcttgttgtagGTTATATCAGGTAAATTATATGCTGGACCTGAAGTAGATGTATGGAGTTGCGGAGTTATATTGTACGCTCTATTATGCGGTACTCTTCCTTTTGATGATG

upper sequence: GRMZM2G107867_T04 (Zea mays), 3'ss of exon 3
lower sequence: Vv08s0040g00720.t01 (Vitis vinifera), 3'ss of exon 5
gtattttattcttattgctgtgagtttgctg-atctatttttttttcctttttagaacaccatgtttcttgatacatagtgagtgttcttttgcagGTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATG
            ||| |  || |  ||| |  ||   ||     |    || |  |  |  ||| |   || ||||  |  |   | ||| ||||||| || ||||   |||||||| |||| |||||||| ||||| ||||||||||| || ||| | | ||||||||| |||||||  ||||| ||||||| ||
-----------gtatgg--gtcaacttgttatataagttgccaatgaacttgtgaataattatgctctgtg-tacaatgaaatactgcttgtgcagGTTATTTCTGAACAACTATATTCTGGTCCTGAGGTTGATGTTTGGAGTTGTGGTGTCATTTTATTTGCTCTTCTCTGTGGAAGGCTTCCTTTTGATGCTG

upper sequence: GRMZM2G107867_T04 (Zea mays), 3'ss of exon 3
lower sequence: Vv14s0108g01230.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------------gtattttattcttattg-ctgtgagtttgctgatctatttttttttcctttttagaacacc-----atgtttcttgatacatagtgagtgttc--ttttgcagGTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATG
                               | ||  |  || |||  || ||| |   | | | ||  ||| |    | | |  | |       |  |||||       || | ||||| |  ||||  |||| |||||||| | | | || || ||||||||||| ||||||||||| || || || ||| | || |||||||||||||| |||||||||||||||||||
gtaaggagtttgcagcattataatataagacaattcctaatttttggttgagagatgagtta-caatactttctaatatatgatgataatggttgaaatttctaaggttctaattagtgtcccattttatagGTTATATCTGGAAGATTGTACGCAGGACCTGAGGTGGATGTATGGAGCTGCGGTGTTATTTTGTACGCTCTTCTTTGTGGTACTCTTCCATTTGATGATG

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|211440538|gb|FL230375.1|FL230375
EST:     GCCATTTTCTGAAGACTAGCTGTGGGAGTCCGAACTATGCTGCTCCAGAG                         GTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGC
genomic: GCCATTTTCTGAAGACTAGCTGTGGGAGTCCGAACTATGCTGCTCCAGAGgtattttatt ... tcttttgcagGTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttcctttttagaacaccatgtttcttgatacatagtgagtgttcttttgcagGTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATG
                         tcttgat  putative branch site (score: 4)
                                          tgttctttt  putative PPT
       tttttagaa  TA-rich tract