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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctgactaacaaatagcttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCT

Basic information

species Zea mays
transcript GRMZM2G000645_T01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 16
gtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctgactaacaaatag--cttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCT
|| |||||||| || || | ||| | |||    |  | |    |||| | ||||   ||||||| ||    |||| | ||||||||| ||||||||||||||||| |||||||||||||||||||| |||||||||||||||||| | || | ||||||  | |||||| |||||||||| 
gtgtgttttcttgataatactgcctgcttattgtc-tgg----tgttgaattcttgaactaacatatttttcttgttgcagTGTCATGGGGTACACATTACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCA

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 16
------gtatgttttctcgaaaacaatgcttcctttcctttgtagca--tctgttaatttctctgactaacaaatagcttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCT
      | |  || |      |  | |      |||   ||| || |    ||   | || ||||  || ||| |   ||  | |||||| || || |||||| | ||| | || ||||||||||||||||| |||||||||||||| ||||||||    || ||  ||||| || |||| || || 
gtaagtgaaacttctgcttggattattcaaagttttaaattgcagtaatcttgactacttttctgtttatcaattttttttct-cagTGTTATGGGATACACACTGCTTTTAAGCTTGATTGAGTACAAGACACTTGTGATGCGTGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATCCCC

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 16
gtatgttttctcgaaaacaatgcttcctttcctttgtagcatct------gttaatttctctgactaacaaatagcttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCT
        |      | ||||| ||    |  ||   |  ||||        ||||     | | |    ||  | ||    |||||| || || |||||  ||||| | ||||||||||| |||||||| ||||| |||||||| ||||||||    || ||  ||||| || |||| || |||
-------gtaagtggatcaatggtttgcattattcaaaatatctcaatgcagtaatcctgattattttttaactgttttactcagTGTTATGGGATACACGCTACTTTTAAGTTTGATTGAATACAAGACACTTGTCATGCGTGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATTCCT

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 16
------gtatgttttctcgaaaacaatgcttcctttcctttgtagca--tctgttaatttctctgactaacaaatagcttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCT
      | |  || |      |  | |      |||   ||| |  |    ||   |||| ||||  || ||| | | ||    |||||| || || |||||| | ||| | || ||||||||||||||||| |||||||||||||| ||||||||    || ||  | ||| |  |||| || || 
gtaagtgaaacttctgcttggattattcaaagttttaaattgcaataatcttgactatttttctgtttatcaa-ttgtttttctcagTGTTATGGGATACACACTGCTTTTAAGCTTGATTGAGTACAAGACACTTGTGATGCGTGGTGATTTGGAAAGGGCCAATGATATTCTGCCATCAATCCCC

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 16
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 16
--------------gtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctgactaacaaatagcttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCT
               |||||||  | || |    || ||  | |    |  |  || || |||  | | |  ||      | |     | ||||||||| || || ||  | || || ||  ||||||| |||||||| ||||||||||| || |||||||||   || ||  |||||||| |  | || |||
gtacgttcctttatatatgtttatttgaga---ctgttttatcttgcatacataatttgctaacatatttccctttttcttgg--gaatgcagTGTCATAGGATATACCCTGCTGCTTAGCCTGATTGAATACAAGACTCTTGTGATGCGAGGCGATTTGGATAGAGCCAATCAAATTTTACCTACAATTCCT

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 16
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 16
gtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctgactaacaaatagctt----ggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCT
||| ||  | | ||      || ||   |   |  |     |||   | |||||    ||        | ||    | | |||||| || |||||||| ||  | || ||  |||||||||||||||| ||||||||||| || ||||| ||  | || |   |||| ||| |  | || |||
gtaagtgct-tagatttgtgtgtttatataattgagattgttctagaagtttctgatgctgttcccctgttttgtggatgcagTGTTATAGGGTACACCTTGTTGCTAAGCCTGATTGAGTACAAGACTCTTGTGATGCGGGGTGATTTAGACAAAGCCAGTGAAATCTTACCTACAATTCCT

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 16
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 20
------gtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctgactaacaaatagcttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCT
        |||||||   |  |  | ||||  |  |  ||||||  |  |  | | |||| || | |    ||   |    ||||||| ||||| ||||| |||||| | |||||||||||||||||||| |||||||||||||| |||||||| || || ||  || | ||| | || || |||
gtaagcagatgttttactgttatgattgctaacaatgttttgta--acttactgacttctgtgtccactttatgatt----acagTGTTATTGGATACACTTTACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCT

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 16
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 16
------gtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctgactaacaaatagctt----------ggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCT
      | |  |||    ||||       |         |||| | || || |||  ||| | | ||  || | | ||            | ||||||||| || ||||| |||||||| |||||||||||||||||||| |||||||||||||| ||  |||| |  || ||  || ||||| | || || || 
gtgagtggacttttggcagaaagggggagtggagggtggttgttgtat-tgctaacatcttt-attattaagttggtttttccttttcaatgcagTGTCATGGGATACACGTTACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCC

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 16
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 16
gtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctga-ctaa-------caaatagcttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCT
||  |    || |  | |    ||||       |    || | ||||  | |   ||| ||||        |  |    |  | |||||| || || || || |||||||| | |||||||||||||||||| ||||| |||||||| || ||  | | |||||   |||||||| | |  || |||
gtgagggagcttgggagctgcacttctgcaatctgactgcttttgttcttgtaattgatctaaatttatttatgttatcttatgcagTGTTATGGGATATACCTTACTTCTCAATTTGATTGAGTACAAGACACTTGTAATGCGTGGAGACTTTCAACGTGCAAGTGAAATTTTACCTTTGATTCCT

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|18965038|gb|BM661357.1|BM661357
EST:     GGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA                         TGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGT
genomic: GGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAAgtatgttttc ... cttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGT
EST: gi|89106492|gb|DY576709.1|DY576709
EST:     GGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA                         TGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGT
genomic: GGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAAgtatgttttc ... cttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGT
EST: gi|22490520|gb|BU050443.1|BU050443
EST:     GGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA                         TGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTT
genomic: GGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAAgtatgttttc ... cttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctttcctttgtagcatctgttaatttctctgactaacaaatagcttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCT
                                gactaac  putative branch site (score: 1)
                   tgttaattt  TA-rich tract