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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcaaatatttatttactacctagatgttaaatatattaatgtttatcttccaaattttatgtaccttttattttcttccagGTGGACAAGCAAAAACTCTAATGTTTGTTCAGATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGTACTTTAAAGTTTGCTGAAAGGGTGTCTGG

Basic information

species Zea mays
transcript GRMZM2G173700_T02
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G173700_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os05g44560.1 (Oryza sativa), 3'ss of exon 17
gtaatcaaatatttatttacta---cctagatgttaaat-atattaatgtttatcttccaaattttatgt-accttttattttcttccagGTGGACAAGCAAAAACTCTAATGTTTGTTCAGATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGTACTTTAAAGTTTGCTGAAAGGGTGTCTGG
|||||||| |||||| ||   |   | |  ||||  | | | ||| ||| ||   ||  || | | || | |     || | |||| |||||||||||||||| || |||||||||||||| ||||||||||||||||||||||||||||| |||||||| ||| ||||||||||||||||||| |||||
gtaatcaattatttagttgaaaaatcatgcatgtggagttagatttatggtt--tttgtaactataatcttataaaataatctcttgcagGTGGACAAGCAAAGACACTAATGTTTGTTCAAATAAATCCTGATGTTGAGTCATATTCAGAGACTATAAGCACTCTAAAGTTTGCTGAAAGGGTTTCTGG

upper sequence: GRMZM2G173700_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA05G35130.1 (Glycine max), 3'ss of exon 15
gtaatcaaatatttatttactacctag-atgttaaatatattaatgtttatct-tccaaatttt---atg------------taccttttattttcttcca--gGTGGACAAGCAAAAACTCTAATGTTTGTTCAGATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGTACTTTAAAGTTTGCTGAAAGGGTGTCTGG
      |||| |||||| |  |  |   |||| | ||   || |   || ||| |  | |||||   |||            |  |||| ||||| || ||  ||||  ||||| || || || ||||||||||| || ||| | || ||    |||||||| |||||  | || ||||||||||||||||||||||| |||||
----gtaaatctttattcatcatttgttatgtcacatgccttgaatcttttctatgtagattttcttatgatctttgactcttgtctttgattttattgcacagGTGACCAAGCGAAGACACTCATGTTTGTTCAAATTAATTCAGACGTAAGTTCATATTCTGAAACACTGAGCACTTTAAAGTTTGCTGAAAGGGTTTCTGG

upper sequence: GRMZM2G173700_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA13G33390.1 (Glycine max), 3'ss of exon 13
----------------------------------------------------------------------------------------------gtaatcaaatatttatttactacctagatgttaaata--tattaatgtttatct-----tccaaattttatgtaccttttattttcttcca--gGTGGACAAGCAAAAACTCTAATGTTTGTTCAGATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGTACTTTAAAGTTTGCTGAAAGGGTGTCTGG
                                                                                              |   |    ||| | |||   || |  ||  || |    ||||  || |||  |     ||||  |   |  ||  ||| ||||| || ||  ||||| || || || || || ||||| || || || ||| | ||| |  |||| | ||| ||| || |||||||||||||||||||||| ||||| |||||
gtaaaatcatagtttatcatttcttaccttgccttgctagtatctaacacttcatgtcttgccttgctagtatgcacaaaagtgaaaaatccttgagtttctttatgtcttttggacttgtattctataccactatttctgattagataagattccatttgaaacatatgtttaattttattgcacagGTGGTCAGGCCAAGACACTCATGTTAGTCCAAATTAATTCAGATTTAAAGTCTTTTTCTGAATCTCTAAGTACTTTAAAGTTTGCTGAGAGGGTTTCTGG

upper sequence: GRMZM2G173700_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA05G37800.1 (Glycine max), 3'ss of exon 17
----------------------------------------gtaatcaaat--atttatttactacctagatgttaaatatattaatgtt-tatcttccaaattttatgtaccttt-----tattttcttccagGTGGACAAGCAAAAACTCTAATGTTTGTTCAGATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGTACTTTAAAGTTTGCTGAAAGGGTGTCTGG
                                         || |    |  |||| ||| | |  | ||| ||||  |||||   ||  |  ||| | || ||    || ||||     |  | | |   |||||| ||||| ||||| || |||||||| ||| | |||||||||||||  |||||||| |||||| |||| || || |||||||||||| |||| |||||
gtaattgttgccattattggtatcaatttacagtattgttatatttggtttcatttgtttgc-attttgat-ttaagcatattgcagtcatggcttactaaattgcaatagctttgtccgttgtatatgatagGTGGTCAAGCGAAAACCCTTATGTTTGTACAGCTTAATCCTGATGTTGCTTCATATTCTGAAACTGTAAGCACCTTGAAGTTTGCTGAACGGGTTTCTGG

upper sequence: GRMZM2G173700_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA08G01800.1 (Glycine max), 3'ss of exon 18
----------------------------------------gtaatcaaat--atttatttactacctagatgttaaatatattaatgt--ttatcttccaaatttta-----tgtaccttttattttcttccagGTGGACAAGCAAAAACTCTAATGTTTGTTCAGATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGTACTTTAAAGTTTGCTGAAAGGGTGTCTGG
                                         || |    |  |||| ||| | |  | ||| ||||  |||||   ||  |    | | |||||  |     | |  |  || |  | ||  |||||| ||||| ||||| || |||||||| ||| | |||||||||||||  |||||||| |||||| |||| || || |||||||||||  |||| || ||
gtaattgttgccattattggtatcaatttacagttttgttatatttggtttcatttgtttgc-attttgat-ttaagcatattgcagtcatggcttactaaattgcaatagctttgtcccttgtaattttatagGTGGTCAAGCGAAAACCCTTATGTTTGTACAGCTTAATCCTGATGTTGCTTCATATTCTGAAACTGTAAGCACCTTGAAGTTTGCTGAGCGGGTTTCCGG

upper sequence: GRMZM2G173700_T01 (Zea mays), 3'ss of exon 14
lower sequence: AT5G41310.1 (Arabidopsis thaliana), 3'ss of exon 15
--gtaatcaaatatttatttactacctagatgttaaat-atattaatgtttatcttccaaattttatgtaccttttattttcttccagGTGGACAAGCAAAAACTCTAATGTTTGTTCAGATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGTACTTTAAAGTTTGCTGAAAGGGTGTCTGG
     || | |||    |  |  |   | || |||  | |||||  || ||   |    | |  |     | ||||| ||| ||  ||| || ||||| |||||||| ||||||||||| || ||||||||||  || |||||| | || ||| |||||||||| || ||||| ||||| || |||||
gtactataagatagacttcaataaaaaaaatattacttgatattgttgcttgcttctttactcct-----ctttttaatttttt--agGAGGGCAAGCGAAAACTCTTATGTTTGTTCAAATTAATCCTGATGAAGATTCATATGCTGAGACTGTAAGTACTTTGAAATTTGCGGAAAGAGTTTCTGG

upper sequence: GRMZM2G173700_T01 (Zea mays), 3'ss of exon 14
lower sequence: Vv17s0000g03700.t01 (Vitis vinifera), 3'ss of exon 17
------------------------------------------------------------------gtaatcaaatatttatttactacctagatgttaaatatattaatgtttatcttccaaatttt-atgtaccttttattttcttccagGTGGACAAGCAAAAACTCTAATGTTTGTTCAGATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGTACTTTAAAGTTTGCTGAAAGGGTGTCTGG
                                                                      | || |||||  |||   || | ||  |     | || |  || || |  |  ||||| || | |   ||  |    | ||||||| |||||||| ||||| |||||||| ||| | |||||||||||  | |||| ||| ||||||  ||||||||| || |||||||| ||||| |||||
gtacttcactgttttccagttgcttttagcaataaatcccttcacctgtcttattgtttcgtcaggactctaaattatttccttagctccca-atagtcctctttttgaacttcatatagcggatttttattttctactttataaactacagGTGGTCAAGCAAAGACTCTTATGTTTGTGCAGCTTAATCCTGATGTGAATTCATTTTCTGAAACTGCAAGTACTTTGAAATTTGCTGAGAGGGTTTCTGG

upper sequence: GRMZM2G173700_T01 (Zea mays), 3'ss of exon 14
lower sequence: Vv02s0025g03480.t01 (Vitis vinifera), 3'ss of exon 18
------------------------------------------------gtaatcaaatatttat-ttactacctagatgttaaatatattaatgtttatcttccaaattttatgt-accttttattttc------ttccagGTGGACAAGCAAAAACTCTAATGTTTGTTCAGATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGTACTTTAAAGTTTGCTGAAAGGGTGTCTGG
                                                || |       || |  ||   |  | ||  ||  |  | ||||  |||   | ||     || | | ||| ||| ||||       ||  ||| || ||||| || || || |||||||| ||| | ||||||||||| || || || || |||||||||||||| || |||||||| || || || |||||
gtacatatccttctggtttttgagtcttgtggttgaaccataccgtttgtcagtgtgctttaagattgggaatttgactttgtagttgttaacattttcttgcctgggcttgtttgaccgtttctttttcctactttatagGAGGTCAAGCGAAGACCCTTATGTTTGTACAGCTTAATCCTGATGTGGATTCCTACTCCGAAACTATAAGTACCTTGAAGTTTGCCGAGAGAGTCTCTGG

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|31353200|gb|CD437557.1|CD437557
EST:     TGTGCCTTATAGAAACAGCAAGTTAACACAAGTTCTTCAAAGTTCTTTAG                         GTGGACAAGCAAAAACTCTAATGTTTGTTCAGATAAATCCTGATGTTGAGT
genomic: TGTGCCTTATAGAAACAGCAAGTTAACACAAGTTCTTCAAAGTTCTTTAGgtaatcaaat ... tttcttccagGTGGACAAGCAAAAACTCTAATGTTTGTTCAGATAAATCCTGATGTTGAGT
EST: gi|31354629|gb|CD438986.1|CD438986
EST:     TGTGCCTTATAGAAACAGCAAGTTAACACAAGTTCTTCAAAGTTCTTTAG                         GTGGACAAGCAAAAACTCTAATGTTTGTTCAGATAAATCCTGATGTTGAGT
genomic: TGTGCCTTATAGAAACAGCAAGTTAACACAAGTTCTTCAAAGTTCTTTAGgtaatcaaat ... tttcttccagGTGGACAAGCAAAAACTCTAATGTTTGTTCAGATAAATCCTGATGTTGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaatatattaatgtttatcttccaaattttatgtaccttttattttcttccagGTGGACAAGCAAAAACTCTAATGTTTGTTCAGATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGTACTTTAAAGTTTGCTGAAAGGGTGTCTGG
       tattaat  putative branch site (score: 2)
                                   taccttttattttctt  putative PPT
     tatattaatgtttatc  TA-rich tract