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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacggttagtacaaaaatgcatatttgatgtgttatcatagttcataatacaatcatgaccaaattactgttctgcagTCTGGTCATAACATTGAAAAAGTCAGGGAAAAAATGGGGGAGCTGATAAAGCAAATGATCAACATTTACTCTCTTCCCAAACTAATTCCCTATATACTTG

Basic information

species Zea mays
transcript GRMZM2G068755_T01
intron # 36
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068755_T01 (Zea mays), 3'ss of exon 36
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 36
-------------------------------------------------------------------------------------------------gtacggttagtacaaaaatgcatatttgatgtgttatcatag-ttcataatacaatcatgaccaaattactgttctgcagTCTGGTCATAACATTGAAAAAGTCAGGGAAAAAATGGGGGAGCTGATAAAGCAAATGATCAACATTTACTCTCTTCCCAAACTAATTCCCTATATACTTG
                                                                                                  ||    |  ||    | ||||   ||    | | ||  ||  ||    || || || | | |||  | ||||  |||||||||| || ||||| ||||||||||| ||||||||||| |||||||||||||||||| ||||||| || |||||||| |||||  | || || ||  | |
gtacatagagtgcacaaatattgattagtgtaatcctgaatcttcccatcagaaacacaggctggagaagtatattcttcagattgatcgaacatatttatttgttatatgccattgcaatctttgcctataattttaaattttcgattcattcctaaacaa-ctgctgtattgcagTCTGGCCACAACATCGAAAAAGTCAGAGAAAAAATGGGAGAGCTGATAAAGCAAATGGTCAACATCTATTCTCTTCCAAAACTTCTCCCATACATTTTGG

upper sequence: GRMZM2G068755_T01 (Zea mays), 3'ss of exon 36
lower sequence: AT2G35630.1 (Arabidopsis thaliana), 3'ss of exon 37
-----------------------------------gtacggttagtacaaaa-atgcatatttgatgtgttatcatag-------ttcataatacaat-----catgaccaaattactgttct----gcagTCTGGTCATAACATTGAAAAAGTCAGGGAAAAAATGGGGGAGCTGATAAAGCAAATGATCAACATTTACTCTCTTCCCAAACTAATTCCCTATATACTTG
                                   ||  |  |  | | ||  || |   |||    |  | |  |||       ||  |  | || |      ||    || |   ||| ||    |||||  || ||||||||||||||||| || ||||||||| |||||||||| ||||| || ||  |    || ||| |    ||      |||||||||  | |
gttaggcatctgatattaatccaatttcctatggtgttggcctctttctaatcattcccgtttatctttctgttttagaaaaagattggtgcttcagtgtctttatatttaactccttgtccttggtgcagTTGGGGCATAACATTGAAAAAGTAAGAGAAAAAATGCGGGAGCTGATGAAGCAGATCATTCAGGCATATTCTGTAGGAAAGACGTATCCCTATATTTTGG

upper sequence: GRMZM2G068755_T01 (Zea mays), 3'ss of exon 36
lower sequence: EFJ11209 (Selaginella moellendorffii), 3'ss of exon 35
gtacggttagtacaaaaatgcatatttgatgtgttatcatagttcataat-acaatcatgaccaaattactgttctgcagTCTGGTCATAACATTGAAAAAGTCAGGGAAAAAATGGGGGAGCTGATAAAGCAAATGATCAACATTTACTCTCTTCCCAAACTAATTCCCTATATACTTG
                                || ||     || ||  |  | |   |  |  |     | | ||||||||||||||||| |||||||| ||  ||||||| ||| |||||||||| |  |  ||      ||| ||| ||    | || ||| || | || ||    |
--------------------------------gtaattgacatttatgcttgcgagtttagctgagcatgtttcctgcagTCTGGTCATAATATTGAAAAGGTTCGGGAAAAGATGCGGGAGCTGATGAGACTCATCTGTTGCATCTACCCTGCATCAAAGCTATTTACGTACATTTGCG

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|33770951|gb|CF273245.1|CF273245
EST:     TGTTGACAGAAGCTGAAGCTGCAATTTTTCTTCCTTGCCTCATAGAGAAG                         TCTGGTCATAACATTGAAAAAGTCAGGGAAAAAATGGGGGAGCTGATAAAG
genomic: TGTTGACAGAAGCTGAAGCTGCAATTTTTCTTCCTTGCCTCATAGAGAAGgtacggttag ... tgttctgcagTCTGGTCATAACATTGAAAAAGTCAGGGAAAAAATGGGGGAGCTGATAAAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgatgtgttatcatagttcataatacaatcatgaccaaattactgttctgcagTCTGGTCATAACATTGAAAAAGTCAGGGAAAAAATGGGGGAGCTGATAAAGCAAATGATCAACATTTACTCTCTTCCCAAACTAATTCCCTATATACTTG
 atttgat  putative branch site (score: 5)
                                            ctgttct  putative PPT
                     ataatacaat  TA-rich tract