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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcatcttttcttcttattttaacatgctacgatagttgccaggtcatgttcttgaaataatccatcttgcagATATTAAAGGCTTTTTAAGTGATGTTAAACCAGCACTTCTAAGTGCCCTGGATACTGAATATGAGAAAAATCCTTTTGAG

Basic information

species Zea mays
transcript GRMZM2G009849_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009849_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 23
gtcatcttttc--ttcttattttaacatgctac--gatagttgcca------ggtcat---gttcttgaaataatccatcttgcagATATTAAAGGCTTTTTAAGTGATGTTAAACCAGCACTTCTAAGTGCCCTGGATACTGAATATGAGAAAAATCCTTTTGAG
||  | |  ||  |||| | ||||| ||| | |  ||||  |||||      | | ||   |||  ||| |||| || || ||||||||| ||||||||  |||||||||| |||||||| ||||| ||| | |||||| ||||||||||||||||||| ||||||
gttctttgctcatttctcaatttaa-atgttgcttgataaatgccaatgcttgattatattgttactgagataaaccttcctgcagATATCAAAGGCTTCCTAAGTGATGTCAAACCAGCGCTTCTCAGTACTCTGGATGCTGAATATGAGAAAAATCCATTTGAG

upper sequence: GRMZM2G009849_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 23
gtcatcttttcttc-ttattttaacatg--ctacgatagttgccaggtcatgttcttgaaataatccatcttgcagATATTAAAGGCTTTTTAAGTGATGTTAAACCAGCACTTCTAAGTGCCCTGGATACTGAATATGAGAAAAATCCTTTTGAG
||||  ||   ||   |||   |   ||   |     | ||      ||| |    | |  |  | |  |||||||| |||||||| ||| | | |||||| ||||| ||||| || |||||||||||||| || |||||||| ||||| ||||||
gtcactttgcgttaactatcaaattttgatttctctcaatttgtttttcaaggctctaaggtttttctccttgcagACATTAAAGGGTTTCTTACTGATGTAAAACCTGCACTGCTCAGTGCCCTGGATACGGAGTATGAGAAGAATCCATTTGAG

upper sequence: GRMZM2G009849_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA10G35140.1 (Glycine max), 3'ss of exon 25
gtcatcttttcttcttattttaacatg---ctacgatagttgccaggtcatgttcttgaaataatccatcttgcagATATTAAAGGCTTTTTAAGTGATGTTAAACCAGCACTTCTAAGTGCCCTGGATACTGAATATGAGAAAAATCCTTTTGAG
||||  ||   ||    ||  ||  |     |     | ||      ||| |    | |  |  | |  |||||||| |||||||| ||| | | |||||| || || ||||| || |||||||||||||| || |||||||| ||||| ||    
gtcactttgcgttaactttcaaattttgatttctctcaattttgttttcaagGCTCTAAGGTTTTTCTCCTTGCAGACATTAAAGGGTTTCTTACTGATGTAAAGCCTGCACTGCTCAGTGCCCTGGATACAGAGTATGAGAAGAATCCATT----

upper sequence: GRMZM2G009849_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT2G35630.1 (Arabidopsis thaliana), 3'ss of exon 23
-----------------------gtcatcttttcttcttattttaacatgctacgatag-ttgccaggtcatgttcttgaaataatccatct-----tgcagATATTAAAGGCTTTTTAAGTGATGTTAAACCAGCACTTCTAAGTGCCCTGGATACTGAATATGAGAAAAATCCTTTTGAG
                       |       ||  ||| | ||     || ||  |||  ||  |    ||     |  || | ||   | |     | |||| |||||||| ||| | | |||||| ||||| ||||| |||||||| || || || |||||||||||||| ||||| |||
gtggctacgaattcctttaagctggttcagctttgtctaaattctgtttggtagaataacttatcttaacactgaatcaaacttatgtttttctgttttcagACATTAAAGGGTTTCTTAATGATGTCAAACCTGCACTACTAAGTGCACTTGACACCGAATATGAGAAAAACCCTTTCGAG

upper sequence: GRMZM2G009849_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ11209 (Selaginella moellendorffii), 3'ss of exon 22
gtcatcttttcttcttattttaacatgctacgatagttgccagg-tcatgttcttgaaataatccatcttgcagATATTAAAGGCTTTTTAAGTGATGTTAAACCAGCACTTCTAAGTGCCCTGGATACTGAATATGAGAAAAATCCTTTTGAG
               | ||| |       | | |   |   | | | | ||| || |  |      | || |||   | ||    ||||| |  ||||| ||||| || |||| ||||||  ||||||| ||||||||||||||||| | ||||
--------------gtttttcagataatgatgttgaatataaagcttacgtttttaagttc-----tgtttcagGCTTGAAGAATTTTTTGACGGATGTGAAACCTGCTCTTCAAAGTGCTTTGGATACCGAATATGAGAAAAATCCCTATGAG

upper sequence: GRMZM2G009849_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ15655 (Selaginella moellendorffii), 3'ss of exon 22
gtcatcttttcttcttattttaacatgctacgatagttgccagg-tcatgttcttgaaataatccatcttgcagATATTAAAGGCTTTTTAAGTGATGTTAAACCAGCACTTCTAAGTGCCCTGGATACTGAATATGAGAAAAATCCTTTTGAG
              || ||   |||    | | |   |   | | | | ||| || |  |      | || |||   | ||    ||||| |  ||||| ||||| || |||| ||||||  ||||||| ||||||||||||||||| | ||||
-------------gtttttcagaca-atgatgttgaatataaagcttacgtttttaagttc-----tgtttcagGCTTGAAGAATTTTTTGACGGATGTGAAACCTGCTCTTCAAAGTGCTTTGGATACCGAATATGAGAAAAATCCCTATGAG

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|19350672|gb|BM895204.1|BM895204
EST:     AAATGCTACTATAAAACTAATTGGGATGCTACATAAGTTTGTGGGCCCAG                         ATATTAAAGGCTTTTTAAGTGATGTTAAACCAGCACTTCTAAGTGCCCTGG
genomic: AAATGCTACTATAAAACTAATTGGGATGCTACATAAGTTTGTGGGCCCAGgtcatctttt ... catcttgcagATATTAAAGGCTTTTTAAGTGATGTTAAACCAGCACTTCTAAGTGCCCTGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaacatgctacgatagttgccaggtcatgttcttgaaataatccatcttgcagATATTAAAGGCTTTTTAAGTGATGTTAAACCAGCACTTCTAAGTGCCCTGGATACTGAATATGAGAAAAATCCTTTTGAG
 ttttaac  putative branch site (score: 2)
                                           tccatctt  putative PPT
                                  ttgaaataat  TA-rich tract