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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagagttttcttattgtgcatcattgtttgttgaaattgtttaaccgaatatatatctcacctaatatgtttttattattttccatgcctcaagGTCAAAGCTTCATACCTATGATGATGTTGTTGAGAGAGTTGCTCGCCAACTTGAATTGGACGATCCAGCGAAAATTCGGCTTACACCCCACAATTGCTAC

Basic information

species Zea mays
transcript GRMZM2G418232_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G418232_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g36470.1 (Oryza sativa), 3'ss of exon 18
gtgagagttttcttattgtgcatcattgtttgttgaaattgtttaaccgaatatatatctcaccta-atatgt----ttttattattttccatgcctcaagGTCAAAGCTTCATACCTATGATGATGTTGTTGAGAGAGTTGCTCGCCAACTTGAATTGGACGATCCAGCGAAAATTCGGCTTACACCCCACAATTGCTAC
        |   | | |    | | |  |  ||| ||| |||||||  |  ||  |||||  | |  || |||    ||   || ||  |||| | | ||||||||| ||||||||||||||||||||||||||||||||||| || || ||||   |||| ||||||||||||||||| || ||| |||| || ||||| 
-------gtgagtgactacaaaacctattgggttcaaactgtttaattggctaattatctagcatgtatgtgtaacgttaatttcttccccattctttaagGTCAAAACTTCATACCTATGATGATGTTGTTGAGAGAGTTGCCCGTCAGCTTGGTGTGGATGATCCAGCGAAAATTCGTCTAACATCCCATAACTGCTAT

upper sequence: GRMZM2G418232_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA02G43930.1 (Glycine max), 3'ss of exon 22
-------------------------------gtgagagttttcttattgt-gcatcattgtttgt------tgaaattgtttaaccgaatatatatctcacctaatatgtttttattattttccatgc------ctcaagGTCAAAGCTTCATACCTATGATGATGTTGTTGAGAGAGTTGCTCGCCAACTTGAATTGGACGATCCAGCGAAAATTCGGCTTACACCCCACAATTGCTAC
                               || ||| ||    |||||  | ||  || ||         || || | ||||        |||   |    |   ||  |  | ||||  ||| |         || ||||||| |||  |||| ||||||||||| || |||| ||| ||||  |||||||  ||||| |||||| | | |||| ||||||| || ||||||||||||
gtaagcattgtgtaatttattggagcaaatcgttagatttaatatattgcagtatttttcttgagaggacatgtaagtatttatatattattatgcttagatttgcatcctcatcttatactccgtatatgaatttctagGTCAAGGCTCTATACATATGATGATGTGGTGGAGAAAGTGGCTCAACAACTTGGTTTGGATGATCCATCCATAATTAGGCTTACCCCTCACAATTGCTAC

upper sequence: GRMZM2G418232_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 14
---------------------------------------gtgagagttttcttattgtgcatcattgtttgt-tgaaattgtttaaccgaatatatatctcacctaatatgttt----ttattattttccatgcctcaa------gGTCAAAGCTTCATACCTATGATGATGTTGTTGAGAGAGTTGCTCGCCAACTTGAATTGGACGATCCAGCGAAAATTCGGCTTACACCCCACAATTGCTAC
                                        ||| | | ||   ||| |  |  |  ||   | || | || ||||     |  |||   |  | |  | |  |     ||||  ||| ||||   | ||      |||||| ||||  ||| ||||||||||| || |||||||| || |  |||||||   |||| |||||| | ||||| ||||||||||| ||||| ||||||
gtaagcatcttggaacttattgggggcaaattgttaagtttgatactatttagattttttactaacgtgcatatgtagttatttatagataattatgcttagcattttgtcctcagtcttatattttcccatatattaatttctagGTCAAGGCTTTTTACGTATGATGATGTGGTGGAGAGAGTAGCCCAACAACTTGGTCTGGATGATCCATCCAAAATACGGCTTACACCACACAACTGCTAC

upper sequence: GRMZM2G418232_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA13G16040.1 (Glycine max), 3'ss of exon 3
gtgagagtttt----cttat-tgtgcatcattgtttg--ttgaaattgtttaac-------cgaatatatatctcacctaatatgttt----ttattattttccatg------cctcaagGTCAAAGCTTCATACCTATGATGATGTTGTTGAGAGAGTTGCTCGCCAACTTGAATTGGACGATCCAGCGAAAATTCGGCTTACACCCCACAATTGCTAC
|| ||  | ||    ||||  || |||  ||||||    |||| | | |||||        | ||| |||      | |  | |  ||    ||||  ||| ||||       | || ||||||| ||||  ||| ||||||||||| || |||||||| || |  |||||||  ||||| |||||  | ||||| ||||||||||| ||||| ||||||
gtaagcatcttgaaacttacatgggcaa-attgttaaatttgatactatttaaattttttactaatttatgctgagcattctgtccttagtcttatactttcccatatgttaacttctagGTCAAGGCTTTTTACATATGATGATGTGGTGGAGAGAGTAGCCCAACAACTTGGTTTGGATGATCCGTCCAAAATACGGCTTACACCACACAACTGCTAC

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|78113609|gb|DV532000.1|DV532000
EST:     TTCCGGTCTTTGGAGAAACCAAAGGATGATGATTTTTCTTTGGAATT                         GTCAAAGCTTCATACCTATGATGATGTTGTTGAGAGAGTTGCTCGCCAACT
genomic: TTCCGGTCTTTGGAGAAACCAAAGGATGATGATTTTTCTTTGGAATTgtgagagttt ... atgcctcaagGTCAAAGCTTCATACCTATGATGATGTTGTTGAGAGAGTTGCTCGCCAACT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaaccgaatatatatctcacctaatatgtttttattattttccatgcctcaagGTCAAAGCTTCATACCTATGATGATGTTGTTGAGAGAGTTGCTCGCCAACTTGAATTGGACGATCCAGCGAAAATTCGGCTTACACCCCACAATTGCTAC
                    acctaat  putative branch site (score: 3)
                                       ttttccat  putative PPT
        aatatatatctcacct  TA-rich tract