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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatcttggaacttattgggggcaaattgttaagtttgatactatttagattttttactaacgtgcatatgtagttatttatagataattatgcttagcattttgtcctcagtcttatattttcccatatattaatttctagGTCAAGGCTTTTTACGTATGATGATGTGGTGGAGAGAGTAGCCCAACAACTTGGTCTGGATGATCCATCCAAAATACGGCTTACACCACACAACTGCTAC

Basic information

species Glycine max
transcript GLYMA20G11330.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 22
gtaagcatcttggaacttattgggggcaaattgttaagtttgatactatttagattttttactaacgtgcatatgtagttatttatagataattatgcttagcattttgtcctcagtcttatattttcccatatattaatttc---tagGTCAAGGCTTTTTACGTATGATGATGTGGTGGAGAGAGTAGCCCAACAACTTGGTCTGGATGATCCATCCAAAATACGGCTTACACCACACAACTGCTAC
                                                    ||    || | ||     || | |  ||||||| | |  ||||  || |  ||||||     |  |||| || |    || | ||  ||||   |||||| | ||||  ||| ||||||||||| || |||||||| || |  ||||||||  ||||||||||||| ||||| || |||||| | |||||||| || 
--------------------------------------------------gtgagggcttgcaaatcactatgtttc-ttatttaaaaa--attaaact-attattttgcaaaaaagcttacatatcaatatttcttgctttcacttagGTCGAAGCTTCATACTTATGATGATGTTGTTGAGAGAGTTGCACGCCAACTTGGCTTGGATGATCCATCAAAAATTCGCCTTACATCTCACAACTGTTAT

upper sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G303655_T01 (Zea mays), 3'ss of exon 12
gtaagcatcttggaacttattgggggcaaattgttaagtttgatactatttagattttttactaacgtgcatatgtagttatttatagataattatgcttagcattttgtcctcagtcttatattttcccatatattaatttctagGTCAAGGCTTTTTACGTATGATGATGTGGTGGAGAGAGTAGCCCAACAACTTGGTCTGGATGATCCATCCAAAATACGGCTTACACCACACAACTGCTAC
                                              ||    ||||    |  ||  ||   |  | ||| |  ||    | |   | || | ||      || |  | | | ||||  | | | || |   ||||||| | ||||  ||| ||||||||||| || |||||||| || || ||||||||  ||||||||||||| || |||||||||||  | ||||| || || 
---------------------------------------------gtaag-ggattgcaaatcaaactgataaactggttttacatttgaactgcagttttgaatcaa---cttaaacatgttttttttcttgttttcac--ctagGTCGAAGCTTCATACATATGATGATGTTGTTGAGAGAGTTGCACATCAACTTGGGTTGGATGATCCATCAAAGATACGGCTTACGTCTCACAATTGTTAT

upper sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 22
gtaagcatcttggaacttattgggggcaaattgttaagtttgatactatttagattttttactaacgtgcatatgtagttatttatagataattatgcttagcattttgtcctcagtcttatattttcccatatattaatttctagGTCAAGGCTTTTTACGTATGATGATGTGGTGGAGAGAGTAGCCCAACAACTTGGTCTGGATGATCCATCCAAAATACGGCTTACACCACACAACTGCTAC
                         | ||    ||     ||| |||  | |  |  |||||  |  || |  |   ||| |   | |  | ||  | || | ||     |  ||  | ||| | || |  | | || | ||  ||||||| ||||  ||| ||||||||||| || |||||||| || ||  |||||||  ||||||||||||| || || ||||||||| | ||||| || || 
-------------------------gtaagggattgcaaatgaaactgataaactggtttac--atttgaactt-cggttttacgttggaactttggttttgaat-----caacatacatatgtgtttct-tgttttcactt--agGTCAAAGCTTCATACTTATGATGATGTTGTTGAGAGAGTTGCACATAAACTTGGGTTGGATGATCCATCAAAGATTCGGCTTACATCTCACAATTGTTAT

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

upper sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 22
gtaagcatcttggaacttattgggggcaaattgttaagtttgatactatttagattttttactaacgtgcatatgtagttatttatagataattatgcttagcattttgtcctcagtct-tatattttcccat--atattaatttctagGTCAAGGCTTTTTACGTATGATGATGTGGTGGAGAGAGTAGCCCAACAACTTGGTCTGGATGATCCATCCAAAATACGGCTTACACCACACAACTGCTAC
                                                                    | |  || ||  ||  || | ||| ||   | |||||| ||     ||| | | || |  |   |  |||| ||| || ||||||| ||||||||| |||||||| ||||| || |||||||| |  || |||||| |||||||||||||||||||  |||| ||| | |||||||| |||
--------------------------------------------------------------------gtaagtgcagaaatcaattg-taacta--atcagcattatgattatagtttatttactagctggtgcatatgaatgtccagGTCAAAGCTTTTTACTTATGATGACGTGGTAGAAAGAGTAGCTCGTCAGCTTGGTTTGGATGATCCATCCAAAATCAGGCTCACATCTCACAACTGTTAC

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|17519525|gb|BM188567.1|BM188567
EST:     CACTTTCGATCTCTGGATAGACCGAAGGAAGATGACTTTTTCCTGGAGAT                         GTCAAGGCTTTTTACGTATGATGATGTGGTGGAGAGAGTAGCCCAACAACT
genomic: CACTTTCGATCTCTGGATAGACCGAAGGAAGATGACTTTTTCCTGGAGATgtaagcatct ... taatttctagGTCAAGGCTTTTTACGTATGATGATGTGGTGGAGAGAGTAGCCCAACAACT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatgcttagcattttgtcctcagtcttatattttcccatatattaatttctagGTCAAGGCTTTTTACGTATGATGATGTGGTGGAGAGAGTAGCCCAACAACTTGGTCTGGATGATCCATCCAAAATACGGCTTACACCACACAACTGCTAC
                                          tattaat  putative branch site (score: 2)
                                                tttct  CT-rich tract
                           ttatattttcccatat  TA-rich tract