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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttactgcttcaagattatttgattggcatattatgagaatttatttcagctatgtcttgttctatctaatacttgtggtgttgaaacttgtagGTGTGCTGGATATCACAGTGAAGCTGATGCTCCTAGCCGGAGACTTGCTAAACCACTAATCTTTTGTAGGACTGAAAGTGACTGCCCTATGGAAAATGGC

Basic information

species Glycine max
transcript GLYMA08G38990.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G38990.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g38010.1 (Oryza sativa), 3'ss of exon 4
----gttagttactgcttcaagattatttgattggcatattatgagaatttatttcagctatgtcttgttctatctaatacttgtggtgttgaaacttgtagGTGTGCTGGATATCACAGTGAAGCTGATGCTCCTAGCCGGAGACTTGCTAAACCACTAATCTTTTGTAGGACTGAAAGTGACTGCCCTATGGAAAATGGC
       |   | | |   |      | |  | | | |  |  ||   ||  |   |   |        |  |   |  || |||  |  |  ||  | ||||||||| |||||| ||||||| ||||||||||| |  || ||| |||| ||||| || ||||| ||||| |||||||||||  |||||||||| ||||| 
taaacaaaaggatttccctacatccttcttctcgtcctcctccgattcttgttgcgaaacaatagaaccttgaaacatgacctgttctagttgaa--tatagGTGTGCAGGATATTACAGTGATGCTGATGCTCCCAATCGAAGAATTGCCAAACCTCTGATCTTCTGTAGAACTGAAAGTGATAGCCCTATGGAGAATGGT

upper sequence: GLYMA08G38990.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g40040.1 (Oryza sativa), 3'ss of exon 5
gttagttactgcttcaaga----ttatttgattggcatattatga--gaatttatt---tcagctatgtcttgttctatctaatacttgtggtgttg----aaacttgtagGTGTGCTGGATATCACAGTGAAGCTGATGCTCCTAGCCGGAGACTTGCTAAACCACTAATCTTTTGTAGGACTGAAAGTGACTGCCCTATGGAAAATGGC
|| || ||  |||| | ||    |  |||| ||   || | ||    |  ||| ||   | ||     || | |   |  | ||| |       |||    |||     ||||||||||| ||  ||||||| ||||||||||| ||||| |||||||  || || ||||||||||| || ||||| |||||  | || ||||| ||||| 
gtaagctaa-gctttaggaaacttcttttgttttatatctcatagctggctttgttgtcttagaatcatcatatggaaaatgataatgtgaacattgttctaaatcatcagGTGTGCTGGCTACTACAGTGATGCTGATGCTCCCAGCCGCAGACTTGGCAAGCCTCTAATCTTTTGCAGAACTGACAGTGATAGTCCCATGGAGAATGGT

upper sequence: GLYMA08G38990.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G147884_T01 (Zea mays), 3'ss of exon 4
gttagttactgcttcaaga--ttatttgattggcatatt---atgagaatttatttcagctatgtcttgttctatctaatacttgt------ggtgttgaaacttgtagGTGTGCTGGATATCACAGTGAAGCTGATGCTCCTAGCCGGAGACTTGCTAAACCACTAATCTTTTGTAGGACTGAAAGTGACTGCCCTATGGAAAATGGC
  || ||  |   | | |   || || |  |   || ||   ||     | | ||||| || ||  |  |  ||| |   | |||        ||  | ||| |   ||||||||||| ||  |||| ||||||||||||||||| || |||||||  || ||  | || ||||| || ||||| |||||  |||| ||||| ||||| 
-gtaatttatatataagggctttcttgggctaaaattttcctattttgctatgtttcaact-tgcatcatcatatttgtaaattgaaaggaaagttattaaattgtcagGTGTGCTGGCTACTACAGCGAAGCTGATGCTCCTAGTCGCAGACTTGGCAAGCCTTTGATATTTTGCAGAACTGAGAGTGATAGCCCCATGGAGAATGGT

upper sequence: GLYMA08G38990.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 4
gttagttactgcttcaagattatttgattggcatattatgaga-atttatttcagc---tatgtcttgttctatcta-atacttgtggtgttgaaacttgta--gGTGTGCTGGATATCACAGTGAAGCTGATGCTCCTAGCCGGAGACTTGCTAAACCACTAATCTTTTGTAGGACTGAAAGTGACTGCCCTATGGAAAATGGC
|||||||||  ||   ||||| ||| |   ||||||  || || |   |  |||     | || |    ||  | || | | | |||    ||   ||| ||  |||||| ||||||||||||||| |||||||||||||| || |||||||| |||||||| ||||||||| | || || ||||| || || ||||||||||| 
gttagttacc-ctgtcagattctttcacatgcatatcctgggagaaaaagctcaatatatgtggcaaactccttttacacattggtgtatgtgcttcttttacagGTGTGTTGGATATCACAGTGATGCTGATGCTCCTAGTCGTAGACTTGCGAAACCACTTATCTTTTGTCGAACCGAGAGTGATTGTCCAATGGAAAATGGT

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|192295328|gb|FG985982.1|FG985982
EST:     ATGAAGAAGAGAGGGATTGAGGATATGGATCTCGTGATGGTAGATCCCTG                         GTGTGCTGGATATCACAGTGAAGCTGATGCTCCTAGCCGGAGACTTGCTAA
genomic: ATGAAGAAGAGAGGGATTGAGGATATGGATCTCGTGATGGTAGATCCCTGgttagttact ... aaacttgtagGTGTGCTGGATATCACAGTGAAGCTGATGCTCCTAGCCGGAGACTTGCTAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttatttcagctatgtcttgttctatctaatacttgtggtgttgaaacttgtagGTGTGCTGGATATCACAGTGAAGCTGATGCTCCTAGCCGGAGACTTGCTAAACCACTAATCTTTTGTAGGACTGAAAGTGACTGCCCTATGGAAAATGGC
                         atctaat  putative branch site (score: 3)
                        tatctaata  TA-rich tract