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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgcatttattgtgttgctgctacacttggaatttgattgcccaaaacttagttaatattgtgatatgtagGGCTTAATGCGAGCTTTCAGAGTTGAAGACCTACCTATTGAGTCCAAGATGTTGACCAAAGCATTAGACGAAGCCCAAAGGAAAGTGGAGAACTATTTCT

Basic information

species Glycine max
transcript GLYMA02G01060.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G01060.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os01g21820.1 (Oryza sativa), 3'ss of exon 14
-------------------gtaatgcatttattgtg------ttgctgctacacttggaatttgattgcccaa-aacttagttaatattgtgatatgtagGGCTTAATGCGAGCTTTCAGAGTTGAAGACCTACCTATTGAGTCCAAGATGTTGACCAAAGCATTAGACGAAGCCCAAAGGAAAGTGGAGAACTATTTCT
                    | |  |||||| || |      |   |   ||| |   ||||  |||| |  | ||| | |  | |  ||   || |||||| || |||| ||| |||||||| ||||| || ||||||||||| |||||| |||| |  ||  |||| ||||| ||| ||||||| |||||||||||||
tcagtactacttgcattagttcaaacatttaatgagagccaataaatagaacagtataaattcaattgtctgataacattgccattcgtgatgtacgtagGGTTTGATGCAAGCCTTCAGAGTCGAAGATCTTCCTATTGAGTCGAAGATGCTGACAAGGGCTCTAGATGAAGCTCAACGGAAAGTTGAGAACTATTTCT

upper sequence: GLYMA02G01060.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv07s0005g02610.t01 (Vitis vinifera), 3'ss of exon 16
------gtaatgcatttattgtgt---tgctgctaca-cttggaatttgattgcccaaaacttagttaatattgtgatatgtagGGCTTAATGCGAGCTTTCAGAGTTGAAGACCTACCTATTGAGTCCAAGATGTTGACCAAAGCATTAGACGAAGCCCAAAGGAAAGTGGAGAACTATTTCT
         |||  ||||  || |    ||  |||||  || | ||||| |||   ||   ||  | | | |||  |  ||||||| || |||   ||||| ||||||||||||||||| |||||||||||||||||||| || ||| |||| ||||| ||  ||||||| ||||| |||||||
gtttagcctatggttttaaagtctattcgccactacagtttaggatttgcttgttaaagggttc-tcatttttgctaattgtagGGTTTGATGACCGCTTTTAGAGTTGAAGACCTACCCATTGAGTCCAAGATGTTGACAAAGGCACTAGATGAAGCACAGCGGAAAGTAGAGAATTATTTCT
















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|19348856|gb|BM893388.1|BM893388
EST:     TAAGTCTTGAAGATAACATATTTCGTATTTTTGGTGGAGATCGAATTCAG                         GGCTTAATGCGAGCTTTCAGAGTTGAAGACCTACCTATTGAGTCCAAGATG
genomic: TAAGTCTTGAAGATAACATATTTCGTATTTTTGGTGGAGATCGAATTCAGgtaatgcatt ... tgatatgtagGGCTTAATGCGAGCTTTCAGAGTTGAAGACCTACCTATTGAGTCCAAGATG
EST: gi|18039565|gb|BM307859.1|BM307859
EST:     TAAGTCTTGAAGATAACATATTTCGTATTTTTGGTGGAGATCGAATTCAG                         GGCTTAATGCGAGCTTTCAGAGTTGAAGACCTACCTATTGAGTCCAAGATG
genomic: TAAGTCTTGAAGATAACATATTTCGTATTTTTGGTGGAGATCGAATTCAGgtaatgcatt ... tgatatgtagGGCTTAATGCGAGCTTTCAGAGTTGAAGACCTACCTATTGAGTCCAAGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgctacacttggaatttgattgcccaaaacttagttaatattgtgatatgtagGGCTTAATGCGAGCTTTCAGAGTTGAAGACCTACCTATTGAGTCCAAGATGTTGACCAAAGCATTAGACGAAGCCCAAAGGAAAGTGGAGAACTATTTCT
                                  agttaat  putative branch site (score: 4)
                           aaaacttagttaatat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgcatttattgtgttgctgctacacttggaatttgattgcccaaaacttagttaatattgtgatatgtagGGCTTAATGCGAGCTTTCAGAGTTGAAGACCTACCTATTGAGTCCAAGATGTTGACCAAAGCATTAGACGAAGCCCAAAGGAAAGTGGAGAACTATTTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA