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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatgttaattgggccaatctcactatcttttcaggaatggatgttccattatcttctctaatgctttgtgtttttctcttccattttttaacagGAAGCTTTAAGGTCAAGAGGTCTGAAGGATGATACAACTTGCCTCGTTGTAGATATTATTCCTTCAGATCATCCCGTGTTGCCAACAATTCCAAGAAAGA

Basic information

species Glycine max
transcript GLYMA20G38270.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38270.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv14s0060g01580.t01 (Vitis vinifera), 3'ss of exon 6
gtgat-gttaattgggccaatctcactatcttttcagg--aatggatgttccattatcttctctaatgctttgtgtttttctcttccattttttaa-cagGAAGCTTTAAGGTCAAGAGGTCTGAAGGATGATACAACTTGCCTCGTTGTAGATATTATTCCTTCAGATCATCCCGTGTTGCCAACAATTCCAAGAAAGA
|| |  | | |   || |  | |  ||  |  | |||    ||  ||||    ||  ||| | |  |   |  | || | |   ||  ||   |   |||||||||||||||||||| ||  |||||||||||||||| ||||| ||||| ||||| ||||| |||||| |||| || || ||  |||  ||||  ||||
gtaacagctgacatgggctctttt-ctgacagtccagactgatccatgtcgacttccctttttttttttatcttattatacctgtctgttcactgttcagGAAGCTTTAAGGTCAAGGGGCTTGAAGGATGATACAACATGCCTAGTTGTTGATATGATTCCATCAGATAATCCTGTCTTACCTCCAACACCAAAGAAGA
















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|10234774|gb|BE803662.1|BE803662
EST:     AGTCATGCCGAGGTGTACCTGCAGAGCTTGCTGCAAAGCTGGTGGTTAAG                         GAAGCTTTAAGGTCAAGAGGGCTGAAGGATGATACAACTTGCCTCGTTGTA
genomic: AGTCATGCCGAGGTGTACCTGCAGAGCTTGCTGCAAAGCTGGTGGTTAAGgtgatgttaa ... tttttaacagGAAGCTTTAAGGTCAAGAGGTCTGAAGGATGATACAACTTGCCTCGTTGTA
EST: gi|22522410|gb|BU081221.1|BU081221
EST:     AGTCATGCCGAGGTGTACCTGCAGAGCTTGCTGCAAAGCTGGTGGTTAAG                         GAAGCTTTAAGGTCAAGAGGTCTGAAGGATGATACAACTTGCCTCGTTGTA
genomic: AGTCATGCCGAGGTGTACCTGCAGAGCTTGCTGCAAAGCTGGTGGTTAAGgtgatgttaa ... tttttaacagGAAGCTTTAAGGTCAAGAGGTCTGAAGGATGATACAACTTGCCTCGTTGTA
EST: gi|18733866|gb|BM527857.1|BM527857
EST:     AGTCATGCCGAGGTGTACCTGCAGAGCTTGCTGCAAAGCTGGTGGTTAAG                         GAAGCTTTAAGGTCAAGAGGTCTGAAGGATGATACAACTTGCCTCGTTGTA
genomic: AGTCATGCCGAGGTGTACCTGCAGAGCTTGCTGCAAAGCTGGTGGTTAAGgtgatgttaa ... tttttaacagGAAGCTTTAAGGTCAAGAGGTCTGAAGGATGATACAACTTGCCTCGTTGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgttccattatcttctctaatgctttgtgtttttctcttccattttttaacagGAAGCTTTAAGGTCAAGAGGTCTGAAGGATGATACAACTTGCCTCGTTGTAGATATTATTCCTTCAGATCATCCCGTGTTGCCAACAATTCCAAGAAAGA
                ctctaat  putative branch site (score: 3)
                      tgctttgtgtttttct  CT-rich tract
                                           attttttaaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatgttaattgggccaatctcactatcttttcaggaatggatgttccattatcttctctaatgctttgtgtttttctcttccattttttaacagGAAGCTTTAAGGTCAAGAGGTCTGAAGGATGATACAACTTGCCTCGTTGTAGATATTATTCCTTCAGATCATCCCGTGTTGCCAACAATTCCAAGAAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA