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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtctcgttatgtagttgttgatgactttctaatagtatttgttctccccttgttattttcccccctgtatttgtattgtaaggtattcctttgacagGTTATGAGTGTTAAGGCTCTTGGAATTGTCATAAAGTTAACACTGTCTGGGATGAATCAGCTAATTTACCCTCAGACTTGGGCATTCACTCTAGTTGTAC

Basic information

species Glycine max
transcript GLYMA16G00560.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G00560.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv12s0035g00720.t01 (Vitis vinifera), 3'ss of exon 5
gtatgtctcgttatgtagttgttgatgactttctaatagtatttgttctccccttgttattttcccccctgtatttgtattgtaaggtattcctttgacagGTTATGAGTGTTAAGGCTCTTGGAATTGTCATAAAGTTAACACTGTCTGGGATGAATCAGCTAATTTACCCTCAGACTTGGGCATTCACTCTAGTTGTAC
||  || | |  || | || |||  | ||||  | |      |||| |||   || ||| ||         | ||||| |||  | | | | || |||||||| ||||||||||| || ||||||||||   | ||||||||| | || || |||||||||||||  || |||||||| ||||| |||||| |||||||| 
gtgcgtattggcatttggtagtttctcacttcttgaa-----ttgtgctctgttt-ttacttctagagtgttgtttgtcttg--atggaatgctctgacagGTCATGAGTGTTAAAGCACTTGGAATTGCTTTGAAGTTAACATTATCAGGAATGAATCAGCTAACATATCCTCAGACATGGGCCTTCACTATAGTTGTAA
















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|38193345|gb|CF922551.1|CF922551
EST:     CACACATAATGGTTTATATTGGTGTTTGTTCCCTTGTAGGTTCTCTAACG                         GTTATGAGTGTTAAGGCTCTTGGAATTGTCATAAAGTTAACACTGTCTGGG
genomic: CACACATAATGGTTTATATTGGTGTTTGTTCCCTTGTAGGTTCTCTAACGgtatgtctcg ... cctttgacagGTTATGAGTGTTAAGGCTCTTGGAATTGTCATAAAGTTAACACTGTCTGGG
EST: gi|120530522|gb|EH258655.1|EH258655
EST:     CACACATAATGGTTTATATTGGTGTTTGTTCCCTTGTAGGTTCTCTAACG                         GTTATGAGTGTTAAGGCTCT-GGAATTGTCATAAAGTTAACACTGTCTGGG
genomic: CACACATAATGGTTTATATTGGTGTTTGTTCCCTTGTAGGTTCTCTAACGgtatgtctcg ... cctttgacagGTTATGAGTGTTAAGGCTCTTGGAATTGTCATAAAGTTAACACTGTCTGGG
EST: gi|208128879|gb|GD927115.1|GD927115
EST:     TGTAGGTTCTCTAACG                         GTTATGAGTGTTAAGGCTCTTGGAATTGTCATAAAGTTAACACTGTCTGGG
genomic: TGTAGGTTCTCTAACGgtatgtctcg ... cctttgacagGTTATGAGTGTTAAGGCTCTTGGAATTGTCATAAAGTTAACACTGTCTGGG
EST: gi|58020349|gb|CX707091.1|CX707091
EST:     CACACATAATGGTTTATATTGGTGGTTGTTCCCTTGTAGGTTCTCTAACG                         GTTATGAGTGTTAAGGCTCTTGGAATTGTCATAAAGTTAACACTGTCTGGG
genomic: CACACATAATGGTTTATATTGGTGTTTGTTCCCTTGTAGGTTCTCTAACGgtatgtctcg ... cctttgacagGTTATGAGTGTTAAGGCTCTTGGAATTGTCATAAAGTTAACACTGTCTGGG
EST: gi|120531881|gb|EH260014.1|EH260014
EST:     CACACATAATGGTTTATATTGGTGTTTGTTCCCTTGTAGGTTCTCTAACG                         GTTATGAGTGTTAAGGCTCTTGGAATTGTCATAAAGTTAACACTGTCTGGG
genomic: CACACATAATGGTTTATATTGGTGTTTGTTCCCTTGTAGGTTCTCTAACGgtatgtctcg ... cctttgacagGTTATGAGTGTTAAGGCTCTTGGAATTGTCATAAAGTTAACACTGTCTGGG
EST: gi|58016807|gb|CX703549.1|CX703549
EST:     ACACATAATGGTTTATA-TGGTGTTTTGTTCCCTNGTAGGTTCTCTAACG                         GTTATGAGTGTTAAGGCTCTTGGAATTGTCATAAAGTTAACACTGTCTGGG
genomic: ACACATAATGGTTTATATTGGTG-TTTGTTCCCTTGTAGGTTCTCTAACGgtatgtctcg ... cctttgacagGTTATGAGTGTTAAGGCTCTTGGAATTGTCATAAAGTTAACACTGTCTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctccccttgttattttcccccctgtatttgtattgtaaggtattcctttgacagGTTATGAGTGTTAAGGCTCTTGGAATTGTCATAAAGTTAACACTGTCTGGGATGAATCAGCTAATTTACCCTCAGACTTGGGCATTCACTCTAGTTGTAC
                                         tattccttt  CT-rich tract
                         tatttgtattgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtctcgttatgtagttgttgatgactttctaatagtatttgttctccccttgttattttcccccctgtatttgtattgtaaggtattcctttgacagGTTATGAGTGTTAAGGCTCTTGGAATTGTCATAAAGTTAACACTGTCTGGGATGAATCAGCTAATTTACCCTCAGACTTGGGCATTCACTCTAGTTGTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT