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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgatggatatgctgacccttatcgtgtgcctcataatatttcaatttagcttacttgtccttttgcctaagctgatttcttacttgatgttattgcagGAGCATGTGAAGGCTCGCTTGCGTGTTCAACTTGCCATGTTATAGTCATG

Basic information

species Glycine max
transcript GLYMA13G17370.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G17370.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os07g01930.1 (Oryza sativa), 3'ss of exon 5
tatgatggatatgctgaccct-tatcgtgtgcctcataatatttcaatttagcttacttgtccttttgcc---taagctgatttcttacttgatgttattgcagGAGCATGTGAAGGCTCGCTTGCGTGTTCAACTTGCCATGTTATAGTCATG
  | || |||    |||   | | |    ||  ||||  ||||     ||  || | || |  || |      |||  || | |  || ||   || | |||||||||||||||||| || |||||||||||||| || ||||| ||||| |||
--ttattgattacttgatgttatttgacatgtttcatg-tattgactattgactgatttttaattgtagttagtaacttggtctagtattttgggt-actgcagGAGCATGTGAAGGTTCACTTGCGTGTTCAACCTGTCATGTCATAGTTATG

upper sequence: GLYMA13G17370.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G013607_T02 (Zea mays), 3'ss of exon 5
tatgatggatatgctgacccttatcgt-gtgcctcataatatttcaatttagcttacttgtc-cttttgcctaagctga--tttcttact--tgatgttattgcagGAGCATGTGAAGGCTCGCTTGCGTGTTCAACTTGCCATGTTATAGTCATG
    ||   ||   |     || |  |  | |||  | || || ||  | | || | ||    || | |   | | | |  || | | ||  ||  | || ||||||||||||||| ||||| ||||||||||| ||||| ||||| ||||| |||
----atcagtacattaggtattgtaatcattcctttttatgttcca--tcaactgattttcagctgtagttcatgataaccttccctgctattgtggctactgcagGAGCATGTGAGGGCTCACTTGCGTGTTCTACTTGTCATGTAATAGTAATG

upper sequence: GLYMA13G17370.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G856338_T01 (Zea mays), 3'ss of exon 1
tatgatggatatgctgacccttatcgt-gtgcctcataatatttcaatt-tagcttacttgtccttttgcctaagctgatttcttact-tgatgt-tattgcagGAGCATGTGAAGGCTCGCTTGCGTGTTCAACTTGCCATGTTATAGTCATG
    ||  |||   |     |  | ||  | |||  | || ||  | |    | ||    |   |  | | | |    ||| | | || |  ||| || ||||||||||||||| || || ||||||||||| ||||| ||||| ||||| |||
----atcaatacattaggtatcgtagtcattcctttttatgttctattcactgattttcagctgtaattcatgataacattccctgctattgtgtctactgcagGAGCATGTGAGGGTTCACTTGCGTGTTCTACTTGTCATGTAATAGTAATG

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|7284255|gb|AW596850.1|AW596850
EST:     TGGAATGTCTATGTTAGAAGCTGCTCATGAAAATGACATTGAACTAGAAG                         GAGCATGTGAAGGCTCGCTTGCGTGTTCAACTTGCCATGTTATAGTCATG
genomic: TGGAATGTCTATGTTAGAAGCTGCTCATGAAAATGACATTGAACTAGAAGgcaagagctt ... gttattgcagGAGCATGTGAAGGCTCGCTTGCGTGTTCAACTTGCCATGTTATAGTCATG
EST: gi|254329164|gb|GR833536.1|GR833536
EST:     TGGAATGTCTATGTTAGAAGCTGCTCATGAAAATGACATTGAACTAGAAG                         GAGCATGTGAAGGCTCGCTTGCGTGTTCAACTTGCCATGTTATAGTCATG
genomic: TGGAATGTCTATGTTAGAAGCTGCTCATGAAAATGACATTGAACTAGAAGgcaagagctt ... gttattgcagGAGCATGTGAAGGCTCGCTTGCGTGTTCAACTTGCCATGTTATAGTCATG
EST: gi|22931821|gb|BU548960.1|BU548960
EST:     TGGAANGTCTATGTTAGAAGCTGCTCATGAAAATGACATTGAACTAGAAG                         GAGCATGTGAAGGCTCGCTTGCGTGTTCAACTTGCCATGNNNTAGTCATG
genomic: TGGAATGTCTATGTTAGAAGCTGCTCATGAAAATGACATTGAACTAGAAGgcaagagctt ... gttattgcagGAGCATGTGAAGGCTCGCTTGCGTGTTCAACTTGCCATGTTATAGTCATG
EST: gi|14125826|gb|BG790264.1|BG790264
EST:     TGGAATGTCTATGTTAGAAGCTGCTCATGAAAATGACATTGAACTAGAAG                         GAGCATGTGAAGGCTCGCTTGCGTGTTCAACTTGCCATGTTATAGTCATG
genomic: TGGAATGTCTATGTTAGAAGCTGCTCATGAAAATGACATTGAACTAGAAGgcaagagctt ... gttattgcagGAGCATGTGAAGGCTCGCTTGCGTGTTCAACTTGCCATGTTATAGTCATG
EST: gi|254329165|gb|GR833537.1|GR833537
EST:     TGGAATGTCTATGTTAGAAGCTGCTCATGAAAATGACATTGAACTAGAAG                         GAGCATGTGAAGGCTCGCTTGCGTGTTCAACTTGCCATGTTATAGTCATG
genomic: TGGAATGTCTATGTTAGAAGCTGCTCATGAAAATGACATTGAACTAGAAGgcaagagctt ... gttattgcagGAGCATGTGAAGGCTCGCTTGCGTGTTCAACTTGCCATGTTATAGTCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttagcttacttgtccttttgcctaagctgatttcttacttgatgttattgcagGAGCATGTGAAGGCTCGCTTGCGTGTTCAACTTGCCATGTTATAGTCATG
                               atttctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgatggatatgctgacccttatcgtgtgcctcataatatttcaatttagcttacttgtccttttgcctaagctgatttcttacttgatgttattgcagGAGCATGTGAAGGCTCGCTTGCGTGTTCAACTTGCCATGTTATAGTCATG

-atgatgg
- - - - - - -ctgaccc
- - - - - - - - - - - - - - tgcctca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgatt