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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcacaaacttcatgcttaggagtaaaaaaactcatgcatataattttaattatctatgtatgatattgatgtttgtttgtgttttactcttgatggccagAATTCACTTGGGAGGATGTGAAAGCTGATAAGCATAGGGAGAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAG

Basic information

species Glycine max
transcript GLYMA02G12330.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G12330.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os08g44440.1 (Oryza sativa), 3'ss of exon 1
----tcacaaacttcatgcttaggagtaaaaaaactcatgcatataat--tttaattatctatgtatgatattgatgtttgtttgtgttttactcttgatggccagAATTCACTTGGGAGGATGTGAAAGCTGATAAGCATAGGGAGAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAG
    |   |   | |  ||||    || | |    |    |||| |||  ||  |  | ||  |||  || |  ||  || | |   |||    ||||     |||||||||  ||||| ||||| || | ||| |||||  | ||||| || || ||||| || || ||||||||||||||||||||||||||||
tgcattgtagcttacgagcttttttgttatatgggttgaacatacaattattagaaaagctcagta-aatctaaatacttttctccttttgttccttg-----cagAATTCAAATGGGATGATGTTAAGGTTGACAAGCACCGAGAGAATTACCTCGGTCATAGCATTAAGGCTCCTGTTGGAAGATGGCAGAAAG

upper sequence: GLYMA02G12330.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G167548_T01 (Zea mays), 3'ss of exon 1
----tcacaaacttcatgcttaggagtaaaaaaactcatgcatataattttaattatctatgtatgatattgatgtttgtt-tgtgttttactcttgatggccagAATTCACTTGGGAGGATGTGAAAGCTGATAAGCATAGGGAGAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAG
    ||   |  |||||| |        |      || |   | ||  |      |  ||     |  | || |  |   | | | ||||| || ||     |||||||||  ||||| |||||||| | ||| |||||| ||||||| || |||||||| ||| | |||||||| ||||| |||||||||||||
gctgtctacattttcatgttccatttgcacttgcttcgtttttgtatgtcatggaacataaaagggtcagtggttctaactgtatattttattcatg-----cagAATTCAAATGGGACGATGTGAAGGTTGACAAGCATCGGGAGAATTACCTTGGTCATAGTGTTAAGGCTCCGGTTGGTAGATGGCAGAAAG

upper sequence: GLYMA02G12330.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G52220.1 (Arabidopsis thaliana), 3'ss of exon 1
tcacaaacttcatgcttaggagtaaaaaaactcatg-catataattttaattatctatg-tatgatattgatgtttgtttgtgttttactcttgatggccagAATTCACTTGGGAGGATGTGAAAGCTGATAAGCATAGGGAGAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAG
  | |   ||  ||   |  |||    |||   | |   || ||  | |  |    ||| |  ||  |  ||   |  |||  |||   | |  |||  ||||||||| |||||| || || || ||||||||  |||||||||||||| | |||||||||||||| || ||||||||||||||||| ||||
--agatcgtttttggcaattagttttcaaatcaaagatgtagaacatgagctgctaatgatgagaactctattactaattgaatttgtttataaatgtgcagAATTCAGTTGGGATGAAGTCAAGGCTGATAAATATAGGGAGAACTATTTGGGTCACAGTATCAAAGCCCCTGTTGGAAGATGGCAAAAAG

upper sequence: GLYMA02G12330.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv13s0101g00090.t01 (Vitis vinifera), 3'ss of exon 1
--tcacaaacttcatgcttaggagtaaaaaaactcatgcatataattttaattatctatgtatgatattgatgtttgtttgtgttttactcttgatggccagAATTCACTTGGGAGGATGTGAAAGCTGATAAGCATAGGGAGAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAG
  ||       ||   ||||  |  || |   |  | || |||  | |  |  |   ||| |||||     |  ||||   | |||| ||  | ||| |||||||| |  ||||| ||||| || | |||||| ||  | ||||||||||||||||||||||||||||| ||||||||||||||||| ||||
tttcttctttctctgtcttactatcaatagggcctaagcctatt-tgtagacaactcatggatgattgaacttcttgtaattatttt-cttgtaatgtccagAATTTAAGTGGGATGATGTCAAGGTTGATAAACACCGAGAGAACTATCTTGGTCACAGTATCAAGGCCCCTGTTGGAAGATGGCAAAAAG

upper sequence: GLYMA02G12330.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S59_322V6.1 (Physcomitrella patens), 3'ss of exon 1
tcacaaacttca-tgcttaggagtaaaaaaactcatgcatataattttaattatctatg-tatgatattgatgtttgtttgtgttttactcttga--tggc--cagAATTCACTTGGGAGGATGTGAAAGCTGATAAGCATAGGGAGAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAG
    ||  |||| ||    | | | |    |  ||| ||      | |     |  ||| |||||      ||| |     | |||||  || |   ||||  |||| || | |||||| ||||| || || || |||||  | ||||| || |||||||||||  ||||||||||||||||  |||||||||| |
----aattttcaatgggatgcaattatggga--cattcaaggtcctctggacgtaaatgatatgaggcgactgtgttgacattttttaaactgggattggctgcagAGTTTAATTGGGATGATGTCAAGGCCGACAAGCACCGCGAGAATTACCTTGGTCACAGCCTCAAGGCTCCTGTTGGGCGATGGCAGAAGG

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|193380891|gb|FK346468.1|FK346468
EST:     GCAGACATGTATCATCCAACAAGAGGTGGCGTTCGTGGTGGTCGAGATAC                         AATTCACTTGGG
genomic: GCAGACATGTATCATCCAACAAGAGGTGGCGTTCGTGGTGGTCGAGAT-Cgtaagtcatg ... tgatggccagAATTCACTTGGG
EST: gi|193391354|gb|FK355035.1|FK355035
EST:     AGCAGACATGTATCATCCAACAAGAGGTGGCGTTCGTGGTGGTCGAGATC                         AATTCACTTGGG
genomic: AGCAGACATGTATCATCCAACAAGAGGTGGCGTTCGTGGTGGTCGAGATCgtaagtcatg ... tgatggccagAATTCACTTGGG
EST: gi|298196401|gb|HO041144.1|HO041144
EST:     AGCAGACATGTATCATCCAACAAGAGGTGGCGTTCGTGGTGGTCGAGATC                         AATTCACTTAGGAGGATGTGAAAGCTGATAAGCATAGGGAGAACTATCTTG
genomic: AGCAGACATGTATCATCCAACAAGAGGTGGCGTTCGTGGTGGTCGAGATCgtaagtcatg ... tgatggccagAATTCACTTGGGAGGATGTGAAAGCTGATAAGCATAGGGAGAACTATCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaattatctatgtatgatattgatgtttgtttgtgttttactcttgatggccagAATTCACTTGGGAGGATGTGAAAGCTGATAAGCATAGGGAGAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAG
                                    ttttactctt  CT-rich tract
             tatgatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcacaaacttcatgcttaggagtaaaaaaactcatgcatataattttaattatctatgtatgatattgatgtttgtttgtgttttactcttgatggccagAATTCACTTGGGAGGATGTGAAAGCTGATAAGCATAGGGAGAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
-cacaaac
- - - - -tcatgct
- - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - -tcatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgt