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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttgagctttgatgctgacactgtaccagattatggaaaactattttttgagctattttttgttttgcagCCTGATACAGTCACAGGGGATATTGTCTTTGTCCTACAACAGAAGGAACACCCAAAGTTCAAACGAAAGGCAGATGACCTTTTTGTAGAACACACATTGT

Basic information

species Glycine max
transcript GLYMA13G38790.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G38790.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0080g01230.t01 (Vitis vinifera), 3'ss of exon 4
-----gtatgttgagctttg--atgctgacactgtaccagattatggaaaactattttttgagctattttttg----ttttgcagCCTGATACAGTCACAGGGGATATTGTCTTTGTCCTACAACAGAAGGAACACCCAAAGTTCAAACGAAAGGCAGATGACCTTTTTGTAGAACACACATTGT
      | || |||   ||   || ||  |  |  |  ||||  | |   |  ||||| |  |||  |||| |    ||||||||||||| |||||||| |||||||| || |||||||| || || |||||||| ||||| |||||  ||||||  |||||||||||||| || ||||| ||||
gtatgttttgatgaatcttataatactatctatagat-agatatttgttgatgattttatctgcttgttttgggtcattttgcagCCTGACACAGTCACTGGGGATATAGTTTTTGTCCTCCAGCAAAAGGAACATCCAAAATTCAAGAGAAAGGGGGATGACCTTTTTGTGGAGCACACCTTGT
















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|4290603|gb|AI441642.1|AI441642
EST:     GCAGAATGGACAGAAGATTACATTCCCTGGTGAAGCTGATGAAGCG                         CCTGATACAGTCACAGGGGATATTGTCTTTGTCCTACAACAGAAGGAACAC
genomic: GCAGAATGGACAGAAGATTACATTCCCTGGTGAAGCTGATGAAGCGgtatgttgag ... tgttttgcagCCTGATACAGTCACAGGGGATATTGTCTTTGTCCTACAACAGAAGGAACAC
EST: gi|192318285|gb|FK010997.1|FK010997
EST:     GAATGCAGAATGGACAGAAGATTACATTCCCTGGTGAAGCTGATGAAGCG                         CCTGATACAGTCACAGGGGATATTGTCTTTGTCCTACAACAGAAGGAACAC
genomic: GAATGCAGAATGGACAGAAGATTACATTCCCTGGTGAAGCTGATGAAGCGgtatgttgag ... tgttttgcagCCTGATACAGTCACAGGGGATATTGTCTTTGTCCTACAACAGAAGGAACAC
EST: gi|6072029|gb|AW101476.1|AW101476
EST:     GAATGCAGAATGGACAGAAGATTACATTCCCTGGTGAAGCTGATGAAGCG                         CCTGATACAGTCACAGGGGATATTGTCTTTGTCCTACAACAGAAGGAACAC
genomic: GAATGCAGAATGGACAGAAGATTACATTCCCTGGTGAAGCTGATGAAGCGgtatgttgag ... tgttttgcagCCTGATACAGTCACAGGGGATATTGTCTTTGTCCTACAACAGAAGGAACAC
EST: gi|24136910|gb|BU927420.1|BU927420
EST:     GAATGCAGAATGGACAGAAGATTACATTCCCTGGTGAAGCTGATGAAGCG                         CCTGATACAGTCACAGGGGATATTGTCTTTGTCCTACAACAGAAGGAACAC
genomic: GAATGCAGAATGGACAGAAGATTACATTCCCTGGTGAAGCTGATGAAGCGgtatgttgag ... tgttttgcagCCTGATACAGTCACAGGGGATATTGTCTTTGTCCTACAACAGAAGGAACAC
EST: gi|193584498|gb|FK538952.1|FK538952
EST:     GAATGCAGAATGGACAGAAGATTACATTCCCTGGTGAAGCTGATGAAGCG                         CCTGATACAGTCACAGGGGATATTGTCTTTGTCCTACAACAGAAGGAACAC
genomic: GAATGCAGAATGGACAGAAGATTACATTCCCTGGTGAAGCTGATGAAGCGgtatgttgag ... tgttttgcagCCTGATACAGTCACAGGGGATATTGTCTTTGTCCTACAACAGAAGGAACAC
EST: gi|193481371|gb|FK447848.1|FK447848
EST:     GAATGCAGAATGGACAGAAGATTACATTCCCTGGTGAAGCTGATGAAGCG                         CCTGATACAGTCACAGGGGATATTGTCTTTGTCCTACAACAGAAGGAACAC
genomic: GAATGCAGAATGGACAGAAGATTACATTCCCTGGTGAAGCTGATGAAGCGgtatgttgag ... tgttttgcagCCTGATACAGTCACAGGGGATATTGTCTTTGTCCTACAACAGAAGGAACAC
EST: gi|33389476|gb|CA852683.1|CA852683
EST:     GAATGCAGAATGGACAGAAGATTACATTCCCTGGTGAAGCTGATGAAGCG                         CCTGATACAGTCACAGGGGATATTGTCTTTGTCCTACAACGGAAGGAACAC
genomic: GAATGCAGAATGGACAGAAGATTACATTCCCTGGTGAAGCTGATGAAGCGgtatgttgag ... tgttttgcagCCTGATACAGTCACAGGGGATATTGTCTTTGTCCTACAACAGAAGGAACAC
EST: gi|208240028|gb|GE042796.1|GE042796
EST:     GAATGCAGAATGGACAGAAGATTACATTCCCTGGTGAAGCTGATGAAGCA                         CCTGATACAGTCACAGGGGATATTGTCTTTGTCCTACAACAGAAGGAACAC
genomic: GAATGCAGAATGGACAGAAGATTACATTCCCTGGTGAAGCTGATGAAGCGgtatgttgag ... tgttttgcagCCTGATACAGTCACAGGGGATATTGTCTTTGTCCTACAACAGAAGGAACAC
EST: gi|7692524|gb|AW760628.1|AW760628
EST:     GAATGCAGAATGGACAGAAGATTACATTCCCTGGTGAAGCTGATGAAGCG                         CCTGATACAGTCACAGGGGATATTGTCTTTGTCCTACAACAGAAGGAACAC
genomic: GAATGCAGAATGGACAGAAGATTACATTCCCTGGTGAAGCTGATGAAGCGgtatgttgag ... tgttttgcagCCTGATACAGTCACAGGGGATATTGTCTTTGTCCTACAACAGAAGGAACAC
EST: gi|298171124|gb|HO016156.1|HO016156
EST:     GAATGCAGAATGGACAGAAGATTACATTCCCTGGTGAAGCTGATGAAGCG                         CCTGATACAGTCACAGGGGATATTGTCTTTGTCCTACAACAGAAGGAACAC
genomic: GAATGCAGAATGGACAGAAGATTACATTCCCTGGTGAAGCTGATGAAGCGgtatgttgag ... tgttttgcagCCTGATACAGTCACAGGGGATATTGTCTTTGTCCTACAACAGAAGGAACAC
EST: gi|298174702|gb|HO014733.1|HO014733
EST:     GAATGCAGAATGGACAGAAGACTACATTCCCTGGTGAAGCTGATGAAGCG                         CCTGATACAGTCACAGGGGATATTGTCTTTGTCCTACAACAGAAGGAACAC
genomic: GAATGCAGAATGGACAGAAGATTACATTCCCTGGTGAAGCTGATGAAGCGgtatgttgag ... tgttttgcagCCTGATACAGTCACAGGGGATATTGTCTTTGTCCTACAACAGAAGGAACAC
EST: gi|15815007|gb|BI787282.1|BI787282
EST:     GAATGCAGAATGGACAGAAGATTACATTCCCTGGTGAAGCTGATGAAGCG                         CCTGATACAGTCACAGGGGATATTGTCTTTGTCCTACAACAGAAGGAACAC
genomic: GAATGCAGAATGGACAGAAGATTACATTCCCTGGTGAAGCTGATGAAGCGgtatgttgag ... tgttttgcagCCTGATACAGTCACAGGGGATATTGTCTTTGTCCTACAACAGAAGGAACAC
EST: gi|18040794|gb|BM309088.1|BM309088
EST:     GAATGCAGAATGGACAGAAGATTACATTCCCTGGTGAAGCTGATGAAGCG                         CCTGATACAGTCACAGGGGATATTGTCTTTGTCCTACAACAGAAGGAACAC
genomic: GAATGCAGAATGGACAGAAGATTACATTCCCTGGTGAAGCTGATGAAGCGgtatgttgag ... tgttttgcagCCTGATACAGTCACAGGGGATATTGTCTTTGTCCTACAACAGAAGGAACAC
EST: gi|208076854|gb|GD877393.1|GD877393
EST:     GAATGCAGAATGGACAGAAGATTACATTCCCTGGTGAAGCTGATGAAGCG                         CCTGATACAGTCACAGGGGATATTGTCTTTGTCCTACAACAGAAGGAACAC
genomic: GAATGCAGAATGGACAGAAGATTACATTCCCTGGTGAAGCTGATGAAGCGgtatgttgag ... tgttttgcagCCTGATACAGTCACAGGGGATATTGTCTTTGTCCTACAACAGAAGGAACAC
EST: gi|16996123|gb|BM085495.1|BM085495
EST:     GAATGCAGAATGGACAGAAGATTACATTCCCTGGTGAAGCTGATGAAGCG                         CCTGATACAGTCACATGGGATATTGTCTTTGTCCTACAACAGAAGGAACAC
genomic: GAATGCAGAATGGACAGAAGATTACATTCCCTGGTGAAGCTGATGAAGCGgtatgttgag ... tgttttgcagCCTGATACAGTCACAGGGGATATTGTCTTTGTCCTACAACAGAAGGAACAC
EST: gi|7925317|gb|AW831404.1|AW831404
EST:     GAATGCAGAATGGACAGAAGATTACATTCCCTGGTGAAGCTGATGAAGCG                         CCTGATACAGTCACAGGGGATATTGTCTTTGTCCTACAACAGAAGGAACAC
genomic: GAATGCAGAATGGACAGAAGATTACATTCCCTGGTGAAGCTGATGAAGCGgtatgttgag ... tgttttgcagCCTGATACAGTCACAGGGGATATTGTCTTTGTCCTACAACAGAAGGAACAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgacactgtaccagattatggaaaactattttttgagctattttttgttttgcagCCTGATACAGTCACAGGGGATATTGTCTTTGTCCTACAACAGAAGGAACACCCAAAGTTCAAACGAAAGGCAGATGACCTTTTTGTAGAACACACATTGT
 tgctgac  putative branch site (score: 2)
                                     ctattttttgtttt  putative PPT
                     aaaactattttttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttgagctttgatgctgacactgtaccagattatggaaaactattttttgagctattttttgttttgcagCCTGATACAGTCACAGGGGATATTGTCTTTGTCCTACAACAGAAGGAACACCCAAAGTTCAAACGAAAGGCAGATGACCTTTTTGTAGAACACACATTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG