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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagatctaatgtacaagacaacatagttttggacttcaagcatcaatgtaaattttcgccctgagaatcaacaacctaactctacttgtttttctcccagGTACCTACATGAAGTTTGTTCACCATCTGTTGTTCATAAGAATATAAAGTCGGCCAACATATTGCTTGATACAGATTTTAATCCTCATCTTTCTGACAGT

Basic information

species Glycine max
transcript GLYMA16G01790.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G01790.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv09s0002g00150.t01 (Vitis vinifera), 3'ss of exon 12
-cagatctaatgtacaagaca-acatagttttggacttcaagcatcaatgtaaattttcgccctgagaatcaacaacctaactctacttgtttttctcccagGTACCTACATGAAGTTTGTTCACCATCTGTTGTTCATAAGAATATAAAGTCGGCCAACATATTGCTTGATACAGATTTTAATCCTCATCTTTCTGACAGT
  | |  ||   |  |    | |  |  ||||| |     |   | | | | | |  |        |  |  |||      | | |   |   || |  ||||||||||||||||||||| ||||||||  |||||||||| ||| | || || || |||||||| || || |||||  | ||||| || ||| | ||| ||
ataaaattagcttggattttacatttgattttgtaacctcattcttactatga-taataatgtgaggggtgcacagtact-caccaagggaacttttatcagGTACCTACATGAAGTTTGCTCACCATCAATTGTTCATAAAAATTTCAAATCAGCTAACATATTACTAGACACAGAGCTCAATCCACACCTTACAGACTGT
















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|10845159|gb|BF068320.1|BF068320
EST:     TATGGAATTCACGAGTGAAAATTGCTTTGGGGGATTGCACGCGCCTTAGA                         GTACCTACATGAAGTTTGTTCACCATCTGTTGTTCATAAGAATATAAAGTC
genomic: TATGGAATTCACGAGTGAAAATTGCTTT-GGGGATTGCACGCGCTTTAGAgtaagttagt ... tttctcccagGTACCTACATGAAGTTTGTTCACCATCTGTTGTTCATAAGAATATAAAGTC
EST: gi|208098688|gb|GD895991.1|GD895991
EST:     ATATGGAATTCACGAGTGAAAATTGCTTTGGGGATTGCACGCGCTTTAGA                         GTACCTACATGAAGTTTGTTCACCATCTGTTGTTCATAAGAATATAA
genomic: ATATGGAATTCACGAGTGAAAATTGCTTTGGGGATTGCACGCGCTTTAGAgtaagttagt ... tttctcccagGTACCTACATGAAGTTTGTTCACCATCTGTTGTTCATAAGAATATAA
EST: gi|15813078|gb|BI785353.1|BI785353
EST:     ATATGGAATTCACGAGTGAAAATTGCTTTGGGGATTGCACGCGCTTTAGA                         GTACCTACATGAAGTTTGTTCACCATCTGTTGTTCATAAGAATATAAAGTC
genomic: ATATGGAATTCACGAGTGAAAATTGCTTTGGGGATTGCACGCGCTTTAGAgtaagttagt ... tttctcccagGTACCTACATGAAGTTTGTTCACCATCTGTTGTTCATAAGAATATAAAGTC
EST: gi|15814309|gb|BI786584.1|BI786584
EST:     ATATGGAATTCACGAGTGAAAATTGCTTTGGGGATTGCACGCGCTTTAGA                         GTACCTACATGAAGT
genomic: ATATGGAATTCACGAGTGAAAATTGCTTTGGGGATTGCACGCGCTTTAGAgtaagttagt ... tttctcccagGTACCTACATGAAGT
EST: gi|24136261|gb|BU926771.1|BU926771
EST:     ATATGGAATTCACGAGTGAAAATTGCTTTGGGGATTGCACGCGCTTTAGA                         GTACCTACATGAAGTTTGTTCACCATCTGTTGTTCATAAGAATATAAAGTC
genomic: ATATGGAATTCACGAGTGAAAATTGCTTTGGGGATTGCACGCGCTTTAGAgtaagttagt ... tttctcccagGTACCTACATGAAGTTTGTTCACCATCTGTTGTTCATAAGAATATAAAGTC
EST: gi|254326942|gb|GR836551.1|GR836551
EST:     ATATGGAATTCACGAGTGAAAATTGCTTTGGGGATTGCACGCGCTTTAGA                         GTACCTACATGAAGTTTGTTCACCATCTGTTGTTCATAAGAATATAAAGTC
genomic: ATATGGAATTCACGAGTGAAAATTGCTTTGGGGATTGCACGCGCTTTAGAgtaagttagt ... tttctcccagGTACCTACATGAAGTTTGTTCACCATCTGTTGTTCATAAGAATATAAAGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtaaattttcgccctgagaatcaacaacctaactctacttgtttttctcccagGTACCTACATGAAGTTTGTTCACCATCTGTTGTTCATAAGAATATAAAGTCGGCCAACATATTGCTTGATACAGATTTTAATCCTCATCTTTCTGACAGT
                            acctaac  putative branch site (score: 2)
                                  ctctacttgtttttct  CT-rich tract
                                        ttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagatctaatgtacaagacaacatagttttggacttcaagcatcaatgtaaattttcgccctgagaatcaacaacctaactctacttgtttttctcccagGTACCTACATGAAGTTTGTTCACCATCTGTTGTTCATAAGAATATAAAGTCGGCCAACATATTGCTTGATACAGATTTTAATCCTCATCTTTCTGACAGT

- - - -aatgtac
- - - - - - - - - - - - - - - - - ttcaagc
- - - - - - - - - - - - - - - - - - - - - -caatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caacaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctacttg