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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatgacttgatataaatttataatacaaccttgtgaagggttaggcaatactccaattatccatgtttatgtttgttaacttctctatcttattaacagaGTGCAAACCATGGGCGATGCAATTGATTTGACTGGTGACGGAGGAGTCATTAAAACCATTGTAAGAAAAAGCAAAGCTGATGCTGTCGGTCCAACAGAAA

Basic information

species Glycine max
transcript GLYMA18G04170.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G04170.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv13s0019g01900.t01 (Vitis vinifera), 3'ss of exon 1
--------------------gatgacttgatataaatttat--aatacaaccttgtgaagggttaggcaatactccaattatccatgtttatgtttgttaacttctctatcttattaacagaGTGCAAACCATGGGCGATGCAATTGATTTGACTGGTGACGGAGGAGTCATTAAAACCATTGTAAGAAAAAGCAAAGCTGATGCTGTCGGTCCAACAGAAA
                    |||   |||   | || | ||  ||| |       |  |    |||    | |||  ||  | ||||||| | ||   |||  |    ||   |     ||||   || ||||||| ||||||||||||||||| || |||||||||||  | || || ||| |||   ||  |||| |||||||                 
ggaaatcattttccttctttgatctgttgggctgaagtgattcaattcgtatcattttacttgtagcagtttctcttat--ttcatgtttcttttgtctaagCTGGTGATTGAAACTTTAGAG---AAGCCATGGGTGATGCAATTGATTTGACCGGGGACGGAGGAGTACTGAAGACAATTATAAAGCAAGCCAAACCTGATGC-----------------
















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|298193802|gb|HO040450.1|HO040450
EST:     TACAGCCTTCTCTCGCTTCGTTCCACCCTTCACCTGAAAAGCAAAAAGGA                         GTGCAAACCATGGGCGATGCAATTGATTTGACTGGTGACGGAGGAGTCATT
genomic: TACAGCCTTCTCTCGCTTCGTTCCACCCTTCACCTGAAAAGCAAAAAGGGttagtctcaa ... tattaacagaGTGCAAACCATGGGCGATGCAATTGATTTGACTGGTGACGGAGGAGTCATT
EST: gi|298188914|gb|HO035607.1|HO035607
EST:     TACAGCCTTCTCTCGCTTCGTTCCACCCTTCACCTGAAAAGCAAAAAGGA                         GTGCAAACCATGGGCGATGCAATTGATTTGACTGGTGACGGAGGAGTCATT
genomic: TACAGCCTTCTCTCGCTTCGTTCCACCCTTCACCTGAAAAGCAAAAAGGGttagtctcaa ... tattaacagaGTGCAAACCATGGGCGATGCAATTGATTTGACTGGTGACGGAGGAGTCATT
EST: gi|298175755|gb|HO018352.1|HO018352
EST:     TACAGCCTTCTCTCGCTTCGTTCCACCCTTCACCTGAAAAGCAAAAAGGA                         GTGCAAACCATGGGCGATGCAATTGATTTGACTGGTGACGGAGGAGTCATT
genomic: TACAGCCTTCTCTCGCTTCGTTCCACCCTTCACCTGAAAAGCAAAAAGGGttagtctcaa ... tattaacagaGTGCAAACCATGGGCGATGCAATTGATTTGACTGGTGACGGAGGAGTCATT
EST: gi|21887331|gb|BQ740544.1|BQ740544
EST:     CCTGAAAAGCAAAAAGGA                         GTGCAAACCATGGGCGATGCAATTGATTTGACTGGTGACGGAGGAGTCATT
genomic: CCTGAAAAGCAAAAAGGGttagtctcaa ... tattaacagaGTGCAAACCATGGGCGATGCAATTGATTTGACTGGTGACGGAGGAGTCATT
EST: gi|298169599|gb|HO020959.1|HO020959
EST:     TACGGCCTTCTCTCGCTTCGTTCCACCCTTCACCTGAAAAGCAAAAAGGA                         GTGCAAACCATGGGCGATGCAATTGATCTGACTGGTGACGGAGGAGTCATT
genomic: TACAGCCTTCTCTCGCTTCGTTCCACCCTTCACCTGAAAAGCAAAAAGGGttagtctcaa ... tattaacagaGTGCAAACCATGGGCGATGCAATTGATTTGACTGGTGACGGAGGAGTCATT
EST: gi|208260921|gb|GE059887.1|GE059887
EST:     TACAGCCTTCTCTCGCTTCGTTCCACCCTTCACCTGAAAAGCAAAAAGGA                         GTGCAAACCATGGGCGATGCAATTGATTTGACTGGTGACGGAGGAGTCATT
genomic: TACAGCCTTCTCTCGCTTCGTTCCACCCTTCACCTGAAAAGCAAAAAGGGttagtctcaa ... tattaacagaGTGCAAACCATGGGCGATGCAATTGATTTGACTGGTGACGGAGGAGTCATT
EST: gi|298171704|gb|HO021296.1|HO021296
EST:     TACAGCCTTCTCTCGCTTCGTTCCACCCTTCACCTGAAAAGCAAAAAGGA                         GTGCAAACCATGGGCGATGCAATTGATTTGACTGGTGACGGAGGAGTCATT
genomic: TACAGCCTTCTCTCGCTTCGTTCCACCCTTCACCTGAAAAGCAAAAAGGGttagtctcaa ... tattaacagaGTGCAAACCATGGGCGATGCAATTGATTTGACTGGTGACGGAGGAGTCATT
EST: gi|298185077|gb|HO030290.1|HO030290
EST:     TACAGCCTTCTCTCGCTTCGTTCCACCCTTCACCTGAAAAGCAAAAAGGA                         GTGCAAACCATGGGCGATGCAATTGATTTGACTGGTGACGGAGGAGTCATT
genomic: TACAGCCTTCTCTCGCTTCGTTCCACCCTTCACCTGAAAAGCAAAAAGGGttagtctcaa ... tattaacagaGTGCAAACCATGGGCGATGCAATTGATTTGACTGGTGACGGAGGAGTCATT
EST: gi|9565709|gb|BE475218.1|BE475218
EST:     TACAGCCTTCTCTCGCTTCGTTCCACCCTTCACCTGAAAAGCAAAAAGGA                         GTGCAAACCATGGGCGATGCAATTGATTTGACTGGTGACGGAGGAGTCATT
genomic: TACAGCCTTCTCTCGCTTCGTTCCACCCTTCACCTGAAAAGCAAAAAGGGttagtctcaa ... tattaacagaGTGCAAACCATGGGCGATGCAATTGATTTGACTGGTGACGGAGGAGTCATT
EST: gi|298169647|gb|HO021007.1|HO021007
EST:     TACAGCCTTCTCTCGCTTCGTTCCACCCTTCACCTGAAAAGCAAAAAGGA                         GTGCAAACCATGGGCGATGCAATTGATTTGACTGGTGACGGAGGAGTCATT
genomic: TACAGCCTTCTCTCGCTTCGTTCCACCCTTCACCTGAAAAGCAAAAAGGGttagtctcaa ... tattaacagaGTGCAAACCATGGGCGATGCAATTGATTTGACTGGTGACGGAGGAGTCATT
EST: gi|18726884|gb|BM523811.1|BM523811
EST:     TACAGCCTTCTCTCGCTTCGTTCCACCCTTCACCTGAAAAGCAAAAAGGA                         GTGCAAACCATGGGCGATGCAATTGATTTGACTGGTGACGGAGGAGTCATT
genomic: TACAGCCTTCTCTCGCTTCGTTCCACCCTTCACCTGAAAAGCAAAAAGGGttagtctcaa ... tattaacagaGTGCAAACCATGGGCGATGCAATTGATTTGACTGGTGACGGAGGAGTCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatactccaattatccatgtttatgtttgttaacttctctatcttattaacagaGTGCAAACCATGGGCGATGCAATTGATTTGACTGGTGACGGAGGAGTCATTAAAACCATTGTAAGAAAAAGCAAAGCTGATGCTGTCGGTCCAACAGAAA
                            tgttaac  putative branch site (score: 2)
                                  cttctctatcttatt  CT-rich tract
                    tttatgtttgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatgacttgatataaatttataatacaaccttgtgaagggttaggcaatactccaattatccatgtttatgtttgttaacttctctatcttattaacagaGTGCAAACCATGGGCGATGCAATTGATTTGACTGGTGACGGAGGAGTCATTAAAACCATTGTAAGAAAAAGCAAAGCTGATGCTGTCGGTCCAACAGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- tgacttg
- - - - - - - - - - - - acaacct
- - - - - - - - - - - - - - - - gtgaagg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgt