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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattttatctgaatttcctccacagaagaaggaatttgacctaaatataatgttgtgtatataatttatttattcatcacatgatgttccttttatttcagGTCAAAACATCAATCAGAACTTTTCCTTCGTCAGCTGAAATAGTACCTGAACCACTGGGTGTTGTGTTGGTCATCTCTGCATGGAACTATCCAATTT

Basic information

species Glycine max
transcript GLYMA06G12010.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G12010.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0001g02440.t01 (Vitis vinifera), 3'ss of exon 4
gtatattttatctgaatttcctccacagaagaaggaatttgacctaaatataatgttgtgtatataatttat--ttattcatcacatgatgttcct-tttatttcagGTCAAAACATCAATCAGAACTTTTCCTTCGTCAGCTGAAATAGTACCTGAACCACTGGGTGTTGTGTTGGTCATCTCTGCATGGAACTATCCAATTT
||| | ||      |  |  ||||  |   ||||   ||      |   || ||||||  |  | | || |   ||||| |   ||  || ||     | ||| ||||| ||||| ||||| | |||||||||||| ||||| ||||||||  | |||||| ||||||| || ||| ||||    |||||||| | |||  | |
gtaaaattgtcacaacctctctcctgattggaagctgtta---tgatgcatcatgttgccttgaaagttgagcattatttaatgcaaaatcttttcactcattgcagGTTAAAACTTCAATAACAACTTTTCCTTCATCAGCAGAAATAGTGTCAGAACCATTGGGTGTAGTATTGATCATTGGAGCATGGAATTTTCCTTTGT
















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|209699810|gb|BW661120.1|BW661120
EST:     CATGTGAAGTCATACTGAAGGAATTGAAACAATGGATGAAGCCAGAAAAG                         GTCAAAACATCAATCAGAACTTTTCCTTCGTCAGCTGAAATAGTACCTGAA
genomic: CATGTGAAGTCATACTGAAGGAATTGAAACAATGGATGAAGCCAGAAAAGgtatatttta ... tttatttcagGTCAAAACATCAATCAGAACTTTTCCTTCGTCAGCTGAAATAGTACCTGAA
EST: gi|213616764|gb|DB971261.1|DB971261
EST:     CATGTGAAGTCATACTGAAGGAATTGAAACAATGGATGAAGCCAGAAAAG                         GTCAAAACATCAATCAGAACTTTTCCTTCGTCAGCTGAAATAGTACCTGAA
genomic: CATGTGAAGTCATACTGAAGGAATTGAAACAATGGATGAAGCCAGAAAAGgtatatttta ... tttatttcagGTCAAAACATCAATCAGAACTTTTCCTTCGTCAGCTGAAATAGTACCTGAA
EST: gi|308098235|gb|HO759976.1|HO759976
EST:     CATGTGAAGTCATACTGAAGGAATTGAAACAATGGATGAAGCCAGAAAAG                         GTCAAAACATCAATCAGAACTTTTCCTTCGTCAGCTGAAATAGT
genomic: CATGTGAAGTCATACTGAAGGAATTGAAACAATGGATGAAGCCAGAAAAGgtatatttta ... tttatttcagGTCAAAACATCAATCAGAACTTTTCCTTCGTCAGCTGAAATAGT
EST: gi|213595059|gb|DB971862.1|DB971862
EST:     CATGTGAAGTCATACTGAAGGAATTGAAACAATGGATGAAGCCAGAAAAG                         GTCAAAACATCAATCAGAACTTTTTTCTTCGTCAGCTGAAATAGTACCTGA
genomic: CATGTGAAGTCATACTGAAGGAATTGAAACAATGGATGAAGCCAGAAAAGgtatatttta ... tttatttcagGTCAAAACATCAATCAGAACTTTTC-CTTCGTCAGCTGAAATAGTACCTGA
EST: gi|254317849|gb|GR826833.1|GR826833
EST:     CATGTGAAGTCATACTGAAGGAATTGAAACAATGGATGAAGCCAGAAAAG                         GTCAAAACATCAATCAGAACTTTTCCTTCGTCAGCTGAAATAGTACCTGAA
genomic: CATGTGAAGTCATACTGAAGGAATTGAAACAATGGATGAAGCCAGAAAAGgtatatttta ... tttatttcagGTCAAAACATCAATCAGAACTTTTCCTTCGTCAGCTGAAATAGTACCTGAA
EST: gi|213591368|gb|DB955716.1|DB955716
EST:     CATGTGAAGTCATACTGAAGGAATTGAAACAATGGATGAAGCCAGAAAAG                         GTCAAAACATCAATCAGAACTTTTCCTTCGTCAGCTGAAATAGTACCTGAA
genomic: CATGTGAAGTCATACTGAAGGAATTGAAACAATGGATGAAGCCAGAAAAGgtatatttta ... tttatttcagGTCAAAACATCAATCAGAACTTTTCCTTCGTCAGCTGAAATAGTACCTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataatgttgtgtatataatttatttattcatcacatgatgttccttttatttcagGTCAAAACATCAATCAGAACTTTTCCTTCGTCAGCTGAAATAGTACCTGAACCACTGGGTGTTGTGTTGGTCATCTCTGCATGGAACTATCCAATTT
                                      tgttccttttatttc  CT-rich tract
           tatataatttatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatattttatctgaatttcctccacagaagaaggaatttgacctaaatataatgttgtgtatataatttatttattcatcacatgatgttccttttatttcagGTCAAAACATCAATCAGAACTTTTCCTTCGTCAGCTGAAATAGTACCTGAACCACTGGGTGTTGTGTTGGTCATCTCTGCATGGAACTATCCAATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA