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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattatgaaaacatgtaacaaatgatttttttattctgagtgttttctttttcaacacttccatcgttgtctcacaaatgtattcattcttttcttgcagTCCAGACGCCACACATGATTTTTACAGGTCTTGAAGATTACAAGGCCAGAGGAACACAAGCAGCCCCTTACTTTACTTTGACCTTTTACACAGAATTTGC

Basic information

species Glycine max
transcript GLYMA12G12960.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G12960.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G34050.1 (Arabidopsis thaliana), 3'ss of exon 3
tattatgaaaacatgtaacaaatgattt-ttttattctgagtgttttctttttcaac----acttccatcgttgtctcacaaatgtattcattctt-ttcttgcagTCCAGACGCCACACATGATTTTTACAGGTCTTGAAGATTACAAGGCCAGAGGAACACAAGCAGCCCCTTACTTTACTTTGACCTTTTACACAGAATTTGC
         | ||| |||   ||| |    || |||   |  ||| | |   ||  |       | |||  |  ||| | | |  |  ||| | || || | |||||  |  |||| |||||||||||||| ||||| ||||| ||||| || |||||||| ||||| || |||||| | |||   ||||| ||||| ||  || |
------tgtaccatttaattcatgttgagcttcattacaacagttatgtaactcggctgaagagttcattatgatcttatataaatggtcagttttattgtggcagTTGAAGCGCCTCACATGATTTTTACTGGTCTCGAAGACTACAAAGCAAGAGGAACTCAAGCGGCTCCTTACCTGACTACAACCTTCTACACTGAGCTTTC

upper sequence: GLYMA12G12960.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv10s0003g00660.t01 (Vitis vinifera), 3'ss of exon 3
--tattatgaaaacatgtaacaaatgatttttttattctgagtgttttctttttcaacacttccatcgttgtctcacaaatgtattcattc---ttttcttgcagTCCAGACGCCACACATGATTTTTACAGGTCTTGAAGATTACAAGGCCAGAGGAACACAAGCAGCCCCTTACTTTACTTTGACCTTTTACACAGAATTTGC
  |  |    || || |||     ||      | |  || || | |   |   | |  |  |  ||  ||||| |||  | |  ||  |||   || || |||||| || | || |||||||||||| || |||||||||||||||||||| |||||||| |||||||| || ||||| ||| | || ||||||||||| |||||
tctcctccttaatca-gtagtgtttgtggaactgaagcttag-gatgaataccttagta--tgaatatttgtc-cactgaagcttttgttcaagttgtcatgcagTTCAAATGCAACACATGATTTTCACTGGTCTTGAAGATTACAAGGCAAGAGGAACTCAAGCAGCTCCCTACTTCACTGTCACTTTTTACACAGACTTTGC
















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|192331188|gb|FK020955.1|FK020955
EST:     TGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTTTGTTCAAG                         TCCAGACGCCACACATGATTTTTACAGGTCTTGAAGATTACAAGGCCAGAG
genomic: TGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTTTGTTCAAGgtttgacaaa ... tttcttgcagTCCAGACGCCACACATGATTTTTACAGGTCTTGAAGATTACAAGGCCAGAG
EST: gi|192300166|gb|FG989288.1|FG989288
EST:     TGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTTTGTTCAAG                         TCCAGACGCCACACATGATTTTTACAGGTCTTGAAGATTACAAGGCCAGAG
genomic: TGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTTTGTTCAAGgtttgacaaa ... tttcttgcagTCCAGACGCCACACATGATTTTTACAGGTCTTGAAGATTACAAGGCCAGAG
EST: gi|17400249|gb|BM177040.1|BM177040
EST:     TGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTTTGTTCAAG                         TCCAGACGCCACACATGATTTTTACAGG
genomic: TGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTTTGTTCAAGgtttgacaaa ... tttcttgcagTCCAGACGCCACACATGATTTTTACAGG
EST: gi|192331203|gb|FK020956.1|FK020956
EST:     TGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTTTGTTCAAG                         TCCAGACGCCACACATGATTTTTACAGGTCTTGAAGATTACAAGGCCAGAG
genomic: TGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTTTGTTCAAGgtttgacaaa ... tttcttgcagTCCAGACGCCACACATGATTTTTACAGGTCTTGAAGATTACAAGGCCAGAG
EST: gi|8827322|gb|BE211052.1|BE211052
EST:     TGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTTTGTTCAAG                         TCCAGACGCCACACATGATTTTTACAGGTCTTGAAGATTACAAGGCCAGAG
genomic: TGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTTTGTTCAAGgtttgacaaa ... tttcttgcagTCCAGACGCCACACATGATTTTTACAGGTCTTGAAGATTACAAGGCCAGAG
EST: gi|298179061|gb|HO024796.1|HO024796
EST:     TGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTTTGTTCAAG                         TCCAGACGCCACACATGATTTTTACAGGTCTTGAAGATTA
genomic: TGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTTTGTTCAAGgtttgacaaa ... tttcttgcagTCCAGACGCCACACATGATTTTTACAGGTCTTGAAGATTA
EST: gi|254320768|gb|GR827217.1|GR827217
EST:     TGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTTTGTTCAAG                         TCCAGACGCCACACATGATTTTTACAGGTCTTGAAGATTACAAGGCCAGAG
genomic: TGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTTTGTTCAAGgtttgacaaa ... tttcttgcagTCCAGACGCCACACATGATTTTTACAGGTCTTGAAGATTACAAGGCCAGAG
EST: gi|254320769|gb|GR827218.1|GR827218
EST:     TGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTTTGTTCAAG                         TCCAGACGCCACACATGATTTTTACAGGTCTTGAAGATTACAAGGCCAGAG
genomic: TGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTTTGTTCAAGgtttgacaaa ... tttcttgcagTCCAGACGCCACACATGATTTTTACAGGTCTTGAAGATTACAAGGCCAGAG
EST: gi|19453517|gb|BM954927.1|BM954927
EST:     TGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTTTGTTCAAG                         TCCAGACGCCACACATGATTTTTACAGGTCTTGAAGATTACAAGGCCAGAG
genomic: TGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTTTGTTCAAGgtttgacaaa ... tttcttgcagTCCAGACGCCACACATGATTTTTACAGGTCTTGAAGATTACAAGGCCAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttttcaacacttccatcgttgtctcacaaatgtattcattcttttcttgcagTCCAGACGCCACACATGATTTTTACAGGTCTTGAAGATTACAAGGCCAGAGGAACACAAGCAGCCCCTTACTTTACTTTGACCTTTTACACAGAATTTGC
                       gtctcac  putative branch site (score: 3)
                                   tattcattcttttctt  putative PPT
                              aaatgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattatgaaaacatgtaacaaatgatttttttattctgagtgttttctttttcaacacttccatcgttgtctcacaaatgtattcattcttttcttgcagTCCAGACGCCACACATGATTTTTACAGGTCTTGAAGATTACAAGGCCAGAGGAACACAAGCAGCCCCTTACTTTACTTTGACCTTTTACACAGAATTTGC

- - - - - -catgtaa
- - - - - - - - - - - - - - - - -ttctgag
- - - - - - - - - - - - - - - - - - - - - - - - - - - -cacttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcattc